Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures

Mammalian ribosomal RNA (rRNA) molecules are highly abundant RNAs, decorated with over 220 different rRNA modifications, changing their chemical and biological properties. Previous works have shown that some types of rRNA modifications can be dynamically regulated; however, a comprehensive analysis of how the mammalian rRNA modification landscape is remodeled across time, cell types and upon disease conditions, remains largely unexplored. Here, we employ direct RNA nanopore sequencing to generate maps of human and mouse rRNA modifications across tissues, developmental stages, cell types and disease conditions. Our analyses reveal multiple rRNA sites that are differentially modified in a tissue- and/or developmental stage-specific manner. Notably, the adult brain exhibits the most distinct rRNA modification patterns, including previously unannotated rRNA modified sites. We then demonstrate that dynamic rRNA modification patterns can be used for tissue and cell type identification, which we hereby term 'epitranscriptomic fingerprinting'. We then explored rRNA modification patterns in normal-tumor matched samples from lung cancer patients, finding that rRNA epitranscriptomic fingerprinting accurately classified clinical samples into normal and tumor groups from only 250 reads per sample, demonstrating the potential of rRNA modifications as diagnostic biomarkers, and revealing rRNA modifications as a rich source of information for tissue, cell type and disease identification. Overall design: Direct-RNA sequencing of rRNA from mouse tissues, cell lines and human matched normal-tumor lung samples.