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Pan-Cancer Analysis of Microbiome Quantitative Trait Loci

生物 微生物群 全基因组关联研究 遗传学 癌症 表达数量性状基因座 数量性状位点 遗传力 遗传建筑学 基因组 计算生物学 基因型 单核苷酸多态性 基因
作者
Can Chen,Yimin Cai,Yizhuo Liu,Shuoni Chen,Yanmin Li,Fuwei Zhang,Ming Zhang,Zequn Lu,Pingting Ying,Jinyu Huang,Linyun Fan,Xiwen Cai,Caibo Ning,Wenzhuo Wang,Yuan Jiang,Heng Zhang,Shuhui Yang,Zhihua Wang,Xiaoyang Wang,Shaokai Zhang,Chaoqun Huang,Bin Xu,Zhenming Fu,Qing Song,Mingjuan Jin,Kun Chen,Hongda Chen,Min Dai,Xiaoping Miao,Xiaojun Yang,Ying Zhu,Jianbo Tian
出处
期刊:Cancer Research [American Association for Cancer Research]
卷期号:82 (19): 3449-3456 被引量:3
标识
DOI:10.1158/0008-5472.can-22-1854
摘要

Microorganisms are commonly detected in tumor tissues, and the species and abundance have been reported to affect cancer initiation, progression, and therapy. Host genetics have been associated with gut microbial abundances, while the relationships between genetic variants and the cancer microbiome still require systematic interrogation. Therefore, identification of cancer microbiome quantitative trait loci (mbQTL) across cancer types might elucidate the contributions of genetic variants to tumor development. Using genotype data from The Cancer Genome Atlas and microbial abundance levels from Kraken-derived data, we developed a computational pipeline to identify mbQTLs in 32 cancer types. This study systematically identified 38,660 mbQTLs across cancers, ranging 50 in endometrial carcinoma to 3,133 in thyroid carcinoma. Furthermore, a strong enrichment of mbQTLs was observed among transcription factor binding sites and chromatin regulatory elements, such as H3K27ac. Notably, mbQTLs were significantly enriched in cancer genome-wide association studies (GWAS) loci and explained an average of 2% for cancer heritability, indicating that mbQTLs could provide additional insights into cancer etiology. Correspondingly, 24,443 mbQTLs overlapping with GWAS linkage disequilibrium regions were identified. Survival analyses identified 318 mbQTLs associated with patient overall survival. Moreover, we uncovered 135,248 microbiome-immune infiltration associations and 166,603 microbiome-drug response associations that might provide clues for microbiome-based biomarkers. Finally, a user-friendly database, Cancer-mbQTL (http://canmbqtl.whu.edu.cn/#/), was constructed for users to browse, search, and download data of interest. This study provides a valuable resource for investigating the roles of genetics and microorganisms in human cancer.This study provides insights into the host-microbiome interactions for multiple cancer types, which could help the research community understand the effects of inherited variants in tumorigenesis and development.
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