Towards routine modopathy diagnostics: advances and clinical application of direct RNA sequencing

Biography

Anna completed her Bachelor’s degree in Biology and specialised in Applied Bioinformatics during her Master’s studies at the Johannes Gutenberg University in Mainz. In 2019, Anna started her PhD at the Leibniz Institute for Resilience.

Abstract

RNA modifications, such as pseudouridine and N6-methyladenosine (m6A), play critical roles in gene regulation and have been increasingly implicated in disease mechanisms, making them promising targets for diagnostics and biomarker discovery. Direct RNA sequencing (DRS) by Oxford Nanopore Technologies enables the analysis of RNA in its native form, offering unique insights into epitranscriptomic features such as RNA modifications. However, the clinical implementation of the earlier DRS chemistry, namely RNA002, has been constrained by low throughput, limited accuracy, and the absence of robust modification detection models. In this study, we evaluate the latest RNA004 chemistry paired with novel basecalling models for pseudouridine and m6A, using diverse RNA samples, including cell lines, synthetic oligonucleotides, and human blood. Notably, we demonstrate the first clinical application of DRS by confirming an aberrant modification pattern in a patient with intellectual developmental disorder carrying truncating mutations in the methyltransferase METTL5. Additionally, the new DRS chemistry significantly improved in throughput, accuracy, and site-specific modification detection performance. These advances highlight the potential of DRS for routine diagnostics and RNA therapeutics quality assessment.