The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants

被引:143
作者
Dohlman, Anders B. [1 ]
Mendoza, Diana Arguijo [1 ]
Ding, Shengli [1 ]
Gao, Michael [2 ]
Dressman, Holly [3 ]
Iliev, Iliyan D. [4 ]
Lipkin, Steven M. [4 ]
Shen, Xiling [1 ]
机构
[1] Duke Univ, Ctr Genom & Computat Biol, Duke Microbiome Ctr, Dept Biomed Engn, Durham, NC 27708 USA
[2] Duke Univ, Duke Inst Hlth Innovat, Durham, NC 27701 USA
[3] Duke Univ, Duke Microbiome Ctr, Dept Mol Genet & Microbiol, Durham, NC 27708 USA
[4] Cornell Univ, Weill Cornell Med Coll, Dept Med, New York, NY 10065 USA
关键词
SET ENRICHMENT ANALYSIS; LYSINE DECARBOXYLASE; COLORECTAL-CANCER; GENE; RNA; EXPRESSION; INTERLEUKIN-6; INFLAMMATION; MECHANISMS; EXTRACTION;
D O I
10.1016/j.chom.2020.12.001
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Studying the microbial composition of internal organs and their associations with disease remains challenging due to the difficulty of acquiring clinical biopsies. We designed a statistical model to analyze the prevalence of species across sample types from The Cancer Genome Atlas (TCGA), revealing that species equiprevalent across sample types are predominantly contaminants, bearing unique signatures from each TCGA-designated sequencing center. Removing such species mitigated batch effects and isolated the tissue-resident microbiome, which was validated by original matched TCGA samples. Gene copies and nucleotide variants can further distinguish mixed-evidence species. We, thus, present The Cancer Microbiome Atlas (TCMA), a collection of curated, decontaminated microbial compositions of oropharyngeal, esophageal, gastrointestinal, and colorectal tissues. This led to the discovery of prognostic species and blood signatures of mucosal barrier injuries and enabled systematic matched microbe-host multi-omic analyses, which will help guide future studies of the microbiome's role in human health and disease.
引用
收藏
页码:281 / +
页数:23
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