Deep Visual Proteomics reveals DNA replication stress as a hallmark of Signet Ring Cell Carcinoma

Background and Aims: Signet-Ring (SR) cell carcinoma (SRCC) is an increasingly prevalent form of gastric cancer, known for its late presentation and poor treatment outcomes. Using our spatial proteomics pipeline, Deep Visual Proteomics (DVP), we aimed to comprehensively explore the SRCC proteome landscape in a single patient to uncover unknown disease mechanisms that could be individually targeted for therapeutic purposes. Methods: We applied DVP, which combines image-based artificial intelligence with automated microdissection and ultra-high sensitivity mass spectrometry, to SR cell-positive tissues from the bladder, seminal vesicle, lymph node, and prostate within a single patient. Results: DVP allowed us to perform in-depth spatial proteome analysis of SRCC presenting in different organs of a single patient. We identified alternations in DNA damage response (DDR) pathways, particularly in the pathways associated with ataxia-telangiectasia mutant (ATR) and DNA mismatch repair (MMR), suggesting replication stress as the leading factor of SRCC mutagenicity. Additionally, we identified an enrichment of immune-related proteins and could observe infiltration of cytotoxic T lymphocytes. Conclusion: Analyzing the SRCC proteome across different organs within a single patient allowed us to confirm known disease patterns and identify novel biological mechanisms contributing to SRCC aggressiveness. Our data provided insights into why chemotherapy was unsuccessful and explained the significant life extension and improved quality of life following PD-1 inhibitor treatment, which led to tumor stasis.