The effects of IDH1 R132H autopalmitoylation on gene expressions in U87 cells

Gain-of-function mutations of isocitrate dehydrogenase 1 (IDH1) lead to neomorphic enzymatic activities and the production of oncometabolite R-2-hydroxyglutarate (2-HG), contributing to the tumorigenesis of several human cancers. It has been shown that fatty acid biosynthesis is required for the growth of IDH1 mutant tumors, but the underlining mechanisms are unclear. We developed new activity-based chemical probes to study protein autopalmitoylation, and identified that the oncogenic IDH1 (R132H) mutant is uniquely autopalmitoylated at cysteine 269 (C269), which is not observed in the wild type IDH1. Molecular dynamic simulations suggest that palmitoylation of the R132H mutant could occur in a hydrophobic pocket, and enhance its dimerization, consistent with our experimental results. In addition, in vitro autopalmitoylated recombinant IDH1 mutant protein showed enhanced enzymatic activities. In cells expressing IDH1 (R132H) mutant, exogenous fatty acids enhance mutant IDH1 activities through promoting C269 autopalmitoylation, and loss of C269 palmitoylation reverses mutant-induced metabolic reprograming and hypermethylation phenotypes, and impairs cell transformation. Interestingly, a clinical IDH1 mutant inhibitor (LY3410738) strongly inhibits autopalmitoylation by binding to the lipid-binding pocket and covalently modifying C269. Our study reveals that autopalmitoylation conferred by oncogenic IDH1 R132H mutation links fatty acid metabolism to the regulation of IDH1 mutant activities, and is a druggable vulnerability of IDH1 mutant cancers. Overall design: To study the effects of IDH1 R132H mutant autopamitoylation on downstream gene expressions, we estabilsed U87 cells exogenously expressing PCDH (vector control), IDH1 R13H (IDH1mt), IDH1mt C269S. We then performed gene expression profiling analysis using data obtained from RNA-seq of these three cells.