Intratumoral microbes correlate with tumor-infiltrating lymphocytes in lung cancer RNAseq.

Nonhuman sequences have been found in many tumors, but their effect on outcomes remains poorly understood. We hypothesize that intratumoral microbes affect the recruitment of immune cells through local immunostimulatory effects including activation nucleic acid sensing pathways. We obtained RNA-seq data from 480 tumor biopsies including melanoma (16), bladder (104), colorectal (20), renal cell carcinoma (20), sarcoma (118), and lung (202) from patients treated at The Ohio State University Comprehensive Cancer Center as part of the Oncology Research Information Exchange Network (ORIEN). Reads were aligned to human and exogenous genomes using TopHat2 and Kraken2/Bracken, respectively. Human gene expression was deconvolved to absolute abundances of immune cells using CIBERSORT. An average of 99.87% of reads aligned to the human reference genome across all samples. Inferred counts of tumor-infiltrating lymphocytes (TILs), and particularly the immune cell types CD8+ T-cells and M1 macrophages, were significantly enriched in lung cancer relative to the other tested cancers (p-values Citation Format: Daniel Spakowicz, Rebecca Hoyd, YunZhou Liu, Janhavi Sahasrabudhe, Malvenderjit J. Singh, Isaac Arefi, Andrew Denney, David Carbone, Xiaokui Mo. Intratumoral microbes correlate with tumor-infiltrating lymphocytes in lung cancer RNAseq [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B30.