Nanopore based RNA methylation profiling of a circulating lung cancer biomarker

The characterisation of circulating nucleic acid biomarkers in liquid biopsy based diagnostics holds great potential to transform the landscape of early cancer detection and screening. In order to overcome the challenges associated with poor sensitivity, these tests are increasingly incorporating information beyond the primary sequence, to include epigenetic, fragmentomic, and other chemical properties to boost performance. RNA, in particular, can be modified with over one hundred different bases at the epitranscriptomic level, offering a rich and currently untapped source of biomarker signal. Here we have developed a method to enable the single molecule methylation profiling of a previously identified lung cancer biomarker ribosomal RNA fragment on the Oxford Nanopore platform. Importantly, we show the differential methylation profile of this blood based RNA fragment between cancer and control patients that may offer additional information for multi-modal liquid biopsies to enable enhanced diagnostic performance.