Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification

Saei, A. A.; Lundin, A.; Lyu, H.; Gharibi, H.; Luo, H.; Teppo, J.; Zhang, X.; Gaetani, M.; Vegvari, A.; Holmdahl, R.; Gygi, S. P.; Zubarev, R. A.

doi:10.1101/2023.08.31.555796

bioRxiv · 10.1101/2023.08.31.555796

Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification

Saei, A. A.·Lundin, A.·Lyu, H.·Gharibi, H.·Luo, H.·Teppo, J.·Zhang, X.·Gaetani, M.·Vegvari, A.·Holmdahl, R.·Gygi, S. P.·Zubarev, R. A.

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Abstract

Multifaceted interrogation of the proteome deepens the system-wide understanding of biological systems; however, mapping the redox changes in the proteome has so far been significantly more challenging than expression and solubility/stability analyses. Here, we devise the first high- throughput redox proteomics approach integrated with expression analysis (REX) and combine it with Proteome Integral Solubility Alteration (PISA) assay. The whole PISA-REX experiment with up to four biological replicates can be multiplexed into a single tandem mass tag TMTpro set. For benchmarking this compact tool, we analyzed HCT116 cells treated with auranofin, showing great improvement compared with previous such studies. Then we applied PISA-REX to study proteome remodeling upon stimulation of human monocytes by interferon . We also studied the proteome changes in plasmacytoid dendritic cells isolated from wild type vs. Ncf1- mutant mice treated with interferon , showing that NCF1 deficiency enhances the STAT1 pathway and modulates the expression, solubility and redox state of interferon-induced proteins. Providing comprehensive multifaceted information on the proteome, the compact PISA-REX has the potential to become an industry standard in proteomics and to open new windows into the biology of health and disease.

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Saei, A. A., Lundin, A., Lyu, H., Gharibi, H., Luo, H., Teppo, J., Zhang, X., Gaetani, M., Vegvari, A., Holmdahl, R., Gygi, S. P., Zubarev, R. A.. 2023-09-01. Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification. https://doi.org/10.1101/2023.08.31.555796

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