Exogenous sequences in tumors and immune cells (exotic): a tool for estimating the microbe abundances in tumor RNAseq data

The microbiome affects cancer, from carcinogenesis to response to treatments. New evidence suggests that microbes are also present in many tumors, though the scope of how they affect tumor biology and clinical outcomes is unclear. A broad survey of tumor microbiome samples across several independent datasets is needed to identify robust correlations for follow-up testing. We created a tool to carefully identify the tumor microbiome within RNAseq datasets and then applied it to samples collected through the Oncology Research Information Exchange Network (ORIEN) and The Cancer Genome Atlas (TCGA). We showed how the processing removes contaminants and batch effects to yield microbe abundances consistent with non-high-throughput sequencing-based approaches. We sought to establish clinical relevance by correlating the microbe abundances with various clinical and tumor measurements, such as age and tumor hypoxia. This process leveraged the two datasets and raised up only the concordant (significant and in the same direction) associations. We identify associations with survival and clinical variables that are highly cancer-specific and relatively few associations with immune composition. Finally, we explore potential mechanisms by which microbes and tumors may interact using a network approach. Alistipes, a common gut commensal, showed the highest network degree centrality and was associated with genes related to metabolism and inflammation. The exotic tool can support the discovery of microbes in tumors in a way that leverages the many existing and growing RNAseq datasets. Statement of SignificanceThe intrinsic tumor microbiome holds great potential for its ability to predict various aspects of cancer biology and as a target for rational manipulation. Here, we describe a tool to quantify microbes from within tumor RNAseq and apply it to two independent datasets. We show new associations with clinical variables that justify biomarker uses and more experimentation into the mechanisms by which tumor microbiomes affect cancer outcomes.