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Piyathilake CJ, Oelschlager DK, Meleth S, Partridge EE, Grizzle WE. Plasma Protein Profiles Differ between Women Diagnosed with Cervical Intraepithelial Neoplasia (CIN) 1 and 3. Cancer Inform 2017. [DOI: 10.1177/117693510600200026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Early detection of precancerous cells in the cervix and their clinical management is the main purpose of cervical cancer prevention and treatment programs. Cytological findings or testing for high risk (HR)-human papillomavirus (HPV) are inadequately sensitive for use in triage of women at high risk for cervical cancer. The current study is an exploratory study to identify candidate surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) mass spectrometry (MS) protein profiles in plasma that may distinguish cervical intraepithelial neoplasia (CIN 3) from CIN 1 among women infected with HR-HPV. We evaluated the SELDI-TOF-MS plasma protein profiles of HR-HPV positive 32 women with CIN 3 (cases) and 28 women with CIN1 (controls). Case-control status was kept blinded and triplicates of each sample and quality control plasma samples were randomized and after robotic sample preparations were run on WCX2 chips. After alignment of mass/charge (m-z values), an iterative method was used to develop a classifier on a training data set that had 28 cases and 22 controls. The classifier developed was used to classify the subjects in a test data set that has six cases and six controls. The classifier separated the cases from controls in the test set with 100% sensitivity and 100% specificity suggesting the possibility of using plasma SELDI protein profiles to identify women who are likely to have CIN 3 lesions.
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Affiliation(s)
- Chandrika J. Piyathilake
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Denise K. Oelschlager
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Sreelatha Meleth
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Edward E. Partridge
- Department of Obstetrics & Gynecology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - William E. Grizzle
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294
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Wang K, Yang T, Wu Q, Zhao X, Nice EC, Huang C. Chemistry-based functional proteomics for drug target deconvolution. Expert Rev Proteomics 2013; 9:293-310. [PMID: 22809208 DOI: 10.1586/epr.12.19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drug target deconvolution, a process that identifies targets to small molecules in complex biological samples, which underlie the biological responses that are observed when a drug is administered, plays an important role in current drug discovery. Despite the fact that genomics and proteomics have provided a flood of information that contributes to the progress of drug target identification and validation, the current approach to drug target deconvolution still poses dilemmas. Chemistry-based functional proteomics, a multidisciplinary strategy, has become the preferred method of choice to deconvolute drug target pools, based on direct interactions between small molecules and their protein targets. This approach has already identified a broad panel of previously undefined enzymes with potential as drug targets and defined targets that can rationalize side effects and toxicity for new drug candidates and existing therapeutics. Herein, the authors discuss both activity-based protein profiling and compound-centric chemical proteomics approaches used in chemistry-based functional proteomics and their applications for the identification and characterization of small molecular targets.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, PR China
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Lippé R. Deciphering novel host-herpesvirus interactions by virion proteomics. Front Microbiol 2012; 3:181. [PMID: 22783234 PMCID: PMC3390586 DOI: 10.3389/fmicb.2012.00181] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 04/27/2012] [Indexed: 12/15/2022] Open
Abstract
Over the years, a vast array of information concerning the interactions of viruses with their hosts has been collected. However, recent advances in proteomics and other system biology techniques suggest these interactions are far more complex than anticipated. One particularly interesting and novel aspect is the analysis of cellular proteins incorporated into mature virions. Though sometimes considered purification contaminants in the past, their repeated detection by different laboratories suggests that a number of these proteins are bona fide viral components, some of which likely contribute to the viral life cycles. The present mini review focuses on cellular proteins detected in herpesviruses. It highlights the common cellular functions of these proteins, their potential implications for host–pathogen interactions, discusses technical limitations, the need for complementing methods and probes potential future research avenues.
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Affiliation(s)
- Roger Lippé
- Department of Pathology and Cell biology, University of Montreal Montreal, QC, Canada
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Santamaría E, Sánchez-Quiles V, Fernández-Irigoyen J, Corrales F. Contribution of MS-Based Proteomics to the Understanding of Herpes Simplex Virus Type 1 Interaction with Host Cells. Front Microbiol 2012; 3:107. [PMID: 22454626 PMCID: PMC3308349 DOI: 10.3389/fmicb.2012.00107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/02/2012] [Indexed: 12/14/2022] Open
Abstract
Like other DNA viruses, herpes simplex virus type 1 (HSV-1) replicates and proliferates in host cells continuously modulating the host molecular environment. Following a sophisticated temporal expression pattern, HSV-1 encodes at least 89 multifunctional proteins that interplay with and modify the host cell proteome. During the last decade, advances in mass spectrometry applications coupled to the development of proteomic separation methods have allowed to partially monitor the impact of HSV-1 infection in human cells. In this review, we discuss the current use of different proteome fractionation strategies to define HSV-1 targets in two major application areas: (i) viral-protein interactomics to decipher viral-protein interactions in host cells and (ii) differential quantitative proteomics to analyze the virally induced changes in the cellular proteome. Moreover, we will also discuss the potential application of high-throughput proteomic approaches to study global proteome dynamics and also post-translational modifications in HSV-1-infected cells that will greatly improve our molecular knowledge of HSV-1 infection.
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Affiliation(s)
- Enrique Santamaría
- Proteomics Unit, Biomedical Research Centre, Navarra Health Service Pamplona, Spain
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Blais DR, Nasheri N, McKay CS, Legault MC, Pezacki JP. Activity-based protein profiling of host-virus interactions. Trends Biotechnol 2011; 30:89-99. [PMID: 21944551 PMCID: PMC7114118 DOI: 10.1016/j.tibtech.2011.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 02/08/2023]
Abstract
Virologists have benefited from large-scale profiling methods to discover new host–virus interactions and to learn about the mechanisms of pathogenesis. One such technique, referred to as activity-based protein profiling (ABPP), uses active site-directed probes to monitor the functional state of enzymes, taking into account post-translational interactions and modifications. ABPP gives insight into the catalytic activity of enzyme families that does not necessarily correlate with protein abundance. ABPP has been used to investigate several viruses and their interactions with their hosts. Differential enzymatic activity induced by viruses has been monitored using ABPP. In this review, we present recent advances and trends involving the use of ABPP methods in understanding host–virus interactions and in identifying novel targets for diagnostic and therapeutic applications.
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Affiliation(s)
- David R. Blais
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Neda Nasheri
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Craig S. McKay
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
| | - Marc C.B. Legault
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
| | - John Paul Pezacki
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
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Zhou S, Liu R, Zhao X, Huang C, Wei Y. Viral proteomics: the emerging cutting-edge of virus research. SCIENCE CHINA-LIFE SCIENCES 2011; 54:502-12. [PMID: 21706410 PMCID: PMC7089374 DOI: 10.1007/s11427-011-4177-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 12/03/2010] [Indexed: 11/21/2022]
Abstract
Viruses replicate and proliferate in host cells while continuously adjusting to and modulating the host environment. They encode a wide spectrum of multifunctional proteins, which interplay with and modify proteins in host cells. Viral genomes were chronologically the first to be sequenced. However, the corresponding viral proteomes, the alterations of host proteomes upon viral infection, and the dynamic nature of proteins, such as post-translational modifications, enzymatic cleavage, and activation or destruction by proteolysis, remain largely unknown. Emerging high-throughput techniques, in particular quantitative or semi-quantitative mass spectrometry-based proteomics analysis of viral and cellular proteomes, have been applied to define viruses and their interactions with their hosts. Here, we review the major areas of viral proteomics, including virion proteomics, structural proteomics, viral protein interactomics, and changes to the host cell proteome upon viral infection.
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Affiliation(s)
- ShengTao Zhou
- Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, China
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Mettenleiter TC, Klupp BG, Granzow H. Herpesvirus assembly: an update. Virus Res 2009; 143:222-34. [PMID: 19651457 DOI: 10.1016/j.virusres.2009.03.018] [Citation(s) in RCA: 293] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 03/28/2009] [Accepted: 03/28/2009] [Indexed: 12/30/2022]
Abstract
The order Herpesvirales contains viruses infecting animals from molluscs to men with a common virion morphology which have been classified into the families Herpesviridae, Alloherpesviridae and Malacoherpesviridae. Herpes virions are among the most complex virus particles containing a multitude of viral and cellular proteins which assemble into nucleocapsid, envelope and tegument. After autocatalytic assembly of the capsid and packaging of the newly replicated viral genome, a process which occurs in the nucleus and resembles head formation and genome packaging in the tailed double-stranded DNA bacteriophages, the nucleocapsid is translocated to the cytoplasm by budding at the inner nuclear membrane followed by fusion of the primary envelope with the outer nuclear membrane. Viral and cellular proteins are involved in mediating this 'nuclear egress' which entails substantial remodeling of the nuclear architecture. For final maturation within the cytoplasm tegument components associate with the translocated nucleocapsid, with themselves, and with the future envelope containing viral membrane proteins in a complex network of interactions resulting in the formation of an infectious herpes virion. The diverse interactions between the involved proteins exhibit a striking redundancy which is still insufficiently understood. In this review, recent advances in our understanding of the molecular processes resulting in herpes virion maturation will be presented and discussed as an update of a previous contribution [Mettenleiter, T.C., 2004. Budding events in herpesvirus morphogenesis. Virus Res. 106, 167-180].
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Viswanathan K, Früh K. Viral proteomics: global evaluation of viruses and their interaction with the host. Expert Rev Proteomics 2008; 4:815-29. [PMID: 18067418 DOI: 10.1586/14789450.4.6.815] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viruses constantly adapt to and modulate the host environment during replication and propagation. Both DNA and RNA viruses encode multifunctional proteins that interact with and modify host cell proteins. While viral genomes were the first complete sequences known, the corresponding proteomes are only now elucidated, with some surprising results. Even more daunting is the task to globally monitor the impact of viral infection on the proteome of the host cell and many technical hurdles must still be overcome in order to facilitate robust and reproducible measurements. Further complicating the picture is the dynamic nature of proteins, including post-translational modifications, enzymatic cleavage and activation or destruction by proteolytic events. Nevertheless, several promising studies have been published using high-throughput methods directly measuring protein abundance. Particularly, quantitative or semiquantitative mass spectrometry-based analysis of viral and cellular proteomes are now being used to characterize viruses and their host interaction. In addition, the full set of interactions between viral and host proteins, the interactome, is beginning to emerge, with often unexpected interactions that need to be carefully validated. In this review, we will discuss two major areas of viral proteomics: first, virion proteomics (such as the protein characterization of viral particles) and second, proteoviromics, including the viral protein interactomics and the quantitative analysis of host cell proteome during viral infection.
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Affiliation(s)
- Kasinath Viswanathan
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, 505 NW, 185th Ave, Beaverton, OR 97006, USA.
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Wu J, Lin Q, Lim TK, Liu T, Hew CL. White spot syndrome virus proteins and differentially expressed host proteins identified in shrimp epithelium by shotgun proteomics and cleavable isotope-coded affinity tag. J Virol 2007; 81:11681-9. [PMID: 17715220 PMCID: PMC2168766 DOI: 10.1128/jvi.01006-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shrimp subcuticular epithelial cells are the initial and major targets of white spot syndrome virus (WSSV) infection. Proteomic studies of WSSV-infected subcuticular epithelium of Penaeus monodon were performed through two approaches, namely, subcellular fractionation coupled with shotgun proteomics to identify viral and host proteins and a quantitative time course proteomic analysis using cleavable isotope-coded affinity tags (cICATs) to identify differentially expressed cellular proteins. Peptides were analyzed by offline coupling of two-dimensional liquid chromatography with matrix-assisted laser desorption ionization-tandem time of flight mass spectrometry. We identified 27, 20, and 4 WSSV proteins from cytosolic, nuclear, and membrane fractions, respectively. Twenty-eight unique WSSV proteins with high confidence (total ion confidence interval percentage [CI%], >95%) were observed, 11 of which are reported here for the first time, and 3 of these novel proteins were shown to be viral nonstructural proteins by Western blotting analysis. A first shrimp protein data set containing 1,999 peptides (ion score, > or =20) and 429 proteins (total ion score CI%, >95%) was constructed via shotgun proteomics. We also identified 10 down-regulated proteins and 2 up-regulated proteins from the shrimp epithelial lysate via cICAT analysis. This is the first comprehensive study of WSSV-infected epithelia by proteomics. The 11 novel viral proteins represent the latest addition to our knowledge of the WSSV proteome. Three proteomic data sets consisting of WSSV proteins, epithelial cellular proteins, and differentially expressed cellular proteins generated in the course of WSSV infection provide a new resource for further study of WSSV-shrimp interactions.
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Affiliation(s)
- Jinlu Wu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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Engwegen JYMN, Gast MCW, Schellens JHM, Beijnen JH. Clinical proteomics: searching for better tumour markers with SELDI-TOF mass spectrometry. Trends Pharmacol Sci 2006; 27:251-9. [PMID: 16600386 DOI: 10.1016/j.tips.2006.03.003] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 01/11/2006] [Accepted: 03/20/2006] [Indexed: 11/22/2022]
Abstract
Recently, the focus of cancer research has expanded from genetic information in the human genome to protein expression analyses. Because this 'proteome' reflects the state of a cell, tissue or organism more accurately, much is expected from proteomics to yield better tumour markers for disease diagnosis and therapy monitoring. Some current proteomic technologies are particularly suitable for protein profiling in the search for new biomarkers. Surface-enhanced laser desorption ionization time-of-flight mass spectrometry has been used frequently, highlighting many new proteins as biomarkers (e.g. for ovarian, breast, prostate and colorectal cancer). However, it is becoming increasingly recognized that reproducibility and validation of these biomarkers should be addressed carefully, as should their origin and identity. If these efforts are made, protein profiling can contribute to the better diagnosis of patients and the optimization of their treatment.
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Affiliation(s)
- Judith Y M N Engwegen
- Department of Pharmacy and Pharmacology, The Netherlands Cancer Institute and Slotervaart Hospital, Louwesweg 6, 1066 EC Amsterdam, The Netherlands.
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