title: Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages.
abstract: Human immunodeficiency virus type 1 (HIV-1) infection remains a worldwide epidemic, and innovative therapies to combat the virus are needed. Developing a host-oriented antiviral strategy capable of targeting the biomolecules that are directly or indirectly required for viral replication may provide advantages over traditional virus-centric approaches. We used quantitative proteomics by SWATH-MS in conjunction with bioinformatic analyses to identify host proteins, with an emphasis on nucleic acid binding and regulatory proteins, which could serve as candidates in the development of host-oriented antiretroviral strategies. Using SWATH-MS, we identified and quantified the expression of 3608 proteins in uninfected and HIV-1-infected monocyte-derived macrophages. Of these 3608 proteins, 420 were significantly altered upon HIV-1 infection. Bioinformatic analyses revealed functional enrichment for RNA binding and processing as well as transcription regulation. Our findings highlight a novel subset of proteins and processes that are involved in the host response to HIV-1 infection. In addition, we provide an original and transparent methodology for the analysis of label-free quantitative proteomics data generated by SWATH-MS that can be readily adapted to other biological systems.
authors.affiliation: Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center , Durham Research Center I, 985800 Nebraska Medical Center Omaha, Nebraska 68198-5800, United States.
authors.forename: Nicole A
authors.initials: NA
authors.lastname: Haverland
authors.forename: Howard S
authors.initials: HS
authors.lastname: Fox
authors.forename: Pawel
authors.initials: P
authors.lastname: Ciborowski
mesh_terms: D002478:Cells, Cultured; D015658:HIV Infections / Q000378:metabolism*; D054884:Host-Pathogen Interactions / Q000502:physiology*; D006801:Humans; D008264:Macrophages / Q000378:metabolism / Q000821:virology; D013058:Mass Spectrometry; D060066:Protein Interaction Maps; D020543:Proteome / Q000032:analysis / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D016601:RNA-Binding Proteins / Q000032:analysis / Q000378:metabolism*; D014157:Transcription Factors / Q000032:analysis / Q000378:metabolism*
chemical_list: D020543:Proteome; D016601:RNA-Binding Proteins; D014157:Transcription Factors