The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants
| Autor: | Steven M. Lipkin, Xiling Shen, Diana Arguijo Mendoza, Anders Dohlman, Holly K. Dressman, Shengli Ding, Michael Gao, Iliyan D. Iliev |
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| Rok vydání: | 2021 |
| Předmět: |
Genetic Markers
Future studies Colorectal cancer Computational biology Disease Biology Microbiology Article 03 medical and health sciences Human health 0302 clinical medicine Virology Cancer genome medicine Humans Microbiome Decontamination Gastrointestinal Neoplasms 030304 developmental biology 0303 health sciences Bacteria Pan cancer Human microbiome Chromosome Mapping High-Throughput Nucleotide Sequencing medicine.disease Gastrointestinal Microbiome Gastrointestinal Tract Parasitology Artifacts 030217 neurology & neurosurgery |
| Zdroj: | Cell Host Microbe |
| ISSN: | 1931-3128 |
| DOI: | 10.1016/j.chom.2020.12.001 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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