Proteome analysis of patients with early onset colorectal cancer in Ireland.

person Mary O Reilly St. Vincents University Hospital, Dublin, Ireland info_outline Mary O Reilly, Aleksandar Kristic, Catherine Murphy, Anna Linehan, Kieran Wynne, Kieran Sheahan, Des C Winter, Ray McDermott, Walter Kolch

Authors person Mary O Reilly St. Vincents University Hospital, Dublin, Ireland info_outline Mary O Reilly, Aleksandar Kristic, Catherine Murphy, Anna Linehan, Kieran Wynne, Kieran Sheahan, Des C Winter, Ray McDermott, Walter Kolch Organizations St. Vincents University Hospital, Dublin, Ireland, Systems Biology Ireland, Dublin, Ireland, St Vincent's University Hospital, Dublin, Ireland, St. Vincent's Hospital, Glenageary, Ireland, Education & Research Centre, St Vincent's University Hospital, Clonmel, Ireland, St. Vincent's University Hospital, Dublin, Ireland Abstract Disclosures Research Funding Institutional Funding Newman Fellowship from University College Dublin, Ireland Background: Early onset colorectal cancer (EOCRC) is defined as colorectal cancer (CRC) in those under the age of 50. The incidence of EOCRC is rising at an alarming rate. Unlike in the USA, screening for CRC in Ireland begins at 60 years of age. It has been hypothesized that the signatures of CRC in younger populations could differ from that in elderly patients. Deep characterization of the tissue using omics profiling, including proteomics, could provide the answer to this question. Moreover, omics profiling could identify new biomarkers for patient stratification and earlier diagnosis. Methods: Forty micrograms of healthy and matched frozen tumors were taken from 8 patients with locally advanced EOCRC for whole proteome analysis. The samples were digested with trypsin and mass spectrometry was performed using data dependent analysis parallel accumulation serial fragmentation (DDA-PASEF). The raw data was searched against the Homo sapiens subset of the Uniprot Swissprot database (reviewed) with the proteomics pipeline software Fragpipe (Version 19.1) Statistical analysis was performed using Perseus software. Results: When we compared proteomes of 8 tumor tissues versus matched normal tissues, out of 5,717 protein IDs, there were more than 1,300 differentially expressed proteins. Our pathway enrichment analysis, using differentially expressed proteins, has identified a number of molecular functions altered in EOCRC samples. The most enriched signaling pathways were associated with FAT10 signaling, neutrophil extracellular trap (NET) signaling and oxidative stress response. The upstream regulator analysis (URA) has identified LASP1 and LONP1 proteins. LASP1 is known to promote CRC progression via the Hippo signaling pathway, while LONP1 is known to play a role in mitochondrial functions, metabolism, and epithelial–mesenchymal transition (EMT) in CRC cells. Importantly, the NET signaling activation in all samples suggests unfavorable immunomodulation that could stimulate cell proliferation and invasiveness. The observed activation of oxidative stress signaling components is in line with the inflammatory nature of CRC, which could signify potential response to immune checkpoint inhibitors. Conclusions: Our findings in a small cohort of patients indicate that proteomics can provide a deeper insight into aberrant signalling in EOCRC. We have identified novel vulnerabilities that might be used as therapeutic targets as well as patient stratification biomarkers. Additional proteome studies with corresponding genomic and transcriptomic analysis are needed to fully understand the potential of this approach.