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Mishra B, Kumar N, Shahid Mukhtar M. A Rice Protein Interaction Network Reveals High Centrality Nodes and Candidate Pathogen Effector Targets. Comput Struct Biotechnol J 2022; 20:2001-2012. [PMID: 35521542 PMCID: PMC9062363 DOI: 10.1016/j.csbj.2022.04.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/10/2022] [Accepted: 04/17/2022] [Indexed: 12/11/2022] Open
Abstract
Network science identifies key players in diverse biological systems including host-pathogen interactions. We demonstrated a scale-free network property for a comprehensive rice protein–protein interactome (RicePPInets) that exhibits nodes with increased centrality indices. While weighted k-shell decomposition was shown efficacious to predict pathogen effector targets in Arabidopsis, we improved its computational code for a broader implementation on large-scale networks including RicePPInets. We determined that nodes residing within the internal layers of RicePPInets are poised to be the most influential, central, and effective information spreaders. To identify central players and modules through network topology analyses, we integrated RicePPInets and co-expression networks representing susceptible and resistant responses to strains of the bacterial pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola (Xoc) and generated a RIce-Xanthomonas INteractome (RIXIN). This revealed that previously identified candidate targets of pathogen transcription activator-like (TAL) effectors are enriched in nodes with enhanced connectivity, bottlenecks, and information spreaders that are located in the inner layers of the network, and these nodes are involved in several important biological processes. Overall, our integrative multi-omics network-based platform provides a potentially useful approach to prioritizing candidate pathogen effector targets for functional validation, suggesting that this computational framework can be broadly translatable to other complex pathosystems.
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Astore C, Zhou H, Jacob J, Skolnick J. Prediction of severe adverse events, modes of action and drug treatments for COVID-19's complications. Sci Rep 2021; 11:20864. [PMID: 34675303 PMCID: PMC8531388 DOI: 10.1038/s41598-021-00368-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/06/2021] [Indexed: 01/08/2023] Open
Abstract
Following SARS-CoV-2 infection, some COVID-19 patients experience severe host driven adverse events. To treat these complications, their underlying etiology and drug treatments must be identified. Thus, a novel AI methodology MOATAI-VIR, which predicts disease-protein-pathway relationships and repurposed FDA-approved drugs to treat COVID-19's clinical manifestations was developed. SARS-CoV-2 interacting human proteins and GWAS identified respiratory failure genes provide the input from which the mode-of-action (MOA) proteins/pathways of the resulting disease comorbidities are predicted. These comorbidities are then mapped to their clinical manifestations. To assess each manifestation's molecular basis, their prioritized shared proteins were subject to global pathway analysis. Next, the molecular features associated with hallmark COVID-19 phenotypes, e.g. unusual neurological symptoms, cytokine storms, and blood clots were explored. In practice, 24/26 of the major clinical manifestations are successfully predicted. Three major uncharacterized manifestation categories including neoplasms are also found. The prevalence of neoplasms suggests that SARS-CoV-2 might be an oncovirus due to shared molecular mechanisms between oncogenesis and viral replication. Then, repurposed FDA-approved drugs that might treat COVID-19's clinical manifestations are predicted by virtual ligand screening of the most frequent comorbid protein targets. These drugs might help treat both COVID-19's severe adverse events and lesser ones such as loss of taste/smell.
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Affiliation(s)
- Courtney Astore
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, N.W., Atlanta, GA, 30332, USA
| | - Hongyi Zhou
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, N.W., Atlanta, GA, 30332, USA
| | - Joshy Jacob
- Emory Vaccine Center, Emory University, Atlanta, GA, 30329, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Microbiology and Immunology, Emory Vaccine Center, School of Medicine, Emory University, Atlanta, GA, 30329, USA
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, N.W., Atlanta, GA, 30332, USA.
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Vandermeulen C, O’Grady T, Wayet J, Galvan B, Maseko S, Cherkaoui M, Desbuleux A, Coppin G, Olivet J, Ben Ameur L, Kataoka K, Ogawa S, Hermine O, Marcais A, Thiry M, Mortreux F, Calderwood MA, Van Weyenbergh J, Peloponese JM, Charloteaux B, Van den Broeke A, Hill DE, Vidal M, Dequiedt F, Twizere JC. The HTLV-1 viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape. PLoS Pathog 2021; 17:e1009919. [PMID: 34543356 PMCID: PMC8483338 DOI: 10.1371/journal.ppat.1009919] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/30/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Viral infections are known to hijack the transcription and translation of the host cell. However, the extent to which viral proteins coordinate these perturbations remains unclear. Here we used a model system, the human T-cell leukemia virus type 1 (HTLV-1), and systematically analyzed the transcriptome and interactome of key effectors oncoviral proteins Tax and HBZ. We showed that Tax and HBZ target distinct but also common transcription factors. Unexpectedly, we also uncovered a large set of interactions with RNA-binding proteins, including the U2 auxiliary factor large subunit (U2AF2), a key cellular regulator of pre-mRNA splicing. We discovered that Tax and HBZ perturb the splicing landscape by altering cassette exons in opposing manners, with Tax inducing exon inclusion while HBZ induces exon exclusion. Among Tax- and HBZ-dependent splicing changes, we identify events that are also altered in Adult T cell leukemia/lymphoma (ATLL) samples from two independent patient cohorts, and in well-known cancer census genes. Our interactome mapping approach, applicable to other viral oncogenes, has identified spliceosome perturbation as a novel mechanism coordinated by Tax and HBZ to reprogram the transcriptome. Tax and HBZ are two viral regulatory proteins encoded by the human T-cell leukemia virus type 1 (HTLV-1) via sense and antisense transcripts, respectively. Both proteins are known to drive oncogenic processes that culminate in a T-cell neoplasm, known as Adult T cell leukemia/lymphoma (ATLL). We measured the effects of Tax and HBZ on host gene expression pathway by analyzing the interactome with cellular transcriptional and post-transcriptional regulators, and the transcriptome and mRNA splicing of cell lines expressing either Tax or HBZ. We compared our results with data obtained from independent cohorts of Japanese and Afro-Caribbean patients, and identified common splicing changes that might represent clinically useful biomarkers for ATLL. Finally, we provide evidence that the viral protein Tax can reprogram initial steps of the T-cell transcriptome diversification by hijacking the U2AF complex, a key cellular regulator of pre-mRNA splicing.
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Affiliation(s)
- Charlotte Vandermeulen
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Tina O’Grady
- Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Jerome Wayet
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Bartimee Galvan
- Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Sibusiso Maseko
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - Majid Cherkaoui
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - Alice Desbuleux
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Georges Coppin
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Julien Olivet
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Lamya Ben Ameur
- Laboratory of Biology and Modeling of the Cell, CNRS UMR 5239, INSERM U1210, University of Lyon, Lyon, France
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Olivier Hermine
- Service Hématologie Adultes, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants Malades, Université de Paris, Laboratoire d’onco-hématologie, Institut Necker-Enfants Malades, INSERM U1151, Université de Paris, Paris, France
| | - Ambroise Marcais
- Service Hématologie Adultes, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants Malades, Université de Paris, Laboratoire d’onco-hématologie, Institut Necker-Enfants Malades, INSERM U1151, Université de Paris, Paris, France
| | - Marc Thiry
- Unit of Cell and Tissue Biology, GIGA Institute, University of Liege, Liege, Belgium
| | - Franck Mortreux
- Laboratory of Biology and Modeling of the Cell, CNRS UMR 5239, INSERM U1210, University of Lyon, Lyon, France
| | - Michael A. Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Johan Van Weyenbergh
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven, Leuven, Belgium
| | | | - Benoit Charloteaux
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Anne Van den Broeke
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
- * E-mail: (AVdB); (DEH); (MV); (FD); (J-CT)
| | - David E. Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail: (AVdB); (DEH); (MV); (FD); (J-CT)
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (AVdB); (DEH); (MV); (FD); (J-CT)
| | - Franck Dequiedt
- Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
- * E-mail: (AVdB); (DEH); (MV); (FD); (J-CT)
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail: (AVdB); (DEH); (MV); (FD); (J-CT)
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Forlani G, Shallak M, Accolla RS, Romanelli MG. HTLV-1 Infection and Pathogenesis: New Insights from Cellular and Animal Models. Int J Mol Sci 2021; 22:ijms22158001. [PMID: 34360767 PMCID: PMC8347336 DOI: 10.3390/ijms22158001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/12/2022] Open
Abstract
Since the discovery of the human T-cell leukemia virus-1 (HTLV-1), cellular and animal models have provided invaluable contributions in the knowledge of viral infection, transmission and progression of HTLV-associated diseases. HTLV-1 is the causative agent of the aggressive adult T-cell leukemia/lymphoma and inflammatory diseases such as the HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). Cell models contribute to defining the role of HTLV proteins, as well as the mechanisms of cell-to-cell transmission of the virus. Otherwise, selected and engineered animal models are currently applied to recapitulate in vivo the HTLV-1 associated pathogenesis and to verify the effectiveness of viral therapy and host immune response. Here we review the current cell models for studying virus–host interaction, cellular restriction factors and cell pathway deregulation mediated by HTLV products. We recapitulate the most effective animal models applied to investigate the pathogenesis of HTLV-1-associated diseases such as transgenic and humanized mice, rabbit and monkey models. Finally, we summarize the studies on STLV and BLV, two closely related HTLV-1 viruses in animals. The most recent anticancer and HAM/TSP therapies are also discussed in view of the most reliable experimental models that may accelerate the translation from the experimental findings to effective therapies in infected patients.
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Affiliation(s)
- Greta Forlani
- Laboratory of General Pathology and Immunology “Giovanna Tosi”, Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (G.F.); (M.S.); (R.S.A.)
| | - Mariam Shallak
- Laboratory of General Pathology and Immunology “Giovanna Tosi”, Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (G.F.); (M.S.); (R.S.A.)
| | - Roberto Sergio Accolla
- Laboratory of General Pathology and Immunology “Giovanna Tosi”, Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (G.F.); (M.S.); (R.S.A.)
| | - Maria Grazia Romanelli
- Department of Biosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
- Correspondence:
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Saha D, Kundu S. A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion. Front Microbiol 2021; 12:613067. [PMID: 33679637 PMCID: PMC7930833 DOI: 10.3389/fmicb.2021.613067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is a leading cause of pneumonia and septicemia across the world. The rapid emergence of multidrug-resistant K. pneumoniae strains necessitates the discovery of effective drugs against this notorious pathogen. However, there is a dearth of knowledge on the mechanisms by which this deadly pathogen subverts host cellular machinery. To fill this knowledge gap, our study attempts to identify the potential mechanisms of host cell subversion by building a K. pneumoniae-human interactome based on rigorous computational methodology. The putative host targets inferred from the predicted interactome were found to be functionally enriched in the host's immune surveillance system and allied functions like apoptosis, hypoxia, etc. A multifunctionality-based scoring system revealed P53 as the most multifunctional protein among host targets accompanied by HIF1A and STAT1. Moreover, mining of host protein-protein interaction (PPI) network revealed that host targets interact among themselves to form a network (TTPPI), where P53 and CDC5L occupy a central position. The TTPPI is composed of several inter complex interactions which indicate that K. pneumoniae might disrupt functional coordination between these protein complexes through targeting of P53 and CDC5L. Furthermore, we identified four pivotal K. pneumoniae-targeted transcription factors (TTFs) that are part of TTPPI and are involved in generating host's transcriptional response to K. pneumoniae-mediated sepsis. In a nutshell, our study identifies some of the pivotal molecular targets of K. pneumoniae which primarily correlate to the physiological response of host during K. pneumoniae-mediated sepsis.
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Affiliation(s)
- Deeya Saha
- Department of Biophysics, Molecular Biology and Bioinformatics, Faculty of Science, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, Faculty of Science, University of Calcutta, Kolkata, India
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6
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Kumar N, Mishra B, Mehmood A, Mohammad Athar, M Shahid Mukhtar. Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis. iScience 2020; 23:101526. [PMID: 32895641 PMCID: PMC7468341 DOI: 10.1016/j.isci.2020.101526] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/30/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
COVID-19 (coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pathophysiology of this virus is complex and largely unknown, we employed a network-biology-fueled approach and integrated transcriptome data pertaining to lung epithelial cells with human interactome to generate Calu-3-specific human-SARS-CoV-2 interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 targets central nodes of the host-viral network, which participate in core functional pathways. Network centrality analyses discover 33 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation, and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host-modifying responses and cytokine storm. Overall, our network-centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into the pathogenicity of SARS-CoV-2 that may help foster effective therapeutic design.
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Affiliation(s)
- Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, 464 Campbell Hall, 1300 University Boulevard, AL 35294, USA
| | - Bharat Mishra
- Department of Biology, University of Alabama at Birmingham, 464 Campbell Hall, 1300 University Boulevard, AL 35294, USA
| | - Adeel Mehmood
- Department of Biology, University of Alabama at Birmingham, 464 Campbell Hall, 1300 University Boulevard, AL 35294, USA.,Department of Computer Science, University of Alabama at Birmingham, 1402 10th Avenue S., Birmingham, AL 35294, USA
| | - Mohammad Athar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, 1720 University Boulevard, AL 35294, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 464 Campbell Hall, 1300 University Boulevard, AL 35294, USA.,Nutrition Obesity Research Center, University of Alabama at Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA.,Department of Surgery, University of Alabama at Birmingham, 1808 7th Avenue S, Birmingham, AL 35294, USA
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7
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Kumar N, Mishra B, Mehmood A, Athar M, Mukhtar MS. Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis. SSRN 2020:3581857. [PMID: 32714115 PMCID: PMC7366800 DOI: 10.2139/ssrn.3581857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/07/2020] [Indexed: 01/02/2023]
Abstract
COVID-19 (Coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the pathophysiology of this deadly virus is complex and largely unknown, we employ a network biology-fueled approach and integrate multiomics data pertaining to lung epithelial cells-specific co-expression network and human interactome to generate Calu-3-specific human-SARS-CoV-2 Interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 target central nodes of host-viral network that participate in core functional pathways. Network centrality analyses discover 28 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host modifying responses and cytokine storm. Overall, our network centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into SARS-CoV-2 pathogenicity that may foster effective therapeutic design. Funding: This work was supported by the National Science Foundation (IOS-1557796) to M.S.M., and U54 ES 030246 from NIH/NIEHS to M. A. Conflict of Interest: The authors declare no competing interests. The authors also declare no financial interests.
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Affiliation(s)
- Nilesh Kumar
- Department of Biology, 464 Campbell Hall, 1300 University Boulevard, University of Alabama at Birmingham, Alabama 35294, USA
| | - Bharat Mishra
- Department of Biology, 464 Campbell Hall, 1300 University Boulevard, University of Alabama at Birmingham, Alabama 35294, USA
| | - Adeel Mehmood
- Department of Biology, 464 Campbell Hall, 1300 University Boulevard, University of Alabama at Birmingham, Alabama 35294, USA
- Department of Computer Science, University of Alabama at Birmingham, 1402 10th Ave. S. , Birmingham, AL 35294, USA
| | - Mohammad Athar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Alabama 35294, USA
| | - M. Shahid Mukhtar
- Department of Biology, 464 Campbell Hall, 1300 University Boulevard, University of Alabama at Birmingham, Alabama 35294, USA
- Nutrition Obesity Research Center, 1675 University Blvd, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Surgery, 1808 7th Ave S, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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The ESCRT-0 Protein HRS Interacts with the Human T Cell Leukemia Virus Type 2 Antisense Protein APH-2 and Suppresses Viral Replication. J Virol 2019; 94:JVI.01311-19. [PMID: 31597781 DOI: 10.1128/jvi.01311-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/01/2019] [Indexed: 01/18/2023] Open
Abstract
The divergent clinical outcomes of human T cell leukemia virus type 1 (HTLV-1) and HTLV-2 infections have been attributed to functional differences in their antisense proteins. In contrast to HTLV-1 bZIP factor (HBZ), the role of the antisense protein of HTLV-2 (APH-2) in HTLV-2 infection is poorly understood. In previous studies, we identified the endosomal sorting complex required for transport 0 (ESCRT-0) subunit HRS as a novel interaction partner of APH-2 but not HBZ. HRS is a master regulator of endosomal protein sorting for lysosomal degradation and is hijacked by many viruses to promote replication. However, no studies to date have shown a link between HTLVs and HRS. In this study, we sought to characterize the interaction between HRS and APH-2 and to investigate the impact of HRS on the life cycle of HTLV-2. We confirmed a direct specific interaction between APH-2 and HRS and showed that the CC2 domain of HRS and the N-terminal domain of APH-2 mediate their interaction. We demonstrated that HRS recruits APH-2 to early endosomes, possibly furnishing an entry route into the endosomal/lysosomal pathway. We demonstrated that inhibition of this pathway using either bafilomycin or HRS overexpression substantially extends the half-life of APH-2 and stabilizes Tax2B expression levels. We found that HRS enhances Tax2B-mediated long terminal repeat (LTR) activation, while depletion of HRS enhances HTLV-2 production and release, indicating that HRS may have a negative impact on HTLV-2 replication. Overall, our study provides important new insights into the role of the ESCRT-0 HRS protein, and by extension the ESCRT machinery and the endosomal/lysosomal pathway, in HTLV-2 infection.IMPORTANCE While APH-2 is the only viral protein consistently expressed in infected carriers, its role in HTLV-2 infection is poorly understood. In this study, we characterized the interaction between the ESCRT-0 component HRS and APH-2 and explored the role of HRS in HTLV-2 replication. HRS is a master regulator of protein sorting for lysosomal degradation, a feature that is manipulated by several viruses to promote replication. Unexpectedly, we found that HRS targets APH-2 and possibly Tax2B for lysosomal degradation and has an overall negative impact on HTLV-2 replication and release. The negative impact of interactions between HTLV-2 regulatory proteins and HRS, and by extension the ESCRT machinery, may represent an important strategy used by HTLV-2 to limit virus production and to promote persistence, features that may contribute to the limited pathogenic potential of this infection.
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Kumar S, Lata KS, Sharma P, Bhairappanavar SB, Soni S, Das J. Inferring pathogen-host interactions between Leptospira interrogans and Homo sapiens using network theory. Sci Rep 2019; 9:1434. [PMID: 30723266 PMCID: PMC6363727 DOI: 10.1038/s41598-018-38329-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/20/2018] [Indexed: 12/19/2022] Open
Abstract
Leptospirosis is the most emerging zoonotic disease of epidemic potential caused by pathogenic species of Leptospira. The bacterium invades the host system and causes the disease by interacting with the host proteins. Analyzing these pathogen-host protein interactions (PHPIs) may provide deeper insight into the disease pathogenesis. For this analysis, inter-species as well as intra-species protein interactions networks of Leptospira interrogans and human were constructed and investigated. The topological analyses of these networks showed lesser connectivity in inter-species network than intra-species, indicating the perturbed nature of the inter-species network. Hence, it can be one of the reasons behind the disease development. A total of 35 out of 586 PHPIs were identified as key interactions based on their sub-cellular localization. Two outer membrane proteins (GpsA and MetXA) and two periplasmic proteins (Flab and GlyA) participating in PHPIs were found conserved in all pathogenic, intermediate and saprophytic spp. of Leptospira. Furthermore, the bacterial membrane proteins involved in PHPIs were found playing major roles in disruption of the immune systems and metabolic processes within host and thereby causing infectious disease. Thus, the present results signify that the membrane proteins participating in such interactions hold potential to serve as effective immunotherapeutic candidates for vaccine development.
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Affiliation(s)
- Swapnil Kumar
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Kumari Snehkant Lata
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Priyanka Sharma
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Shivarudrappa B Bhairappanavar
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Subhash Soni
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Jayashankar Das
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India.
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Yamagishi M, Fujikawa D, Watanabe T, Uchimaru K. HTLV-1-Mediated Epigenetic Pathway to Adult T-Cell Leukemia-Lymphoma. Front Microbiol 2018; 9:1686. [PMID: 30087673 PMCID: PMC6066519 DOI: 10.3389/fmicb.2018.01686] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), the first reported human oncogenic retrovirus, is the etiologic agent of highly aggressive, currently incurable diseases such as adult T-cell leukemia-lymphoma (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1 proteins, including Tax and HBZ, have been shown to have critical roles in HTLV-1 pathogenicity, yet the underlying mechanisms of HTLV-1-driven leukemogenesis are unclear. The frequent disruption of genetic and epigenetic gene regulation in various types of malignancy, including ATL, is evident. In this review, we illustrate a focused range of topics about the establishment of HTLV-1 memory: (1) genetic lesion in the Tax interactome pathway, (2) gene regulatory loop/switch, (3) disordered chromatin regulation, (4) epigenetic lock by the modulation of epigenetic factors, (5) the loss of gene fine-tuner microRNA, and (6) the alteration of chromatin regulation by HTLV-1 integration. We discuss the persistent influence of Tax-dependent epigenetic changes even after the disappearance of HTLV-1 gene expression due to the viral escape from the immune system, which is a remaining challenge in HTLV-1 research. The summarized evidence and conceptualized description may provide a better understanding of HTLV-1-mediated cellular transformation and the potential therapeutic strategies to combat HTLV-1-associated diseases.
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Affiliation(s)
- Makoto Yamagishi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Dai Fujikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Toshiki Watanabe
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kaoru Uchimaru
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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11
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Vázquez-Ulloa E, Lizano M, Sjöqvist M, Olmedo-Nieva L, Contreras-Paredes A. Deregulation of the Notch pathway as a common road in viral carcinogenesis. Rev Med Virol 2018; 28:e1988. [PMID: 29956408 DOI: 10.1002/rmv.1988] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/27/2018] [Accepted: 05/23/2018] [Indexed: 12/15/2022]
Abstract
The Notch pathway is a conserved signaling pathway and a form of direct cell-cell communication related to many biological processes during development and adulthood. Deregulation of the Notch pathway is involved in many diseases, including cancer. Almost 20% of all cancer cases have an infectious etiology, with viruses responsible for at least 1.5 million new cancer cases per year. Seven groups of viruses have been classified as oncogenic: hepatitis B and C viruses (HBV and HCV respectively), Epstein-Barr virus (EBV), Kaposi sarcoma-associated herpesvirus (KSHV), human T lymphotropic virus (HTLV-1), human papillomavirus (HPV), and Merkel cell polyomavirus (MCPyV). These viruses share the ability to manipulate a variety of cell pathways that are critical in proliferation and differentiation, leading to malignant transformation. Viral proteins interact directly or indirectly with different members of the Notch pathway, altering their normal function. This review focuses exclusively on the direct interactions of viral oncoproteins with Notch elements, providing a deeper understanding of the dual behavior of the Notch pathway as activator or suppressor of neoplasia in virus-related cancers.
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Affiliation(s)
- Elenaé Vázquez-Ulloa
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Tecnológico Nacional de México, Instituto Tecnológico de Gustavo A. Madero, Mexico City, Mexico
| | - Marcela Lizano
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Marika Sjöqvist
- Faculty of Science and Engineering, Biosciences, Åbo Akademi University, Turku, Finland
| | - Leslie Olmedo-Nieva
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adriana Contreras-Paredes
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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12
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Nourani E, Khunjush F, Sevilgen FE. Virus–human protein–protein interaction prediction using Bayesian matrix factorization and projection techniques. Biocybern Biomed Eng 2018. [DOI: 10.1016/j.bbe.2018.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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The Enterococcus faecalis virulence factor ElrA interacts with the human Four-and-a-Half LIM Domains Protein 2. Sci Rep 2017; 7:4581. [PMID: 28676674 PMCID: PMC5496941 DOI: 10.1038/s41598-017-04875-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
The commensal bacterium Enterococcus faecalis is a common cause of nosocomial infections worldwide. The increasing prevalence of multi-antibiotic resistant E. faecalis strains reinforces this public health concern. Despite numerous studies highlighting several pathology-related genetic traits, the molecular mechanisms of E. faecalis virulence remain poorly understood. In this work, we studied 23 bacterial proteins that could be considered as virulence factors or involved in the Enterococcus interaction with the host. We systematically tested their interactions with human proteins using the Human ORFeome library, a set of 12,212 human ORFs, in yeast. Among the thousands of tested interactions, one involving the E. faecalis virulence factor ElrA and the human protein FHL2 was evidenced by yeast two-hybrid and biochemically confirmed. Further molecular characterizations allowed defining an FHL2-interacting domain (FID) of ElrA. Deletion of the FID led to an attenuated in vivo phenotype of the mutated strain clearly indicating that this interaction is likely to contribute to the multifactorial virulence of this opportunistic pathogen. Altogether, our results show that FHL2 is the first host cellular protein directly targeted by an E. faecalis virulence factor and that this interaction is involved in Enterococcus pathogenicity.
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14
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Chan CP, Kok KH, Jin DY. Human T-Cell Leukemia Virus Type 1 Infection and Adult T-Cell Leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1018:147-166. [PMID: 29052136 DOI: 10.1007/978-981-10-5765-6_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the first retrovirus discovered to cause adult T-cell leukemia (ATL), a highly aggressive blood cancer. HTLV-1 research in the past 35 years has been most revealing in the mechanisms of viral oncogenesis. HTLV-1 establishes a lifelong persistent infection in CD4+ T lymphocytes. The infection outcome is governed by host immunity. ATL develops in 2-5% of infected individuals 30-50 years after initial exposure. HTLV-1 encodes two oncoproteins Tax and HBZ, which are required for initiation of cellular transformation and maintenance of cell proliferation, respectively. HTLV-1 oncogenesis is driven by a clonal selection and expansion process during which both host and viral factors cooperate to impair genome stability, immune surveillance, and other mechanisms of tumor suppression. A better understanding of HTLV-1 biology and leukemogenesis will reveal new strategies and modalities for ATL prevention and treatment.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Kin-Hang Kok
- Department of Microbiology, The University of Hong Kong, 145 Pokfulam Road, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
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15
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Wright DG, Marchal C, Hoang K, Ankney JA, Nguyen ST, Rushing AW, Polakowski N, Miotto B, Lemasson I. Human T-cell leukemia virus type-1-encoded protein HBZ represses p53 function by inhibiting the acetyltransferase activity of p300/CBP and HBO1. Oncotarget 2016; 7:1687-706. [PMID: 26625199 PMCID: PMC4811490 DOI: 10.18632/oncotarget.6424] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/15/2015] [Indexed: 01/31/2023] Open
Abstract
Adult T-cell leukemia (ATL) is an often fatal malignancy caused by infection with the complex retrovirus, human T-cell Leukemia Virus, type 1 (HTLV-1). In ATL patient samples, the tumor suppressor, p53, is infrequently mutated; however, it has been shown to be inactivated by the viral protein, Tax. Here, we show that another HTLV-1 protein, HBZ, represses p53 activity. In HCT116 p53+/+ cells treated with the DNA-damaging agent, etoposide, HBZ reduced p53-mediated activation of p21/CDKN1A and GADD45A expression, which was associated with a delay in G2 phase-arrest. These effects were attributed to direct inhibition of the histone acetyltransferase (HAT) activity of p300/CBP by HBZ, causing a reduction in p53 acetylation, which has be linked to decreased p53 activity. In addition, HBZ bound to, and inhibited the HAT activity of HBO1. Although HBO1 did not acetylate p53, it acted as a coactivator for p53 at the p21/CDKN1A promoter. Therefore, through interactions with two separate HAT proteins, HBZ impairs the ability of p53 to activate transcription. This mechanism may explain how p53 activity is restricted in ATL cells that do not express Tax due to modifications of the HTLV-1 provirus, which accounts for a majority of patient samples.
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Affiliation(s)
- Diana G Wright
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - Claire Marchal
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216, CNRS, Paris, France
| | - Kimson Hoang
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - John A Ankney
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie T Nguyen
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - Amanda W Rushing
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - Nicholas Polakowski
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
| | - Benoit Miotto
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216, CNRS, Paris, France.,INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Lemasson
- Brody School of Medicine, Department of Microbiology and Immunology, East Carolina University, Greenville, NC, USA
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16
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Enhanced Stabilization of MCL1 by the Human T-Cell Leukemia Virus Type 1 bZIP Factor Is Modulated by Blocking the Recruitment of Cullin 1 to the SCF Complex. Mol Cell Biol 2016; 36:3075-3085. [PMID: 27697867 DOI: 10.1128/mcb.00450-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/23/2016] [Indexed: 11/20/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is an oncogenic retrovirus that is the etiological agent of adult T-cell leukemia (ATL). The HTLV-1 basic leucine zipper factor (HBZ), which is encoded by the minus strand of the provirus, is constitutively expressed in all ATL patient cells and likely contributes to the development and maintenance of ATL. Furthermore, the overexpression of the myeloid cell leukemia 1 (MCL1) protein is frequently observed in hematological cancers as well as several other types of cancers. Here, we found that the expression of HBZ in cells stabilized MCL1 protein expression and suppressed the MCL1-mediated release of cytochrome c from the mitochondria. This effect was mediated by inhibition of the ubiquitin-dependent degradation of MCL1. In a serial binding assay, HBZ interacted with cullin 1 (CUL1) through a head-to-tail interaction. The association between CUL1 and Skp1, which serves as the molecular scaffold for the components of SCF ubiquitin ligase complexes, was markedly repressed in the presence of HBZ. Mechanistic analysis indicated that HBZ abrogated the CUL1 association with Skp1, which in turn promoted the cellular expression of MCL1. This novel function of HBZ likely plays a role in the viral pathogenesis of HTLV-1 and provides important insights into our understanding of the development of ATL.
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17
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Moles R, Bai XT, Chaib-Mezrag H, Nicot C. WRN-targeted therapy using inhibitors NSC 19630 and NSC 617145 induce apoptosis in HTLV-1-transformed adult T-cell leukemia cells. J Hematol Oncol 2016; 9:121. [PMID: 27829440 PMCID: PMC5103433 DOI: 10.1186/s13045-016-0352-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/03/2016] [Indexed: 12/30/2022] Open
Abstract
Background Human T-cell leukemia virus type 1 (HTLV-1) infection is associated with adult T-cell leukemia/lymphoma (ATLL), a lymphoproliferative malignancy with a dismal prognosis and limited therapeutic options. Recent evidence shows that HTLV-1-transformed cells present defects in both DNA replication and DNA repair, suggesting that these cells might be particularly sensitive to treatment with a small helicase inhibitor. Because the “Werner syndrome ATP-dependent helicase” encoded by the WRN gene plays important roles in both cellular proliferation and DNA repair, we hypothesized that inhibition of WRN activity could be used as a new strategy to target ATLL cells. Methods Our analysis demonstrates an apoptotic effect induced by the WRN helicase inhibitor in HTLV-1-transformed cells in vitro and ATL-derived cell lines. Inhibition of cellular proliferation and induction of apoptosis were demonstrated with cell cycle analysis, XTT proliferation assay, clonogenic assay, annexin V staining, and measurement of mitochondrial transmembrane potential. Results Targeted inhibition of the WRN helicase induced cell cycle arrest and apoptosis in HTLV-1-transformed leukemia cells. Treatment with NSC 19630 (WRN inhibitor) induces S-phase cell cycle arrest, disruption of the mitochondrial membrane potential, and decreased expression of anti-apoptotic factor Bcl-2. These events were associated with activation of caspase-3-dependent apoptosis in ATL cells. We identified some ATL cells, ATL-55T and LMY1, less sensitive to NSC 19630 but sensitive to another WRN inhibitor, NSC 617145. Conclusions WRN is essential for survival of ATL cells. Our studies suggest that targeting the WRN helicase with small inhibitors is a novel promising strategy to target HTLV-1-transformed ATL cells.
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Affiliation(s)
- R Moles
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - X T Bai
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - H Chaib-Mezrag
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - C Nicot
- Department of Pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA. .,Department of Pathology and Laboratory Medicine, Center for Viral Oncology, KU Cancer Center, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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18
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Kheirabadi M, Taghdir M. Is unphosphorylated Rex, as multifunctional protein of HTLV-1, a fully intrinsically disordered protein? An in silico study. Biochem Biophys Rep 2016; 8:14-22. [PMID: 28955936 PMCID: PMC5613702 DOI: 10.1016/j.bbrep.2016.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 02/01/2023] Open
Abstract
Intracellularlocation of a viral unspliced mRNA in host cell is a crucial factor for normal life of the virus. Rex is a neucleo-cytoplasmic shuffling protein of Human T-cell Leukemia Virus-1(HTLV-1)which has important role in active transport of cargo-containing RNA from nucleus to cytoplasm. Therefore, it plays a crucial role in the disease development by the virus. In spite of its importance, the 3d-structurephosphorylated and unphosphorylated of this protein has not been determined. In this study, first we predicted whether Rex protein is an ordered or disordered protein. In second step protein 3Dstructure of Rex was obtained. The content of disorder-promoting amino acids, flexibility, hydrophobicity, short linear motifs (SLiMs) and protein binding regions and probability of Rex crystallization were calculated by various In Silico methods. The3D models of Rex protein were obtained by various In Silico methods, such as homology modeling, threading and ab initio, including; I-TASSER, LOMETS, SPARSKS, ROBBETA and QUARK servers. By comparing and analyzing Qmean, z-scores and energy levels of selected models, the best structures with highest favored region in Ramachandran plot (higher than 90%) was refined with MODREFINER software. In silico analysis of Rex physicochemical properties and also predicted SLiMs and binding regions sites confirms that unphosphorylated Rex protein in HTLV-1 as Rev protin in HIV is wholly disordered protein belongs to the class of intrinsically disordered proteins with extended disorder (native coils, native pre-molten globules). Physico-chemical properties of Rex protein were confirmed unphosphorilated Rex protein is a wholly intrinsically disordered protein. The 3d-structure model of Rex protein was determined.
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Affiliation(s)
- Mitra Kheirabadi
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, 9617976487 Sabzevar, Iran
| | - Majid Taghdir
- Departmentof Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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19
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Mei S, Zhang K. Computational discovery of Epstein-Barr virus targeted human genes and signalling pathways. Sci Rep 2016; 6:30612. [PMID: 27470517 PMCID: PMC4965740 DOI: 10.1038/srep30612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/05/2016] [Indexed: 12/22/2022] Open
Abstract
Epstein-Barr virus (EBV) plays important roles in the origin and the progression of human carcinomas, e.g. diffuse large B cell tumors, T cell lymphomas, etc. Discovering EBV targeted human genes and signaling pathways is vital to understand EBV tumorigenesis. In this study we propose a noise-tolerant homolog knowledge transfer method to reconstruct functional protein-protein interactions (PPI) networks between Epstein-Barr virus and Homo sapiens. The training set is augmented via homolog instances and the homolog noise is counteracted by support vector machine (SVM). Additionally we propose two methods to define subcellular co-localization (i.e. stringent and relaxed), based on which to further derive physical PPI networks. Computational results show that the proposed method achieves sound performance of cross validation and independent test. In the space of 648,672 EBV-human protein pairs, we obtain 51,485 functional interactions (7.94%), 869 stringent physical PPIs and 46,050 relaxed physical PPIs. Fifty-eight evidences are found from the latest database and recent literature to validate the model. This study reveals that Epstein-Barr virus interferes with normal human cell life, such as cholesterol homeostasis, blood coagulation, EGFR binding, p53 binding, Notch signaling, Hedgehog signaling, etc. The proteome-wide predictions are provided in the supplementary file for further biomedical research.
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Affiliation(s)
- Suyu Mei
- Software College, Shenyang Normal University, Shenyang, 110034, China
| | - Kun Zhang
- Department of Computer Science, Xavier University of Louisiana, New Orleans, LA 70125, USA
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20
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Daakour S, Hajingabo LJ, Kerselidou D, Devresse A, Kettmann R, Simonis N, Dequiedt F, Twizere JC. Systematic interactome mapping of acute lymphoblastic leukemia cancer gene products reveals EXT-1 tumor suppressor as a Notch1 and FBWX7 common interactor. BMC Cancer 2016; 16:335. [PMID: 27229929 PMCID: PMC4882867 DOI: 10.1186/s12885-016-2374-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Perturbed genotypes in cancer can now be identified by whole genome sequencing of large number of diverse tumor samples, and observed gene mutations can be used for prognosis and classification of cancer subtypes. Although mutations in a few causative genes are directly linked to key signaling pathways perturbation, a global understanding of how known cancer genes drive oncogenesis in human is difficult to assess. METHODS We collected available information about mutated genes in Acute Lymphoblastic Leukemia (ALL). Validated human protein interactions (PPI) were collected from IntAct, HPRD and BioGRID interactomics databases, or obtained using yeast two-hybrid screening assay. RESULTS We have mapped interconnections between 116 cancer census gene products associated with ALL. Combining protein-protein interactions data and cancer-specific gene mutations information, we observed that 63 ALL-gene products are interconnected and identified 37 human proteins interacting with at least 2 ALL-gene products. We highlighted exclusive and coexistence genetic alterations in key signaling pathways including the PI3K/AKT and the NOTCH pathways. We then used different cell lines and reporter assay systems to validate the involvement of EXT1 in the Notch pathway. CONCLUSION We propose that novel ALL-gene candidates can be identified based on their functional association with well-known cancer genes. We identified EXT1, a gene not previously linked to ALL via mutations, as a common interactor of NOTCH1 and FBXW7 regulating the NOTCH pathway in an FBXW7-dependend manner.
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Affiliation(s)
- Sarah Daakour
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Leon Juvenal Hajingabo
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium.,Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles (ULB), Bruxelles, B-1050, Belgium
| | - Despoina Kerselidou
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Aurelie Devresse
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Richard Kettmann
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Nicolas Simonis
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles (ULB), Bruxelles, B-1050, Belgium
| | - Franck Dequiedt
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium
| | - Jean-Claude Twizere
- Laboratory of Protein Signaling and Interactions, Molecular Biology in Diseases Unit, GIGA-Research, University of Liège, Liège, B-4000, Belgium.
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21
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Wang C, Long W, Peng C, Hu L, Zhang Q, Wu A, Zhang X, Duan X, Wong CCL, Tanaka Y, Xia Z. HTLV-1 Tax Functions as a Ubiquitin E3 Ligase for Direct IKK Activation via Synthesis of Mixed-Linkage Polyubiquitin Chains. PLoS Pathog 2016; 12:e1005584. [PMID: 27082114 PMCID: PMC4833305 DOI: 10.1371/journal.ppat.1005584] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/29/2016] [Indexed: 11/29/2022] Open
Abstract
The HTLV-1 oncoprotein Tax plays a key role in CD4+ T cell transformation by promoting cell proliferation and survival, mainly through permanent activation of the NK-κB pathway and induction of many NF-κB target genes. Elucidating the underlying molecular mechanism is therefore critical in understanding HTLV-1-mediated transformation. Current studies have suggested multiple but controversial mechanisms regarding Tax-induced IKK activation mainly due to blending of primary Tax-induced IKK activation events and secondary IKK activation events induced by cytokines secreted by the primary Tax-induced IKK-NF-κB activation events. We reconstituted Tax-stimulated IKK activation in a cell-free system to dissect the essential cellular components for primary IKK activation by Tax and studied the underlying biochemical mechanism. We found that Tax is a putative E3 ubiquitin ligase, which, together with UbcH2, UhcH5c, or UbcH7, catalyzes the assembly of free mixed-linkage polyubiquitin chains. These free mixed-linkage polyubiquitin chains are then responsible for direct IKK activation by binding to the NEMO subunit of IKK. Our studies revealed the biochemical function of Tax in the process of IKK activation, which utilizes the minimal cellular ubiquitination components for NF-κB activation. Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/HAM), a distinct neurological disorder with inflammatory symptoms and incomplete paralysis of the limbs, and adult T-cell leukemia/lymphoma (ATL), a highly aggressive malignant proliferation of CD4+ T lymphocytes. Both TSP/HAM and ATL are mainly driven by the activation of IκB kinase (IKK)-NF-κB stimulated by HTLV-1 oncoprotein Tax. The molecular mechanism by which Tax activates IKK remains unclear. Here, we found that Tax is an E3 ubiquitin ligase, which, together with its cognate ubiquitin-conjugating enzymes (E2s) UbcH2, UhcH5c, or UbcH7, catalyzes the assembly of unanchored free mixed-linkage polyubiquitin chains. The polyubiquitin chains can activate IKK complex directly by binding to the NEMO subunit. Our studies uncovered the essential cellular factors hijacked by HTLV-1 for infection and pathogenesis, as well as the biochemical function and the underlying mechanism of Tax in the process of IKK activation. Our work might shed light on potential development of therapeutics for TSP/HAM and ATL.
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Affiliation(s)
- Chong Wang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wenying Long
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chao Peng
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Lin Hu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiong Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ailing Wu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoqing Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaotao Duan
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Catherine C. L. Wong
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yuetsu Tanaka
- Department of Immunology, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa, Japan
| | - Zongping Xia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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Molecular Mechanisms of HTLV-1 Cell-to-Cell Transmission. Viruses 2016; 8:74. [PMID: 27005656 PMCID: PMC4810264 DOI: 10.3390/v8030074] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/20/2016] [Accepted: 03/04/2016] [Indexed: 12/14/2022] Open
Abstract
The tumorvirus human T-cell lymphotropic virus type 1 (HTLV-1), a member of the delta-retrovirus family, is transmitted via cell-containing body fluids such as blood products, semen, and breast milk. In vivo, HTLV-1 preferentially infects CD4⁺ T-cells, and to a lesser extent, CD8⁺ T-cells, dendritic cells, and monocytes. Efficient infection of CD4⁺ T-cells requires cell-cell contacts while cell-free virus transmission is inefficient. Two types of cell-cell contacts have been described to be critical for HTLV-1 transmission, tight junctions and cellular conduits. Further, two non-exclusive mechanisms of virus transmission at cell-cell contacts have been proposed: (1) polarized budding of HTLV-1 into synaptic clefts; and (2) cell surface transfer of viral biofilms at virological synapses. In contrast to CD4⁺ T-cells, dendritic cells can be infected cell-free and, to a greater extent, via viral biofilms in vitro. Cell-to-cell transmission of HTLV-1 requires a coordinated action of steps in the virus infectious cycle with events in the cell-cell adhesion process; therefore, virus propagation from cell-to-cell depends on specific interactions between cellular and viral proteins. Here, we review the molecular mechanisms of HTLV-1 transmission with a focus on the HTLV-1-encoded proteins Tax and p8, their impact on host cell factors mediating cell-cell contacts, cytoskeletal remodeling, and thus, virus propagation.
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Nakano K, Watanabe T. HTLV-1 Rex Tunes the Cellular Environment Favorable for Viral Replication. Viruses 2016; 8:58. [PMID: 26927155 PMCID: PMC4810248 DOI: 10.3390/v8030058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/09/2016] [Accepted: 02/09/2016] [Indexed: 12/18/2022] Open
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) Rex is a viral RNA binding protein. The most important and well-known function of Rex is stabilizing and exporting viral mRNAs from the nucleus, particularly for unspliced/partially-spliced mRNAs encoding the structural proteins essential for viral replication. Without Rex, these unspliced viral mRNAs would otherwise be completely spliced. Therefore, Rex is vital for the translation of structural proteins and the stabilization of viral genomic RNA and, thus, for viral replication. Rex schedules the period of extensive viral replication and suppression to enter latency. Although the importance of Rex in the viral life-cycle is well understood, the underlying molecular mechanism of how Rex achieves its function has not been clarified. For example, how does Rex protect unspliced/partially-spliced viral mRNAs from the host cellular splicing machinery? How does Rex protect viral mRNAs, antigenic to eukaryotic cells, from cellular mRNA surveillance mechanisms? Here we will discuss these mechanisms, which explain the function of Rex as an organizer of HTLV-1 expression based on previously and recently discovered aspects of Rex. We also focus on the potential influence of Rex on the homeostasis of the infected cell and how it can exert its function.
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Affiliation(s)
- Kazumi Nakano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan.
| | - Toshiki Watanabe
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan.
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Maheshwari S, Brylinski M. Template-based identification of protein–protein interfaces using eFindSitePPI. Methods 2016; 93:64-71. [DOI: 10.1016/j.ymeth.2015.07.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/12/2015] [Accepted: 07/29/2015] [Indexed: 11/26/2022] Open
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Yang R, Motin VL. Yersinia pestis in the Age of Big Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 918:257-272. [PMID: 27722866 DOI: 10.1007/978-94-024-0890-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
As omics-driven technologies developed rapidly, genomics, transcriptomics, proteomics, metabolomics and other omics-based data have been accumulated in unprecedented speed. Omics-driven big data in biology have changed our way of research. "Big science" has promoted our understanding of biology in a holistic overview that is impossibly achieved by traditional hypothesis-driven research. In this chapter, we gave an overview of omics-driven research on Y. pestis, provided a way of thinking on Yersinia pestis research in the age of big data, and made some suggestions to integrate omics-based data for systems understanding of Y. pestis.
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Affiliation(s)
- Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, No. Dongdajie, Fengtai, Beijing, 100071, China.
| | - Vladimir L Motin
- Departments of Pathology and Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
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Kusano S, Yoshimitsu M, Hachiman M, Ikeda M. I-mfa domain proteins specifically interact with HTLV-1 Tax and repress its transactivating functions. Virology 2015; 486:219-27. [PMID: 26469549 DOI: 10.1016/j.virol.2015.09.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 05/31/2015] [Accepted: 09/25/2015] [Indexed: 12/21/2022]
Abstract
The I-mfa domain proteins HIC (also known as MDFIC) and I-mfa (also known as MDFI) are candidate tumor suppressor genes that are involved in cellular and viral transcriptional regulation. Here, we show that HIC and I-mfa directly interact with human T-cell leukemia virus type-1 (HTLV-1) Tax protein in vitro. In addition, HIC and I-mfa repress Tax-dependent transactivation of an HTLV-1 long terminal repeat (LTR) reporter construct in COS-1, Jurkat and high-Tax-producing HTLV-1-infected T cells. HIC also interacts with Tax through its I-mfa domain in vivo and represses Tax-dependent transactivation of HTLV-1 LTR and NF-κB reporter constructs in an interaction-dependent manner. Furthermore, we show that HIC decreases the nuclear distribution and stimulates the proteasomal degradation of Tax. These data reveal that HIC specifically interacts with HTLV-1 Tax and negatively regulates Tax transactivational activity by altering its subcellular distribution and stability.
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Affiliation(s)
- Shuichi Kusano
- Division of Persistent and Oncogenic Viruses, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan.
| | - Makoto Yoshimitsu
- Division of Hematology and Immunology, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Miho Hachiman
- Division of Hematology and Immunology, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Masanori Ikeda
- Division of Persistent and Oncogenic Viruses, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
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SIRT1 Suppresses Human T-Cell Leukemia Virus Type 1 Transcription. J Virol 2015; 89:8623-31. [PMID: 26063426 DOI: 10.1128/jvi.01229-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/02/2015] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Human T-cell leukemia virus type 1 (HTLV-1)-associated diseases are poorly treatable, and HTLV-1 vaccines are not available. High proviral load is one major risk factor for disease development. HTLV-1 encodes Tax oncoprotein, which activates transcription from viral long terminal repeats (LTR) and various types of cellular promoters. Counteracting Tax function might have prophylactic and therapeutic benefits. In this work, we report on the suppression of Tax activation of HTLV-1 LTR by SIRT1 deacetylase. The transcriptional activity of Tax on the LTR was largely ablated when SIRT1 was overexpressed, but Tax activation of NF-κB was unaffected. On the contrary, the activation of the LTR by Tax was boosted when SIRT1 was depleted. Treatment of cells with resveratrol shunted Tax activity in a SIRT1-dependent manner. The activation of SIRT1 in HTLV-1-transformed T cells by resveratrol potently inhibited HTLV-1 proviral transcription and Tax expression, whereas compromising SIRT1 by specific inhibitors augmented HTLV-1 mRNA expression. The administration of resveratrol also decreased the production of cell-free HTLV-1 virions from MT2 cells and the transmission of HTLV-1 from MT2 cells to uninfected Jurkat cells in coculture. SIRT1 associated with Tax in HTLV-1-transformed T cells. Treatment with resveratrol prevented the interaction of Tax with CREB and the recruitment of CREB, CRTC1, and p300 to Tax-responsive elements in the LTR. Our work demonstrates the negative regulatory function of SIRT1 in Tax activation of HTLV-1 transcription. Small-molecule activators of SIRT1 such as resveratrol might be considered new prophylactic and therapeutic agents in HTLV-1-associated diseases. IMPORTANCE Human T-cell leukemia virus type 1 (HTLV-1) causes a highly lethal blood cancer or a chronic debilitating disease of the spinal cord. Treatments are unsatisfactory, and vaccines are not available. Disease progression is associated with robust expression of HTLV-1 genes. Suppressing HTLV-1 gene expression might have preventive and therapeutic benefits. It is therefore critical that host factors controlling HTLV-1 gene expression be identified and characterized. This work reveals a new host factor that suppresses HTLV-1 gene expression and a natural compound that activates this suppression. Our findings not only provide new knowledge of the host control of HTLV-1 gene expression but also suggest a new strategy of using natural compounds for prevention and treatment of HTLV-1-associated diseases.
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Huo T, Liu W, Guo Y, Yang C, Lin J, Rao Z. Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. BMC Bioinformatics 2015; 16:100. [PMID: 25887594 PMCID: PMC4456996 DOI: 10.1186/s12859-015-0535-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/13/2015] [Indexed: 12/28/2022] Open
Abstract
Background Emergence of multiple drug resistant strains of M. tuberculosis (MDR-TB) threatens to derail global efforts aimed at reigning in the pathogen. Co-infections of M. tuberculosis with HIV are difficult to treat. To counter these new challenges, it is essential to study the interactions between M. tuberculosis and the host to learn how these bacteria cause disease. Results We report a systematic flow to predict the host pathogen interactions (HPIs) between M. tuberculosis and Homo sapiens based on sequence motifs. First, protein sequences were used as initial input for identifying the HPIs by ‘interolog’ method. HPIs were further filtered by prediction of domain-domain interactions (DDIs). Functional annotations of protein and publicly available experimental results were applied to filter the remaining HPIs. Using such a strategy, 118 pairs of HPIs were identified, which involve 43 proteins from M. tuberculosis and 48 proteins from Homo sapiens. A biological interaction network between M. tuberculosis and Homo sapiens was then constructed using the predicted inter- and intra-species interactions based on the 118 pairs of HPIs. Finally, a web accessible database named PATH (Protein interactions of M. tuberculosis and Human) was constructed to store these predicted interactions and proteins. Conclusions This interaction network will facilitate the research on host-pathogen protein-protein interactions, and may throw light on how M. tuberculosis interacts with its host. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0535-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tong Huo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Wei Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Pharmacy, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Pharmacy, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Pharmacy, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China. .,College of Life Sciences, Nankai University, Tianjin, 300071, China. .,Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
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Jain P, Lavorgna A, Sehgal M, Gao L, Ginwala R, Sagar D, Harhaj EW, Khan ZK. Myocyte enhancer factor (MEF)-2 plays essential roles in T-cell transformation associated with HTLV-1 infection by stabilizing complex between Tax and CREB. Retrovirology 2015; 12:23. [PMID: 25809782 PMCID: PMC4374383 DOI: 10.1186/s12977-015-0140-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 01/15/2015] [Indexed: 12/17/2022] Open
Abstract
Background The exact molecular mechanisms regarding HTLV-1 Tax-mediated viral gene expression and CD4 T-cell transformation have yet to be fully delineated. Herein, utilizing virus-infected primary CD4+ T cells and the virus-producing cell line, MT-2, we describe the involvement and regulation of Myocyte enhancer factor-2 (specifically MEF-2A) during the course of HTLV-1 infection and associated disease syndrome. Results Inhibition of MEF-2 expression by shRNA and its activity by HDAC9 led to reduced viral replication and T-cell transformation in correlation with a heightened expression of MEF-2 in ATL patients. Mechanistically, MEF-2 was recruited to the viral promoter (LTR, long terminal repeat) in the context of chromatin, and constituted Tax/CREB transcriptional complex via direct binding to the HTLV-1 LTR. Furthermore, an increase in MEF-2 expression was observed upon infection in an extent similar to CREB (known Tax-interacting transcription factor), and HATs (p300, CBP, and p/CAF). Confocal imaging confirmed MEF-2 co-localization with Tax and these proteins were also shown to interact by co-immunoprecipitation. MEF-2 stabilization of Tax/CREB complex was confirmed by a novel promoter-binding assay that highlighted the involvement of NFAT (nuclear factor of activated T cells) in this process via Tax-mediated activation of calcineurin (a calcium-dependent serine-threonine phosphatase). MEF-2-integrated signaling pathways (PI3K/Akt, NF-κB, MAPK, JAK/STAT, and TGF-β) were also activated during HTLV-1 infection of primary CD4+ T cells, possibly regulating MEF-2 activity. Conclusions We demonstrate the involvement of MEF-2 in Tax-mediated LTR activation, viral replication, and T-cell transformation in correlation with its heightened expression in ATL patients through direct binding to DNA within the HTLV-1 LTR. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0140-1) contains supplementary material, which is available to authorized users.
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Mei S, Zhu H. A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks. Sci Rep 2015; 5:8034. [PMID: 25620466 PMCID: PMC5379509 DOI: 10.1038/srep08034] [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: 09/02/2014] [Accepted: 12/22/2014] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interaction (PPI) prediction is generally treated as a problem of binary classification wherein negative data sampling is still an open problem to be addressed. The commonly used random sampling is prone to yield less representative negative data with considerable false negatives. Meanwhile rational constraints are seldom exerted on model selection to reduce the risk of false positive predictions for most of the existing computational methods. In this work, we propose a novel negative data sampling method based on one-class SVM (support vector machine, SVM) to predict proteome-wide protein interactions between HTLV retrovirus and Homo sapiens, wherein one-class SVM is used to choose reliable and representative negative data, and two-class SVM is used to yield proteome-wide outcomes as predictive feedback for rational model selection. Computational results suggest that one-class SVM is more suited to be used as negative data sampling method than two-class PPI predictor, and the predictive feedback constrained model selection helps to yield a rational predictive model that reduces the risk of false positive predictions. Some predictions have been validated by the recent literature. Lastly, gene ontology based clustering of the predicted PPI networks is conducted to provide valuable cues for the pathogenesis of HTLV retrovirus.
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Affiliation(s)
- Suyu Mei
- 1] Software College, Shenyang Normal University, Shenyang, 110034, China [2] Bioinformatics Section, School of Biomedical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Hao Zhu
- Bioinformatics Section, School of Biomedical Sciences, Southern Medical University, Guangzhou, 510515, China
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31
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Lemmens I, Lievens S, Tavernier J. MAPPIT, a mammalian two-hybrid method for in-cell detection of protein-protein interactions. Methods Mol Biol 2015; 1278:447-55. [PMID: 25859968 DOI: 10.1007/978-1-4939-2425-7_29] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
MAPPIT (MAmmalian Protein-Protein Interaction Trap) is a two-hybrid technology that facilitates the detection and analysis of interactions between proteins in living mammalian cells. The system is based on type 1 cytokine receptor signaling. The bait protein of interest is fused to a chimeric signaling-deficient cytokine receptor, the signaling competence of which is restored upon recruitment of a prey protein that is coupled to a functional cytokine receptor domain. MAPPIT exhibits an excellent signal-to-noise ratio, detects a wide variety of protein-protein interactions (PPIs) including transient and indirect interactions, and has been shown to be highly complementary to other two-hybrid methods with respect to the interactions it can detect. Variants of the method were developed to allow large-scale PPI screening, mapping of protein interaction interfaces, PPI inhibitor screening and drug profiling. This chapter describes a basic 4-day MAPPIT protocol for the analysis of interaction between two designated proteins.
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Affiliation(s)
- Irma Lemmens
- Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000, Ghent, Belgium
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32
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Martins CPS, Gomes OA, Martins ML, de Carvalho LD, de Souza JG, Da Fonseca FG, dos Santos RGS, Andrade MS, Zani CL, de Souza-Fagundes EM, Barbosa-Stancioli EF. A reduction of viral mRNA, proteins and induction of altered morphogenesis reveals the anti-HTLV-1 activity of the labdane-diterpene myriadenolide in vitro. BMC Microbiol 2014; 14:331. [PMID: 25539906 PMCID: PMC4302425 DOI: 10.1186/s12866-014-0331-2] [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: 07/02/2014] [Accepted: 12/17/2014] [Indexed: 01/01/2023] Open
Abstract
Background Human T-lymphotropic virus 1 (HTLV-1) has been associated with leukemia/lymphoma (ATL) and myelopathy/tropical spastic paraparesis (HAM/TSP), in addition to other inflammatory diseases as well as infection complications. Therapeutic approaches for HTLV-1-related pathologies are limited. The labdane diterpene myriadenolide (AMY) is a natural product that exhibit biological activities, such as anti-inflammatory and antiviral activity as reported for HIV and herpesvirus. Results We demonstrated that this natural product was able to inhibit the expression of gag-pol mRNA and substantially reduced the expression of the structural proteins p19 and gp46. Comparison of treated and untreated cells shows that AMY alters both the morphology and the release of viral particles. The Atomic Force Microscopy assay showed that the AMY treatment reduced the number of particles on the cell surface by 47%. Conclusion We demonstrated that the labdane diterpene myriadenolide reduced the expression of the structural proteins and the budding of viral particles, besides induces altered morphogenesis of HTLV-1, conferring on AMY a new antiviral activity that may be useful for the development of new compounds with specific anti-HTLV-1 activity.
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Affiliation(s)
- Camila Pacheco Silveira Martins
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil. .,Interdisciplinary HTLV Research Group - GIPH - Fundação HEMOMINAS, Belo Horizonte, Minas Gerais, Brazil.
| | - Orlando Abreu Gomes
- Núcleo de Ciências Exatas - FACE - Universidade FUMEC, Belo Horizonte, Minas Gerais, Brazil.
| | - Marina Lobato Martins
- Interdisciplinary HTLV Research Group - GIPH - Fundação HEMOMINAS, Belo Horizonte, Minas Gerais, Brazil. .,Serviço de Pesquisa, Fundação HEMOMINAS, Belo Horizonte, Minas Gerais, Brazil.
| | - Luciana Debortoli de Carvalho
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil. .,Interdisciplinary HTLV Research Group - GIPH - Fundação HEMOMINAS, Belo Horizonte, Minas Gerais, Brazil.
| | - Jaqueline Gontijo de Souza
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil. .,Interdisciplinary HTLV Research Group - GIPH - Fundação HEMOMINAS, Belo Horizonte, Minas Gerais, Brazil.
| | - Flavio Guimaraes Da Fonseca
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil.
| | - Rodrigo Gonçalves Silva dos Santos
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil. .,Interdisciplinary HTLV Research Group - GIPH - Fundação HEMOMINAS, Belo Horizonte, Minas Gerais, Brazil.
| | | | - Carlos Leomar Zani
- Centro de Pesquisas Renè Rachou, FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil.
| | - Elaine Maria de Souza-Fagundes
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Edel Figueiredo Barbosa-Stancioli
- Laboratório de Virologia Básica e Aplicada (LVBA), Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil. .,Interdisciplinary HTLV Research Group - GIPH - Fundação HEMOMINAS, Belo Horizonte, Minas Gerais, Brazil.
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Alibek K, Irving S, Sautbayeva Z, Kakpenova A, Bekmurzayeva A, Baiken Y, Imangali N, Shaimerdenova M, Mektepbayeva D, Balabiyev A, Chinybayeva A. Disruption of Bcl-2 and Bcl-xL by viral proteins as a possible cause of cancer. Infect Agent Cancer 2014; 9:44. [PMID: 25699089 PMCID: PMC4333878 DOI: 10.1186/1750-9378-9-44] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023] Open
Abstract
The Bcl proteins play a critical role in apoptosis, as mutations in family members interfere with normal programmed cell death. Such events can cause cell transformation, potentially leading to cancer. Recent discoveries indicate that some viral proteins interfere with Bcl proteins either directly or indirectly; however, these data have not been systematically described. Some viruses encode proteins that reprogramme host cellular signalling pathways controlling cell differentiation, proliferation, genomic integrity, cell death, and immune system recognition. This review analyses and summarises the existing data and discusses how viral proteins interfere with normal pro- and anti-apoptotic functions of Bcl-2 and Bcl-xL. Particularly, this article focuses on how viral proteins, such as Herpesviruses, HTLV-1, HPV and HCV, block apoptosis and how accumulation of such interference predisposes cancer development. Finally, we discuss possible ways to prevent and treat cancers using a combination of traditional therapies and antiviral preparations that are effective against these viruses.
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Affiliation(s)
- Kenneth Alibek
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan ; National Medical Holding, 2 Syganak Street, Astana, 010000 Kazakhstan
| | - Stephanie Irving
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Zarina Sautbayeva
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Ainur Kakpenova
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Aliya Bekmurzayeva
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Yeldar Baiken
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Nurgul Imangali
- School of Science and Technology, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Madina Shaimerdenova
- School of Science and Technology, Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Damel Mektepbayeva
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Arnat Balabiyev
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
| | - Aizada Chinybayeva
- Nazarbayev University Research and Innovation System (NURIS), Nazarbayev University, 53 Kabanbay Batyr Avenue, Astana, 010000 Kazakhstan
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Halehalli RR, Nagarajaram HA. Molecular principles of human virus protein-protein interactions. ACTA ACUST UNITED AC 2014; 31:1025-33. [PMID: 25417202 DOI: 10.1093/bioinformatics/btu763] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/12/2014] [Indexed: 01/01/2023]
Abstract
MOTIVATION Viruses, from the human protein-protein interaction network perspective, target hubs, bottlenecks and interconnected nodes enriched in certain biological pathways. However, not much is known about the general characteristic features of the human proteins interacting with viral proteins (referred to as hVIPs) as well as the motifs and domains utilized by human-virus protein-protein interactions (referred to as Hu-Vir PPIs). RESULTS Our study has revealed that hVIPs are mostly disordered proteins, whereas viral proteins are mostly ordered proteins. Protein disorder in viral proteins and hVIPs varies from one subcellular location to another. In any given viral-human PPI pair, at least one of the two proteins is structurally disordered suggesting that disorder associated conformational flexibility as one of the characteristic features of virus-host interaction. Further analyses reveal that hVIPs are (i) slowly evolving proteins, (ii) associated with high centrality scores in human-PPI network, (iii) involved in multiple pathways, (iv) enriched in eukaryotic linear motifs (ELMs) associated with protein modification, degradation and regulatory processes, (v) associated with high number of splice variants and (vi) expressed abundantly across multiple tissues. These aforementioned findings suggest that conformational flexibility, spatial diversity, abundance and slow evolution are the characteristic features of the human proteins targeted by viral proteins. Hu-Vir PPIs are mostly mediated via domain-motif interactions (DMIs) where viral proteins employ motifs that mimic host ELMs to bind to domains in human proteins. DMIs are shared among viruses belonging to different families indicating a possible convergent evolution of these motifs to help viruses to adopt common strategies to subvert host cellular pathways. AVAILABILITY AND IMPLEMENTATION Hu-Vir PPI data, DDI and DMI data for human-virus PPI can be downloaded from http://cdfd.org.in/labpages/computational_biology_datasets.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rachita Ramachandra Halehalli
- Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500001, India and Graduate School, Manipal University, Manipal, 576104, Karnataka, India
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Identification and characterization of HTLV-1 HBZ post-translational modifications. PLoS One 2014; 9:e112762. [PMID: 25389759 PMCID: PMC4229220 DOI: 10.1371/journal.pone.0112762] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/14/2014] [Indexed: 11/19/2022] Open
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) is estimated to infect 15–25 million people worldwide, with several areas including southern Japan and the Caribbean basin being endemic. The virus is the etiological agent of debilitating and fatal diseases, for which there is currently no long-term cure. In the majority of cases of leukemia caused by HTLV-1, only a single viral gene, hbz, and its cognate protein, HBZ, are expressed and their importance is increasingly being recognized in the development of HTLV-1-associated disease. We hypothesized that HBZ, like other HTLV-1 proteins, has properties and functions regulated by post-translational modifications (PTMs) that affect specific signaling pathways important for disease development. To date, PTM of HBZ has not been described. We used an affinity-tagged protein and mass spectrometry method to identify seven modifications of HBZ for the first time. We examined how these PTMs affected the ability of HBZ to modulate several pathways, as measured using luciferase reporter assays. Herein, we report that none of the identified PTMs affected HBZ stability or its regulation of tested pathways.
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Guirimand T, Delmotte S, Navratil V. VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. Nucleic Acids Res 2014; 43:D583-7. [PMID: 25392406 PMCID: PMC4383936 DOI: 10.1093/nar/gku1121] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
VirHostNet release 2.0 (http://virhostnet.prabi.fr) is a knowledgebase dedicated to the network-based exploration of virus–host protein–protein interactions. Since the previous VirhostNet release (2009), a second run of manual curation was performed to annotate the new torrent of high-throughput protein–protein interactions data from the literature. This resource is shared publicly, in PSI-MI TAB 2.5 format, using a PSICQUIC web service. The new interface of VirHostNet 2.0 is based on Cytoscape web library and provides a user-friendly access to the most complete and accurate resource of virus–virus and virus–host protein–protein interactions as well as their projection onto their corresponding host cell protein interaction networks. We hope that the VirHostNet 2.0 system will facilitate systems biology and gene-centered analysis of infectious diseases and will help to identify new molecular targets for antiviral drugs design. This resource will also continue to help worldwide scientists to improve our knowledge on molecular mechanisms involved in the antiviral response mediated by the cell and in the viral strategies selected by viruses to hijack the host immune system.
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Affiliation(s)
- Thibaut Guirimand
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Stéphane Delmotte
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France UMR5558, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
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Mukai R, Ohshima T. HTLV-1 bZIP factor suppresses the centromere protein B (CENP-B)-mediated trimethylation of histone H3K9 through the abrogation of DNA-binding ability of CENP-B. J Gen Virol 2014; 96:159-164. [PMID: 25281565 DOI: 10.1099/vir.0.070201-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human T-cell leukaemia virus type-1 (HTLV-1) infection causes adult T-cell leukaemia (ATL). The viral protein HTLV-1 bZIP factor (HBZ) is constitutively expressed in ATL cells, suggesting that HBZ plays a major role in the pathogenesis of HTLV-1-associated disease. Here, we identified centromere protein B (CENP-B) as a novel interacting partner of HBZ. HBZ and CENP-B associate with their central regions in cells. Furthermore, overexpression of HBZ abrogated the DNA-binding activity of CENP-B to the α-satellite DNA region containing the CENP-B box motif, which in turn inhibited the CENP-B-mediated trimethylation of histone H3K9 in T-cells.
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Affiliation(s)
- Risa Mukai
- Graduate School of Engineering, Tokushima Bunri University, Sanuki, Kagawa, Japan
| | - Takayuki Ohshima
- Faculty of Pharmaceutical Science at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa, Japan.,Graduate School of Engineering, Tokushima Bunri University, Sanuki, Kagawa, Japan
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38
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Bergiers I, Lambert B, Daakour S, Twizere JC, Rezsohazy R. Hox protein interactions: screening and network building. Methods Mol Biol 2014; 1196:319-48. [PMID: 25151173 DOI: 10.1007/978-1-4939-1242-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Understanding the mode of action of Hox proteins requires the identification of molecular and cellular pathways they take part in. This includes to characterize the networks of protein-protein interactions involving Hox proteins. In this chapter we propose a strategy and methods to map Hox interaction networks, from yeast two-hybrid and high-throughput yeast two-hybrid interaction screening to bioinformatic analyses based on the software platform Cytoscape.
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Affiliation(s)
- Isabelle Bergiers
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-5 box L7.07.10, Louvain-la-Neuve, 1348, Belgium
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Mei S, Zhu H. Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens. BMC Bioinformatics 2014; 15:245. [PMID: 25037487 PMCID: PMC4133621 DOI: 10.1186/1471-2105-15-245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 07/14/2014] [Indexed: 11/15/2022] Open
Abstract
Background Human T-cell leukemia viruses (HTLV) tend to induce some fatal human diseases like Adult T-cell Leukemia (ATL) by targeting human T lymphocytes. To indentify the protein-protein interactions (PPI) between HTLV viruses and Homo sapiens is one of the significant approaches to reveal the underlying mechanism of HTLV infection and host defence. At present, as biological experiments are labor-intensive and expensive, the identified part of the HTLV-human PPI networks is rather small. Although recent years have witnessed much progress in computational modeling for reconstructing pathogen-host PPI networks, data scarcity and data unavailability are two major challenges to be effectively addressed. To our knowledge, no computational method for proteome-wide HTLV-human PPI networks reconstruction has been reported. Results In this work we develop Multi-instance Adaboost method to conduct homolog knowledge transfer for computationally reconstructing proteome-wide HTLV-human PPI networks. In this method, the homolog knowledge in the form of gene ontology (GO) is treated as auxiliary homolog instance to address the problems of data scarcity and data unavailability, while the potential negative knowledge transfer is automatically attenuated by AdaBoost instance reweighting. The cross validation experiments show that the homolog knowledge transfer in the form of independent homolog instances can effectively enrich the feature information and substitute for the missing GO information. Moreover, the independent tests show that the method can validate 70.3% of the recently curated interactions, significantly exceeding the 2.1% recognition rate by the HT-Y2H experiment. We have used the method to reconstruct the proteome-wide HTLV-human PPI networks and further conducted gene ontology based clustering of the predicted networks for further biomedical research. The gene ontology based clustering analysis of the predictions provides much biological insight into the pathogenesis of HTLV retroviruses. Conclusions The Multi-instance AdaBoost method can effectively address the problems of data scarcity and data unavailability for the proteome-wide HTLV-human PPI interaction networks reconstruction. The gene ontology based clustering analysis of the predictions reveals some important signaling pathways and biological modules that HTLV retroviruses are likely to target. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-245) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suyu Mei
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
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40
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Yu X, Bian X, Throop A, Song L, Moral LD, Park J, Seiler C, Fiacco M, Steel J, Hunter P, Saul J, Wang J, Qiu J, Pipas JM, LaBaer J. Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions. Am J Cancer Res 2014; 4:808-22. [PMID: 24955142 PMCID: PMC4063979 DOI: 10.7150/thno.8255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/27/2014] [Indexed: 12/24/2022] Open
Abstract
Throughout the long history of virus-host co-evolution, viruses have developed delicate strategies to facilitate their invasion and replication of their genome, while silencing the host immune responses through various mechanisms. The systematic characterization of viral protein-host interactions would yield invaluable information in the understanding of viral invasion/evasion, diagnosis and therapeutic treatment of a viral infection, and mechanisms of host biology. With more than 2,000 viral genomes sequenced, only a small percent of them are well investigated. The access of these viral open reading frames (ORFs) in a flexible cloning format would greatly facilitate both in vitro and in vivo virus-host interaction studies. However, the overall progress of viral ORF cloning has been slow. To facilitate viral studies, we are releasing the initiation of our panviral proteome collection of 2,035 ORF clones from 830 viral genes in the Gateway® recombinational cloning system. Here, we demonstrate several uses of our viral collection including highly efficient production of viral proteins using human cell-free expression system in vitro, global identification of host targets for rubella virus using Nucleic Acid Programmable Protein Arrays (NAPPA) containing 10,000 unique human proteins, and detection of host serological responses using micro-fluidic multiplexed immunoassays. The studies presented here begin to elucidate host-viral protein interactions with our systemic utilization of viral ORFs, high-throughput cloning, and proteomic technologies. These valuable plasmid resources will be available to the research community to enable continued viral functional studies.
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Mukai R, Ohshima T. HTLV-1 HBZ positively regulates the mTOR signaling pathway via inhibition of GADD34 activity in the cytoplasm. Oncogene 2014; 33:2317-28. [PMID: 23708656 DOI: 10.1038/onc.2013.181] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 03/30/2013] [Accepted: 04/01/2013] [Indexed: 12/11/2022]
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) infection causes adult T-cell leukemia (ATL). Modulation of the transcriptional control of cellular genes by HTLV-1 is thought to be associated with the development of ATL. The viral protein HTLV-1 basic leucine-zipper factor (HBZ) has been shown to dysregulate the activity of cellular transcription factors. Here, we demonstrate that HBZ is exported from the nucleus to the cytoplasm, where it activates the mammalian target of rapamycin (mTOR) signaling pathway through an association with growth arrest and DNA damage gene 34 (GADD34). The N-terminal region of HBZ interacts with the C-terminal region of GADD34. HBZ contains a functional nuclear export signal (NES) sequence within its N-terminal region and it is exported from the nucleus via the CRM1-dependent pathway. Nuclear export of HBZ is essential for its interaction with GADD34 and increased phosphorylation of S6 kinase, which is an established downstream target of the mTOR pathway. Starvation-induced autophagy is significantly suppressed by the overexpression of HBZ. These findings indicate that HBZ is actively exported to the cytoplasm, where it dysregulates the function of cellular factors.
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Affiliation(s)
- R Mukai
- Faculty of Engineering, Tokushima Bunri University, Sanuki, Kagawa, Japan
| | - T Ohshima
- 1] Faculty of Engineering, Tokushima Bunri University, Sanuki, Kagawa, Japan [2] Faculty of Pharmaceutical Science at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa, Japan
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42
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Rachita HR, Nagarajaram HA. Viral proteins that bridge unconnected proteins and components in the human PPI network. ACTA ACUST UNITED AC 2014; 10:2448-58. [DOI: 10.1039/c4mb00219a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Viral proteins bridging unconnected components of the Hu-PPI network play a crucial role in viral replication and hence form attractive targets for therapeutic interventions.
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Affiliation(s)
- H. R. Rachita
- Centre for DNA Fingerprinting and Diagnostics
- Gruhakalpa
- Hyderabad 500001, India
| | - H. A. Nagarajaram
- Centre for DNA Fingerprinting and Diagnostics
- Gruhakalpa
- Hyderabad 500001, India
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43
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Anupam R, Doueiri R, Green PL. The need to accessorize: molecular roles of HTLV-1 p30 and HTLV-2 p28 accessory proteins in the viral life cycle. Front Microbiol 2013; 4:275. [PMID: 24062732 PMCID: PMC3774995 DOI: 10.3389/fmicb.2013.00275] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/24/2013] [Indexed: 11/25/2022] Open
Abstract
Extensive studies of human T-cell leukemia virus (HTLV)-1 and HTLV-2 over the last three decades have provided detailed knowledge on viral transformation, host–viral interactions and pathogenesis. HTLV-1 is the etiological agent of adult T cell leukemia and multiple neurodegenerative and inflammatory diseases while HTLV-2 disease association remains elusive, with few infected individuals displaying neurodegenerative diseases similar to HTLV-1. The HTLV group of oncoretroviruses has a genome that encodes structural and enzymatic proteins Gag, Pro, and Env, regulatory proteins Tax and Rex, and several accessory proteins from the pX region. Of these proteins, HTLV-1 p30 and HTLV-2 p28 are encoded by the open reading frame II of the pX region. Like most other accessory proteins, p30 and p28 are dispensable for in vitro viral replication and transformation but are required for efficient viral replication and persistence in vivo. Both p30 and p28 regulate viral gene expression at the post-transcriptional level whereas p30 can also function at the transcriptional level. Recently, several reports have implicated p30 and p28 in multiple cellular processes, which provide novel insight into HTLV spread and survival and ultimately pathogenesis. In this review we summarize and compare what is known about p30 and p28, highlighting their roles in viral replication and viral pathogenesis.
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Affiliation(s)
- Rajaneesh Anupam
- Center for Retrovirus Research, The Ohio State University Columbus, OH, USA ; Department of Veterinary Biosciences, The Ohio State University Columbus, OH, USA
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Forlani G, Abdallah R, Accolla RS, Tosi G. The MHC-II transactivator CIITA, a restriction factor against oncogenic HTLV-1 and HTLV-2 retroviruses: similarities and differences in the inhibition of Tax-1 and Tax-2 viral transactivators. Front Microbiol 2013; 4:234. [PMID: 23986750 PMCID: PMC3749491 DOI: 10.3389/fmicb.2013.00234] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 07/30/2013] [Indexed: 11/13/2022] Open
Abstract
The activation of CD4(+) T helper cells is strictly dependent on the presentation of antigenic peptides by MHC class II (MHC-II) molecules. MHC-II expression is primarily regulated at the transcriptional level by the AIR-1 gene product CIITA (class II transactivator). Thus, CIITA plays a pivotal role in the triggering of the adaptive immune response against pathogens. Besides this well known function, we recently found that CIITA acts as an endogenous restriction factor against HTLV-1 (human T cell lymphotropic virus type 1) and HTLV-2 oncogenic retroviruses by targeting their viral transactivators Tax-1 and Tax-2, respectively. Here we review our findings on CIITA-mediated inhibition of viral replication and discuss similarities and differences in the molecular mechanisms by which CIITA specifically counteracts the function of Tax-1 and Tax-2 molecules. The dual function of CIITA as a key regulator of adaptive and intrinsic immunity represents a rather unique example of adaptation of host-derived factors against pathogen infections during evolution.
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Affiliation(s)
| | | | - Roberto S. Accolla
- Laboratory of General Pathology and Immunology, Department of Surgical and Morphological Sciences, University of InsubriaVarese, Italy
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Muller M, Cassonnet P, Favre M, Jacob Y, Demeret C. A comparative approach to characterize the landscape of host-pathogen protein-protein interactions. J Vis Exp 2013:e50404. [PMID: 23893119 DOI: 10.3791/50404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Significant efforts were gathered to generate large-scale comprehensive protein-protein interaction network maps. This is instrumental to understand the pathogen-host relationships and was essentially performed by genetic screenings in yeast two-hybrid systems. The recent improvement of protein-protein interaction detection by a Gaussia luciferase-based fragment complementation assay now offers the opportunity to develop integrative comparative interactomic approaches necessary to rigorously compare interaction profiles of proteins from different pathogen strain variants against a common set of cellular factors. This paper specifically focuses on the utility of combining two orthogonal methods to generate protein-protein interaction datasets: yeast two-hybrid (Y2H) and a new assay, high-throughput Gaussia princeps protein complementation assay (HT-GPCA) performed in mammalian cells. A large-scale identification of cellular partners of a pathogen protein is performed by mating-based yeast two-hybrid screenings of cDNA libraries using multiple pathogen strain variants. A subset of interacting partners selected on a high-confidence statistical scoring is further validated in mammalian cells for pair-wise interactions with the whole set of pathogen variants proteins using HT-GPCA. This combination of two complementary methods improves the robustness of the interaction dataset, and allows the performance of a stringent comparative interaction analysis. Such comparative interactomics constitute a reliable and powerful strategy to decipher any pathogen-host interplays.
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Affiliation(s)
- Mandy Muller
- Unité de Génétique, Papillomavirus et Cancer Humain (GPCH), Institut Pasteur
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Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013; 138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 511] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
Abstract
Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design. We give a comprehensive assessment of the analytical tools of network topology and dynamics. The state-of-the-art use of chemical similarity, protein structure, protein-protein interaction, signaling, genetic interaction and metabolic networks in the discovery of drug targets is summarized. We propose that network targeting follows two basic strategies. The "central hit strategy" selectively targets central nodes/edges of the flexible networks of infectious agents or cancer cells to kill them. The "network influence strategy" works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved by targeting the neighbors of central nodes/edges. It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates. We review the recent boom in network methods helping hit identification, lead selection optimizing drug efficacy, as well as minimizing side-effects and drug toxicity. Successful network-based drug development strategies are shown through the examples of infections, cancer, metabolic diseases, neurodegenerative diseases and aging. Summarizing >1200 references we suggest an optimized protocol of network-aided drug development, and provide a list of systems-level hallmarks of drug quality. Finally, we highlight network-related drug development trends helping to achieve these hallmarks by a cohesive, global approach.
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Affiliation(s)
- Peter Csermely
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary.
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Chan CP, Siu YT, Kok KH, Ching YP, Tang HMV, Jin DY. Group I p21-activated kinases facilitate Tax-mediated transcriptional activation of the human T-cell leukemia virus type 1 long terminal repeats. Retrovirology 2013; 10:47. [PMID: 23622267 PMCID: PMC3651266 DOI: 10.1186/1742-4690-10-47] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 04/23/2013] [Indexed: 12/12/2022] Open
Abstract
Background Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell leukemia and tropical spastic paraparesis. HTLV-1 encodes transactivator protein Tax that interacts with various cellular factors to modulate transcription and other biological functions. Additional cellular mediators of Tax-mediated transcriptional activation of HTLV-1 long terminal repeats (LTR) remain to be identified and characterized. Results In this study, we investigated the regulatory role of group I p21-activated kinases (Paks) in Tax-induced LTR activation. Both wild-type and kinase-dead mutants of Pak3 were capable of potentiating the activity of Tax to activate LTR transcription. The effect of Paks on the LTR was attributed to the N-terminal regulatory domain and required the action of CREB, CREB-regulating transcriptional coactivators (CRTCs) and p300/CREB-binding protein. Paks physically associated with Tax and CRTCs. Paks were recruited to the LTR in the presence of Tax. siRNAs against either Pak1 or Pak3 prevented the interaction of Tax with CRTC1 and the recruitment of Tax to the LTR. These siRNAs also inhibited LTR-dependent transcription in HTLV-1-transformed MT4 cells and in cells transfected with an infectious clone of HTLV-1. Conclusion Group I Paks augment Tax-mediated transcriptional activation of HTLV-1 LTR in a kinase-independent manner.
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Affiliation(s)
- Ching-Ping Chan
- Department of Biochemistry, The University of Hong Kong, 3/F Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong
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The four and a half LIM family members are novel interactants of the human T-cell leukemia virus type 1 Tax oncoprotein. J Virol 2013; 87:7435-44. [PMID: 23616667 DOI: 10.1128/jvi.00070-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia (ATL). The viral regulatory protein Tax1 plays a pivotal role in T-cell transformation and ATL development. Previous studies in our laboratory, using the yeast 2-hybrid approach to screen a T-cell library for Tax1-interacting partners, identified the cellular Four and a Half Lim domain protein 3 (FHL3) as a possible Tax1-interacting candidate. FHL3 is a member of the FHL family of proteins, which function as transcriptional coactivators and cytoskeleton regulators and have a role in cancer progression and development. The aim of this study was to investigate the physical and functional interaction between Tax1 and members of the FHL family of proteins. We show that Tax1 and FHL3 interact both in vitro and in vivo. Furthermore, both FHL1 and -2 also interact with Tax1. We have demonstrated that FHL3 enhances Tax1-mediated activation of the viral long terminal repeat (LTR) without affecting basal activity and that FHL1 to -3 regulate NF-κB activation by Tax1 in a cell-specific manner. In addition, we have found that the interaction between Tax1 and FHL1 to -3 affects the localization of these proteins, leading to their redistribution in cells. Tax1 also affected FHL3 cytoskeleton function by increasing FHL3-mediated cell spreading. Overall, our results suggest that the interaction between Tax1 and the FHL family alters both the transactivating activity and the subcellular localization of Tax1 and provide new insights into molecular mechanisms that underlie the oncogenic nature of this HTLV-1 protein.
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Tang HMV, Gao WW, Chan CP, Siu YT, Wong CM, Kok KH, Ching YP, Takemori H, Jin DY. LKB1 tumor suppressor and salt-inducible kinases negatively regulate human T-cell leukemia virus type 1 transcription. Retrovirology 2013; 10:40. [PMID: 23577667 PMCID: PMC3640950 DOI: 10.1186/1742-4690-10-40] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 04/02/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Human T-cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia (ATL). Treatment options are limited and prophylactic agents are not available. We have previously demonstrated an essential role for CREB-regulating transcriptional coactivators (CRTCs) in HTLV-1 transcription. RESULTS In this study we report on the negative regulatory role of LKB1 tumor suppressor and salt-inducible kinases (SIKs) in the activation of HTLV-1 long terminal repeats (LTR) by the oncoprotein Tax. Activation of LKB1 and SIKs effectively blunted Tax activity in a phosphorylation-dependent manner, whereas compromising these kinases, but not AMP-dependent protein kinases, augmented Tax function. Activated LKB1 and SIKs associated with Tax and suppressed Tax-induced LTR activation by counteracting CRTCs and CREB. Enforced expression of LKB1 or SIK1 in cells transfected with HTLV-1 molecular clone pX1MT repressed proviral transcription. On the contrary, depletion of LKB1 in pX1MT-transfected cells and in HTLV-1-transformed T cells boosted the expression of Tax. Treatment of HTLV-1 transformed cells with metformin led to LKB1/SIK1 activation, reduction in Tax expression, and inhibition of cell proliferation. CONCLUSIONS Our findings revealed a new function of LKB1 and SIKs as negative regulators of HTLV-1 transcription. Pharmaceutical activation of LKB1 and SIKs might be considered as a new strategy in anti-HTLV-1 and anti-ATL therapy.
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Affiliation(s)
- Hei-Man Vincent Tang
- Department of Biochemistry, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
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Medina MÁ. Systems biology for molecular life sciences and its impact in biomedicine. Cell Mol Life Sci 2013; 70:1035-53. [PMID: 22903296 PMCID: PMC11113420 DOI: 10.1007/s00018-012-1109-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/24/2012] [Accepted: 07/25/2012] [Indexed: 01/02/2023]
Abstract
Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.
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Affiliation(s)
- Miguel Ángel Medina
- Department of Molecular Biology and Biochemistry, University of Málaga, Malaga, Spain.
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