Tonight, I watched Jade Foster from the University of Southampton in the UK present at London Calling 2024. The session’s title was “Identifying m6A RNA modifications in neuroblastoma cell lines.” They explained that epitranscriptomics describes the modification of RNA molecules. There are over 150 RNA modifications determined by readers, writers, and erasers! This process is disrupted in cancer. Foster focused on neuroblastoma, as it is a common childhood solid cancer. There is evidence that m6A modifications are involved in neuroblastoma. Oxford Nanopore sequencing is the only technology that allows direct RNA sequencing. The initial workflow used RNA002 and MinION R9.4.1 flow cells. RNA from neuroblastoma cell lines were extracted with trizol. Five micrograms were put into the total RNA prep and split across four flow cells on the GridION. M6A modifications were identified. Genes shared between the two cell lines analyzed that had M6A modifications were further studied. Next, the team used a PromethION P2 Solo. The group used 1 ug total RNA and the RNA004 chemistry to analyze TH-MYCN mouse-derived cell lines. With this approach, more coverage was obtained, and novel, highly modified transcripts were found. The power of RNA004 chemistry and PromethION P2 Solo were highlighted by this research.
