Global Proteomic Analysis of Colorectal Cancers Stratified by Microsatellite Instability Subtype Reveals Protein Differences

Lynch syndrome, historically known as hereditary nonpolyposis colorectal cancer, is caused by germline mutations in the DNA mismatch repair (MMR) genes, MLH1, MSH2 (EPCAM), MSH6, and PMS2. While the genetic changes associated with Lynch syndrome have previously been characterized, there have not been studies of the associated proteomic alterations, in part because of the limited availability of primary samples and the absence of in vitro model systems. In this study, the first large-scale tissue proteomic assessment of Lynch syndrome samples as well as three other subtypes of colorectal cancer was completed with specimens from the Ohio Colorectal Cancer Prevention Initiative. The cohort contained three groups of microsatellite unstable (MSI-high) colorectal cancer (CRC) patients (Lynch syndrome, double somatic MMR mutation, and MLH1 hypermethylation) and a group of microsatellite stable (MSS) CRC patients. A total of 122 tumor and complimentary normal mucosa samples from 61 patients were evaluated using label-free bottom-up proteomic analysis identifying 7,352 proteins. Hierarchical clustering analysis of the global proteome showed that the MSS group was significantly different than the three MSI-high groups. Of the 1,607 proteins found to be dysregulated within CRC patients, 648 proteins were specific to Lynch syndrome and 260 proteins were dysregulated across all four subtypes studied. Further examination of dysregulated proteins in response to age of diagnosis and patient's sex assigned at birth were also evaluated. This study fills a critical gap as the first proteomic characterization of Lynch syndrome samples to date. Data are available via ProteomeXchange with identifier PXD073693.