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A sensitive S-Trap-based approach to the analysis of T cell lipid raft proteome
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Edité par CCSD ; American Society for Biochemistry and Molecular Biology -
International audience. The analysis of T cell lipid raft proteome is challenging due to the highly dynamic nature of rafts and the hydrophobic character of raft-resident proteins. We explored an innovative strategy for bottom-up lipid raftomics based on suspension trapping (S-trap) sample preparation. Mouse T cells were prepared from splenocytes by negative immunoselection and rafts were isolated by a detergent-free method and OptiPrep gradient ultracentrifugation. Microdomains enriched in Flotillin-1, LAT and cholesterol were subjected to proteomic analysis through an optimized protocol based on STrap and high pH fractionation, followed by nano-LC-MS/MS. Using this method, we identified 2680 proteins in the raft-rich fraction and established a database of 894 T cell raft proteins. We then performed a differential analysis on the raft-rich fraction from non-stimulated vs. anti-CD3/CD28 TCR-stimulated T cells. Our results revealed 42 proteins present in one condition and absent in the other. For the first time, we performed a proteomic analysis on rafts from ex-vivo T cells obtained from individual mice, before and after TCR activation. This work demonstrates that the proposed method utilizing an Strap based approach for sample preparation increases the specificity and sensitivity of lipid raftomics. Data are available via ProteomeXchange with identifier PXD016476.
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