Identifying m6A RNA modifications in neuroblastoma cell lines

Abstract

Neuroblastoma is a childhood cancer in which half of patients are classified as high-risk, are already in advanced disease, and have a poor outcome despite intensive treatment. Epitranscriptomics is a relatively novel field of genomics that describes the modification of RNA molecules, of which there are thought to be over 150 different types of RNA modifications, most of which are unexplored. The technology advancements by Oxford Nanopore sequencing have provided tools to look in depth at native RNA, including RNA modifications. The most characterised modification of mRNA is N6-methyladenosine (m6A), thought to regulate normal gene expression but it is widely disrupted in cancer and believed to be heavily involved in immune activation and response to immunotherapies. There is evidence to suggest m6A modifications are involved in neuroblastoma biology, susceptibility, and prognosis. This project aimed to use direct RNA sequencing to identify and characterise m6A RNA modifications in human and mouse model neuroblastoma cell lines. Using bioinformatic tools we identified and interpreted m6A RNA modifications and characterised target genes in the cell lines analysed. Some of these m6A modified genes were shared across cell lines, as well as observing novel isoforms and alternative splicing around some of the modification sites. Many of the genes that were identified as being m6A modified, have been implicated in neuroblastoma and more broadly in cancer previously. A gene ontology analysis showed significant enrichment in important biological processes. Further analysis is needed to understand the significance of these RNA modifications in neuroblastoma.

Biography

Dr. Jade Forster is an early career researcher at the University of Southampton, UK. Her expertise and research is based in translational and personalised genomic medicine in primarily cancer and rare disease genomics. Jade’s current research focuses on using nanopore sequencing to better understand and characterise RNA modifications and splicing events at bulk and single-cell transcriptomic levels, in neuroblastoma and in response to immunotherapy drugs.