PT - JOURNAL ARTICLE AU - Seungyeul Yoo AU - Quan Chen AU - Li Wang AU - Wenhui Wang AU - Ankur Chakravarthy AU - Rita Busuttil AU - Alex Boussioutas AU - Dan Liu AU - Junjun She AU - Tim R. Fenton AU - Jiangwen Zhang AU - Xiaodan Fan AU - Suet-Yi Leung AU - Jun Zhu TI - Molecular and cellular heterogeneity of gastric cancer explained by methylation-driven key regulators AID - 10.1101/2020.01.27.920744 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.01.27.920744 4099 - http://biorxiv.org/content/early/2020/01/28/2020.01.27.920744.short 4100 - http://biorxiv.org/content/early/2020/01/28/2020.01.27.920744.full AB - Gastric cancer (GC) is a heterogeneous disease of diverse genetic, genomic, and epigenetic alterations. Tumor microenvironment (TME) also contributes to the heterogeneity of GC. To investigate GC heterogeneity, we developed an Integrative Sequential Causality Test (ISCT) to identify key regulators of GC by integrating DNA methylation, copy number variation, and transcriptomic data. Applying ISCT to three GC cohorts containing methylation, CNV and transcriptomic data, 11 common methylation-driven key regulators (ADHFE1, CDO1, CRYAB, FSTL1, GPT, PKP3, PTPRCAP, RAB25, RHOH, SFN, and SORD) were identified. Based on these 11 genes, gastric tumors were clustered into 3 clusters which were associated with known molecular subtypes, Lauren classification, tumor stage, and patient survival, suggesting significance of the methylation-driven key regulators in molecular and histological heterogeneity of GC. We further showed that chemotherapy benefit was different in the 3 GC clusters and varied depending on the tumor stage. Both immune/stromal proportions in TME and tumor cell genomic variations contributed to expression variations of the 11 methylation-driven key regulators and to the GC heterogeneity.