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 <em>FAM3D</em>, 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 <em>UBD</em>, 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.本仓库为Park等人2022年发表于《iScience》的论文《Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis》补充材料的一部分。摘要：迄今为止，尚无多组学（multi-omic）分析能够解析胃癌发生过程中胃内微生物组与胃黏膜基因表达之间的复杂关联。本研究采用多组学方法，全面刻画了胃癌发生不同阶段（即健康状态、胃炎阶段、胃癌阶段）中微生物组与宿主基因表达的关联关系，并揭示了疾病特异性的关联特征。例如，仅在胃炎阶段，螺杆菌科（Helicobacteraceae）与*FAM3D*的表达呈显著正相关，而*FAM3D*此前已被证实与胃肠道炎症密切相关。此外，仅在胃癌组织而非毗邻的胃炎组织中，毛螺菌科（Lachnospiraceae）与*UBD*的表达呈显著正相关，*UBD*可调控有丝分裂与细胞周期时长。进一步研究发现，与胃炎阶段相比，胃癌组织中B细胞丰度更低，这或许提示胃癌发生过程中存在此前未被报道的免疫逃逸机制。本整合分析全面阐述了胃癌发生通路中的微生物、宿主转录组及免疫细胞特征。