药物基因组学
表达数量性状基因座
免疫系统
增强子
生物
计算生物学
数量性状位点
医学
全基因组关联研究
肿瘤科
生物信息学
作者
Zhao Zhang,Mei Luo,Qiang Li,Yuan Liu,Charles Lussier,Jian Zhang,Youqiong Ye,An-Yuan Guo,Leng Han
出处
期刊:Cancer Research
[American Association for Cancer Research]
日期:2022-03-01
卷期号:82 (5): 785-790
标识
DOI:10.1158/0008-5472.can-21-2058
摘要
Enhancer RNAs (eRNA) regulate gene expression and play critical roles in cancer. Using large-scale omics data from The Cancer Genome Atlas (TCGA), we systematically investigated the impact of genetic variants on eRNA expression and identified approximately 1 million eRNA quantitative trait loci (eRNA-QTL) as cis- and trans-acting. Over 16,000 eRNA-QTLs were associated with patient overall survival. Assessing the impact of eRNAs on more than 1,000 imputed anticancer drug responses across approximately 10,000 patients with cancer revealed more than 7 million significant associations. Furthermore, approximately 240,000 significant associations were identified between eRNA expression and immune cell abundance deconvoluted by TIMER, CIBERSORT, ImmuCellAI, and ImmuneCellGSVA. Finally, a user-friendly data portal was generated: Genetic, Pharmacogenomic, and Immune Landscapes of eRNAs (GPIeR; https://hanlab.tamhsc.edu/GPIeR/). GPIeR is a large-scale multidimensional data portal that can be used to explore eRNA-associated genetic variants, drug responses, and immune infiltration, with the purpose of facilitating functional and clinical investigations of eRNAs in cancer.This study provides insights into the impact of the enhancer RNA (eRNA) landscape on patient outcome, the immune microenvironment, and drug response across cancers and develops a multidimensional data portal to facilitate eRNA research.
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