Quantitative Proteomic Analysis of Enriched Nuclear Fractions from BK Polyomavirus-Infected Primary Renal Proximal Tubule Epithelial Cells

• Published in: Journal of proteome research 2015-10, Vol.14 (10), p.4413-4424
• Main Authors: Justice, Joshua L, Verhalen, Brandy, Kumar, Ranjit, Lefkowitz, Elliot J, Imperiale, Michael J, Jiang, Mengxi
• Format: Article
• Language: English
• Subjects: amino acids; BK Virus - physiology; cell culture; Cell Nucleus - chemistry; Cell Nucleus - metabolism; Cell Nucleus - pathology; Cell Nucleus - virology; Chromatography, Liquid; DNA Damage; DNA Repair; epithelial cells; Epithelial Cells - metabolism; Epithelial Cells - pathology; Epithelial Cells - virology; Gene Expression Regulation; Gene Regulatory Networks; genes; Host-Pathogen Interactions; host-pathogen relationships; human diseases; Human polyomavirus 1; Humans; immunocompromised population; Isotope Labeling; Kidney Tubules, Proximal - metabolism; Kidney Tubules, Proximal - pathology; Kidney Tubules, Proximal - virology; liquid chromatography; microarray technology; Molecular Sequence Annotation; Primary Cell Culture; proteins; proteome; Proteome - genetics; Proteome - isolation & purification; Proteome - metabolism; proteomics; Signal Transduction; stable isotopes; Tandem Mass Spectrometry; transcription (genetics); Transcription, Genetic; Western blotting
• ISSN: 1535-3893; 1535-3907; 1535-3907
• DOI: 10.1021/acs.jproteome.5b00737

Polyomaviruses are a family of small DNA viruses that are associated with a number of severe human diseases, particularly in immunocompromised individuals. The detailed virus–host interactions during lytic polyomavirus infection are not fully understood. Here, we report the first nuclear proteomic study with BK polyomavirus (BKPyV) in a primary renal proximal tubule epithelial cell culture system using stable isotope labeling by amino acids in cell culture (SILAC) proteomic profiling coupled with liquid chromatography–tandem mass spectrometry. We demonstrated the feasibility of SILAC labeling in these primary cells and subsequently performed reciprocal labeling-infection experiments to identify proteins that are altered by BKPyV infection. Our analyses revealed specific proteins that are significantly up- or down-regulated in the infected nuclear proteome. The genes encoding many of these proteins were not identified in a previous microarray study, suggesting that differential regulation of these proteins may be independent of transcriptional control. Western blotting experiments verified the SILAC proteomic findings. Finally, pathway and network analyses indicated that the host cell DNA damage response signaling and DNA repair pathways are among the cellular processes most affected at the protein level during polyomavirus infection. Our study provides a comprehensive view of the host nuclear proteomic changes during polyomavirus lytic infection and suggests potential novel host factors required for a productive polyomavirus infection.