Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification.
Amir A SaeiAlbin LundinHezheng LyuHassan GharibiHuqiao LuoJaakko TeppoXuepei ZhangMassimiliano GaetaniÁkos VégváriRikard HolmdahlSteven P GygiRoman A ZubarevPublished in: Advanced science (Weinheim, Baden-Wurttemberg, Germany) (2024)
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, the first high-throughput redox proteomics approach integrated with expression analysis (REX) is devised and combined with the 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, HCT116 cells treated with auranofin are analyzed, showing great improvement compared with previous studies. PISA-REX is then applied to study proteome remodeling upon stimulation of human monocytes by interferon α (IFN-α). Applying this tool to study the proteome changes in plasmacytoid dendritic cells (pDCs) isolated from wild-type versus Ncf1-mutant mice treated with interferon α, shows 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.
Keyphrases
- dendritic cells
- wild type
- high throughput
- poor prognosis
- regulatory t cells
- immune response
- healthcare
- endothelial cells
- public health
- risk assessment
- high resolution
- binding protein
- induced apoptosis
- cell cycle arrest
- cell proliferation
- high glucose
- adipose tissue
- cell death
- newly diagnosed
- oxidative stress
- high fat diet induced
- electron transfer
- high density
- case control