Borchmann, Sven ORCID: 0000-0001-6662-6864 (2021). An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer. Microbiome, 9 (1). LONDON: BMC. ISSN 2049-2618

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Abstract

Background: Host tissue infections by bacteria and viruses can cause cancer. Known viral carcinogenic mechanisms are disruption of the host genome via genomic integration and expression of oncogenic viral proteins. An important bacterial carcinogenic mechanism is chronic inflammation. Massively parallel sequencing now routinely generates datasets large enough to contain detectable traces of bacterial and viral nucleic acids of taxa that colonize the examined tissue or are integrated into the host genome. However, this hidden resource has not been comprehensively studied in large patient cohorts. Methods: In the present study, 3025 whole genome sequencing datasets and, where available, corresponding RNA-seq datasets are leveraged to gain insight into novel links between viruses, bacteria, and cancer. Datasets were obtained from multiple International Cancer Genome Consortium studies, with additional controls added from the 1000 genome project. A customized pipeline based on KRAKEN was developed and validated to identify bacterial and viral sequences in the datasets. Raw results were stringently filtered to reduce false positives and remove likely contaminants. Results: The resulting map confirms known links and expands current knowledge by identifying novel associations. Moreover, the detection of certain bacteria or viruses is associated with profound differences in patient and tumor phenotypes, such as patient age, tumor stage, survival, and somatic mutations in cancer genes or gene expression profiles. Conclusions: Overall, these results provide a detailed, unprecedented map of links between viruses, bacteria, and cancer that can serve as a reference for future studies and further experimental validation.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Borchmann, SvenUNSPECIFIEDorcid.org/0000-0001-6662-6864UNSPECIFIED
URN: urn:nbn:de:hbz:38-569077
DOI: 10.1186/s40168-021-01039-4
Journal or Publication Title: Microbiome
Volume: 9
Number: 1
Date: 2021
Publisher: BMC
Place of Publication: LONDON
ISSN: 2049-2618
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
HELICOBACTER-PYLORI INFECTION; EPSTEIN-BARR-VIRUS; HEPATITIS-B-VIRUS; HUMAN-PAPILLOMAVIRUS; PROPIONIBACTERIUM-ACNES; DNA; MICROBIOME; CONTAMINATION; CARCINOMA; GENOMEMultiple languages
MicrobiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/56907

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