Chemical Proteomics of Reactive Cysteine Residues in Two Disease Models

Abstract

Cysteine residues perform many essential cellular functions, including nucleophilic and redox catalysis, metal coordination, structural stabilization and cellular protection. Cysteine-related mutations are oftentimes related to diseases due to the amino acid’s functional importance. This has led cysteine to become a focus of small molecule drug discovery. A comparison of the cysteine proteome of diseased cells versus healthy cells can elucidate novel cysteine residues that play an important role in progressing the disease state. Two disease models were chosen to be the focus of this proteomic study; breast cancer through the human epithelial MCF10 progression series and immunoactivation through the Raw 246.7 mouse macrophage cell line. Comparative proteomics with mass spectrometry revealed several changes within the cysteine proteome when the cells were diseased. Some cysteines had changes in reactivity, most likely indicating a loss or gain of a modification or disulfide bond. Other cysteines showed increased labeling due to an increase in the overall expression of the protein encompassing the cysteine residue. Further follow-up of an interesting hit from the Raw cell comparison, immune responsive gene 1 (IRG1), was conducted. IRG1 produces itaconate from cis-aconitate under inflammatory conditions, disrupting the citric acid cycle. IRG1 was confirmed to have increased expression following activation of the macrophage cells by lipopolysaccharides. It was also successfully recombinantly expressed in and purified from Escherichia coli for use in an activity assay to determine if the cysteine labeled in the mass spectrometry experiment is essential for the protein function. With additional knowledge of cysteines that help progress disease states, new small molecule inhibitors can be developed to target these cysteines and impede the function that is beneficial for the disease.