Development of (chemical)proteomics strategies to uncover the role and regulation of protein lipidation in Neurodegenerative disorders, inflammation and cancer.

^{Figure 1, Schematic representation of our dual-method strategy to study S-palmitoylation in neuronal cells}

Acyl-biotin exchange (ABE) and lipid metabolic labelling (LML), both coupled with mass spectrometry proteomics, are indirect but powerful methods for analyzing protein long chain S-acylation. However, these methods are prone to false positive identifications, which can compromise the accuracy of S-palmitoylation analysis. To overcome this limitation, we use the orthogonality of both ABE and LML, and use both approaches in parallel to study bona fide S-palmitoylated proteins and sites. Furthermore, we continuously optimize and refine these proteomics strategies to better understand the role of S-palmitoylation in neurodegenerative disorders and cancer.

^{Figure 2, S-palmitoylation profiling of (neuronal) SH-SY5Y cells during RA-induced neuronal differentiation. (A) Heatmap of the relative abundance of 1151 S-acylated proteins found in all three time points. (B) Volcano plot of the LFQ proteomics analysis of S-acylated proteins in SH-SY5Y cells at t = 7 enriched with the ABE workflow (±RA). Proteins decreased in S-palmitoylated protein abundance during differentiation are pink, and proteins increased are green. Dashed line represents the Student’s unpaired t-test significance cut-off (FDR 0.01, S0 0.5, and n = 3 biological replicates). (C) GO cellular component analysis for proteins increased in S-palmitoylated protein abundance at t = 7 (FDR <0.05, ABE). (D) Volcano plot of the LFQ proteomics analysis of alk-16-labeled proteins in SH-SY5Y cells at t = 7 enriched with LML workflow (±RA). Proteins decreased in S-palmitoylated protein abundance during differentiation are pink, and proteins increased are green. Dashed line represents the Student’s unpaired t-test significance cut-off (FDR 0.01, S0 0.5, and n = 3 biological replicates).}