Data and code for "Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis" by Park et al., iScience 2022

This repository is a part of the supplementary document in Park et al., "Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis" published in iScience 2022.

Abstract: To date, there has been no multi-omic analysis characterizing the intricate relationships between the intragastric microbiome and gastric mucosal gene expression in gastric carcinogenesis. Using multi-omic approaches, we provide a comprehensive view of the connections between the microbiome and host gene expression in distinct stages of gastric carcinogenesis (i.e., healthy, gastritis, cancer). We uncover associations specific to disease states. For example, uniquely in gastritis, Helicobacteraceae is highly correlated with the expression of FAM3D, which has been previously implicated in gastrointestinal inflammation. Additionally, in gastric cancer but not in adjacent gastritis, Lachnospiraceae is highly correlated with the expression of UBD, which regulates mitosis and cell cycle time. Furthermore, lower abundances of B cells in gastric cancer compared to gastritis may suggest a previously unidentified immune evasion process in gastric carcinogenesis. Our integrative analysis provides the most comprehensive description of microbial, host transcriptomic, and immune cell factors of the gastric carcinogenesis pathway.