Multi omic stratification of the missense variant cysteinome
Cancer genomes are rife with genetic variants; one key outcome of this variation is gain-of-cysteine, which is the most frequently acquired amino acid due to missense variants in COSMIC. Acquired cysteines are also both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain uncharacterized. Here, we pair cysteine chemoproteomics, a technique that enables proteome-wide pinpointing of functional, redox sensitive, and potentially druggable residues, with genomics to reveal the hidden landscape of cysteine acquisition. For both cancer and healthy genomes, we find that cysteine acquisition is a ubiquitous consequence of genetic variation that is further elevated in the context of decreased DNA repair. Our chemoproteogenomics platform integrates chemoproteomic, whole exome, and RNAseq data, with a customized two-stage false detection rate (FDR) error control -based FragPipe enabled proteomic search, further enabled with a user friendly FragPipe interface. By deploying chemoproteogenomics across 11 total cell lines, we identify gain of cysteines, including those liganded by electrophilic druglike molecules. Reference cysteines proximal to missense variants were also found to be pervasive, supporting further heretofore untapped opportunities for proteoform-specific chemical probe development campaigns. Many of the identified acquired cysteines, particularly those in mismatch repair deficient (dMMR) cell lines, were found to be predicted to be highly deleterious, providing evidence for likely functional and therapeutic relevance. The sample-matched combinatorial variant databases built into chemoproteogenomics afforded enhanced coverage and enabled identification of highly reactive and ligandable cysteine residues in the highly polymorphic MHC-Class I complexes, including for pathogenic alleles.