Integrative omics analysis reveals effective stratification and potential prognosis markers of pan-gastrointestinal cancers

Gastrointestinal (GI) tract cancers are the most common malignant cancers with high mortality rate. Pan-cancer multi-omics data fusion provides a powerful strategy to examine commonalities and differences among various cancer types and benefits for the identification of pan-cancer drug targets. Herein, we conducted an integrative omics analysis on The Cancer Genome Atlas pan-GI samples including six carcinomas and stratified into 9 clusters, i.e. 5 single-type-dominant clusters and 4 mixed clusters, the clustering reveals the molecular features of different subtypes, other than the organ and cell-of-origin classifications. Especially the mixed clusters revealed the homogeneity of pan-GI cancers. We demonstrated that the prognosis differences among pan-GI subtypes based on multi-omics integration are more significant than clustering by single-omics. The potential prognostic markers for pan-GI stratification were identified by proportional hazards model, such as PSCA (for colorectal and stomach cancer) and PPP1CB (for liver and pancreatic cancer), which have prominent prognostic power supported by high concordance index.