Systems biology and OMIC data integration to understand gastrointestinal cancers

Abstract

Gastrointestinal (GI) cancers are a set of diverse diseases affecting many parts/ organs. The five most frequent GI cancer types are esophageal, gastric cancer (GC), liver cancer, pancreatic cancer, and colorectal cancer (CRC); together, they give rise to 5 million new cases and cause the death of 3.5 million people annually. We provide information about molecular changes crucial to tumorigenesis and the behavior and prognosis. During the formation of cancer cells, the genomic changes are microsatellite instability with multiple chromosomal arrangements in GC and CRC. The genomically stable subtype is observed in GC and pancreatic cancer. Besides these genomic subtypes, CRC has epigenetic modification (hypermethylation) associated with a poor prognosis. The pathway information highlights the functions shared by GI cancers such as apoptosis; focal adhesion; and the p21-activated kinase, phosphoinositide 3-kinase/Akt, transforming growth factor beta, and Toll-like receptor signaling pathways. These pathways show survival, cell proliferation, and cell motility. In addition, the immune response and inflammation are also essential elements in the shared functions. We also retrieved information on protein-protein interaction from the STRING database, and found that proteins Akt1, catenin beta 1 (CTNNB1), E1A binding protein P300, tumor protein p53 (TP53), and TP53 binding protein 1 (TP53BP1) are central nodes in the network. The protein expression of these genes is associated with overall survival in some GI cancers. The low TP53BP1 expression in CRC, high EP300 expression in esophageal cancer, and increased expression of Akt1/TP53 or low CTNNB1 expression in GC are associated with a poor prognosis. The Kaplan Meier plotter database also confirmed the association between expression of the five central genes and GC survival rates. In conclusion, GI cancers are very diverse at the molecular level. However, the shared mutations and protein pathways might be used to understand better and reveal diagnostic/prognostic or drug targets.

Keywords: Cellular pathways; Gastrointestinal cancers; Genome; OMIC data; Prognosis; Protein-protein interaction.

Figure 1

Protein-protein interaction of genes with mutations associated with gastrointestinal cancers. The nodes represent the genes, and the edges represent the protein interactions. The network was built using information from experimental data only from the STRING database[110]. The node size represents the number of protein interactions (degree), indicating the node’s centrality.

Figure 2

Prognostic value of Akt1, catenin beta 1, tumor protein p53 for gastric cancer (A) and hepatocellular carcinoma (B) in Kaplan Meier plotter (https://kmplot.com)[142]. Kaplan-Meier survival curves for patients of gastric cancer and hepatocellular carcinoma with high and low indicated gene expression. CTNNB1: Catenin beta 1; TP53: Tumor protein p53.