Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages

Nicole A. Haverland, Howard S Fox, Pawel S Ciborowski

Research output: Contribution to journalArticle

45 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2109-2119
Number of pages11
JournalJournal of proteome research
Volume13
Issue number4
DOIs
StatePublished - Apr 4 2014

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Macrophages
Viruses
Proteomics
Nucleic Acids
HIV-1
Carrier Proteins
Virus Diseases
Computational Biology
Proteins
Bioinformatics
Investigational Therapies
Antiviral Agents
Biomolecules
Biological systems
RNA
Transcription
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Keywords

  • DHX15
  • HDAC
  • HIV
  • MDM
  • NCOR
  • SWATH
  • YBOX1
  • macrophage
  • spliceosome
  • z -test

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

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