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      Proteomics, biomarkers, and HIV‐1: A current perspective

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          Abstract

          Despite more than three decades of extensive research, HIV‐1 infection although well controlled with cART, remains incurable. Multifactorial complexity of the viral life‐cycle poses great challenges in understanding molecular mechanisms underlying this infection and the development of biomarkers, which we hope will lead us to its eradication. For a more in‐depth understanding of how the virus interacts with host target cells, T cells and macrophages, proteomic profiling techniques that offer strategies to investigate the proteome in its entirety were employed. Here, we review proteomic studies related to HIV‐1 infection and discuss perspectives and limitations of proteomic and systems biology approaches in future studies.

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          Most cited references87

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          Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present.

          Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.
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            Infectious HIV-1 assembles in late endosomes in primary macrophages

            Although human immunodeficiency virus type 1 (HIV-1) is generally thought to assemble at the plasma membrane of infected cells, virions have been observed in intracellular compartments in macrophages. Here, we investigated virus assembly in HIV-1–infected primary human monocyte-derived macrophages (MDM). Electron microscopy of cryosections showed virus particles, identified by their morphology and positive labeling with antibodies to the viral p17, p24, and envelope proteins, in intracellular vacuoles. Immunolabeling demonstrated that these compartments contained the late endosomal marker CD63, which was enriched on vesicles within these structures and incorporated into the envelope of budding virions. The virus-containing vacuoles were also labeled with antibodies against LAMP-1, CD81, and CD82, which were also incorporated into the viral envelope. To assess the cellular source of infectious viruses derived from MDM, virus-containing media from infected cells were precipitated with specific antibodies. Only antibodies against antigens found in late endosomes precipitated infectious virus, whereas antibodies against proteins located primarily on the cell surface did not. Our data indicate that most of the infectious HIV produced by primary macrophages is assembled on late endocytic membranes and acquires antigens characteristic of this compartment. This notion has significant implications for understanding the biology of HIV and its cell–cell transmission.
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              Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards.

              A new method is presented for quantifying proteomic and metabolomic profile data by liquid chromatography-mass spectrometry (LC-MS) with electrospray ionization. This biotechnology provides differential expression measurements and enables the discovery of biological markers (biomarkers). Work presented here uses human serum but is applicable to any fluid or tissue. The approach relies on linearity of signal versus molecular concentration and reproducibility of sample processing. There is no use of isotopic labeling or chemically similar standard materials. Linear standard curves are reported for a variety of compounds introduced into human serum. As a measure of analytical reproducibility for proteome and metabolome sampling, median coefficients of variation of 25.7 and 23.8%, respectively, were determined for approximately 3400 molecular ions (not counting their numerous isotopes) from 25 independently processed human serum samples, corresponding to a total of 85000 individual molecular ion measurements.
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                Author and article information

                Journal
                Proteomics Clin Appl
                Proteomics Clin Appl
                10.1002/(ISSN)1862-8354
                PRCA
                Proteomics. Clinical Applications
                John Wiley and Sons Inc. (Hoboken )
                1862-8346
                1862-8354
                08 July 2015
                February 2016
                : 10
                : 2 , Proteomics and HIV ( doiID: 10.1002/prca.v10.2 )
                : 110-125
                Affiliations
                [ 1 ] Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical Center Omaha NE 68198USA
                Author notes
                [*] [* ] Correspondence: Dr. Pawel Ciborowski, Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA

                E‐mail: pciborowski@ 123456unmc.edu

                Article
                PRCA1682
                10.1002/prca.201500002
                4666820
                26033875
                ff50a2e4-c9b7-4918-90d7-75ced3e4be5b
                © 2015 The Authors. PROTEOMICS ‐ Clinical Applications Published by WILEY‐VCH Verlag GmbH & Co. KGaA

                This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 07 January 2015
                : 17 March 2015
                : 27 May 2015
                Page count
                Pages: 16
                Funding
                Funded by: National Institutes of Health
                Award ID: R01 DA030962
                Award ID: P30 MH062261
                Categories
                Review
                Review
                Custom metadata
                2.0
                prca1682
                February 2016
                Converter:WILEY_ML3GV2_TO_NLMPMC version:4.7.6 mode:remove_FC converted:04.02.2016

                Molecular biology
                biomarker,body fluids,hiv,macrophage,systems biology,t cell
                Molecular biology
                biomarker, body fluids, hiv, macrophage, systems biology, t cell

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