@article{3924bb8f66654d8695f9f800d279e086,
title = "SWATH-MS and MRM: Quantification of Ras-related proteins in HIV-1 infected and methamphetamine-exposed human monocyte-derived macrophages (hMDM)",
abstract = "HIV-1 infection of macrophages is a multistep and multifactorial process that has been shown to be enhanced by exposure to methamphetamine (Meth). In this study, we sought to identify the underlying mechanisms of this effect by quantifying the effect of Meth on the proteome of HIV-1-infected macrophages using sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) approach. The analyses identified several members of the Rab family of proteins as being dysregulated by Meth treatment, which was confirmed by bioinformatic analyses that indicated substantial alteration of vesicular transport pathways. Validation of the SWATH-MS was performed using an MRM based approach, which confirmed that Meth exposure affects expression of the Rab proteins. However, the pattern of expression changes were highly dynamic, and displayed high donor-to-donor variability. Surprisingly a similar phenomenon was observed for Actin. Our results demonstrate that Meth affects vesicular transport pathways, suggesting a possible molecular mechanism underlying its effect on HIV infection hMDM and a potential broader effect of Meth on cellular homeostasis.",
keywords = "HIV, MRM, Rab proteins, SWATH-MS, macrophages",
author = "Katarzyna Macur and Sarah Zieschang and Shulei Lei and Brenda Morsey and Spencer Jaquet and Michael Belshan and Fox, {Howard S.} and Pawel Ciborowski",
note = "Funding Information: The authors would like to thank Dr. Katarzyna Lech for her help in preparing graphics for Figure 1, Mr. Andrew Schissel for technical assistance, Dr. James Eudy (sequencing by the UNMC Genomics Core Facility, which receives partial support from the Nebraska Research Network In Functional Genomics NE-INBRE P20GM103427-14 and the Fred & Pamela Buffett Cancer Center - P30CA036727), and Drs. Peng Xiao, Meng Niu and Babu Guda (bioinformatic pipeline from the UNMC Bioinformatics and Systems Biology Core). The MS analyses were performed at the University of Nebraska Medical Center MS and Proteomics Core Facility, which is administrated through the Office of the Vice Chancellor for Research and supported by state funds from the Nebraska Research Initiative (NRI). Financial support was provided by National Institutes of Health grants: R01 DA043258 and P30 MH062261. Funding Information: The authors would like to thank Dr. Katarzyna Lech for her help in preparing graphics for Figure 1 , Mr. Andrew Schissel for technical assistance, Dr. James Eudy (sequencing by the UNMC Genomics Core Facility, which receives partial support from the Nebraska Research Network In Functional Genomics NE‐INBRE P20GM103427‐14 and the Fred & Pamela Buffett Cancer Center ‐ P30CA036727), and Drs. Peng Xiao, Meng Niu and Babu Guda (bioinformatic pipeline from the UNMC Bioinformatics and Systems Biology Core). The MS analyses were performed at the University of Nebraska Medical Center MS and Proteomics Core Facility, which is administrated through the Office of the Vice Chancellor for Research and supported by state funds from the Nebraska Research Initiative (NRI). Financial support was provided by National Institutes of Health grants: R01 DA043258 and P30 MH062261. Publisher Copyright: {\textcopyright} 2021 Wiley-VCH GmbH",
year = "2021",
month = aug,
doi = "10.1002/pmic.202100005",
language = "English (US)",
volume = "21",
journal = "Proteomics",
issn = "1615-9853",
publisher = "Wiley-VCH Verlag",
number = "15",
}