Analysis of Unmapped RNA-seq Data from Cancer Spatial Transcriptome to Decipher Cancer Microbiome

Abstract Recent research increasingly emphasizes the importance of the microbiome in the development and progression of cancer. Thus, exploring the microbiome modulation in tumor microenvironment and understanding its composition and function are becoming important. The introduction of spatial transcriptomics has provided new insights into microbiome research, as it enables how microbiome affects tumor microenvironment. In this study, we analyzed the spatial distribution of microbial RNA observed through PathSeq and our extended method for unmapped RNA reads in oral squamous cell carcinoma, head and neck cancer, and colorectal cancer samples. Our novel method is designed to identify and classify microbial RNA, using a custom reference that includes species-specific microbial 16S rRNA sequences to enhance the accuracy of species-level microbiome analysis. The results of this study showed a potential for a deeper understanding of the microbial distribution and their functional roles within cancer tissues. These findings will reevaluate the role of the microbiome in cancer research, providing an insight for the development of microbiome-based therapies in the future. Competing Interest Statement Hongyoon Choi and Kwon Joong Na are the co-founders and shareholders of Portrai, Inc. Footnotes ↵* Lead contact