Understanding the epigenetics of brain tumors is vital, as it allows distinguishing tumors with unprecedented precision, guiding precise classification and tailored therapeutic approaches. Consequently, methylation has even been incorporated as a diagnostic criterion in the WHO Classification of Brain Tumors 2021.
A paramount tool when using DNA methylation for classification – especially for brain tumors – is the Heidelberg classifier, developed by the research group coordinating DC2M-TAEC (available on www.molecularneuropathology.org) This computer algorithm assigns any given specimen to the correct diagnosis based on its methylation data. However, using this algorithm currently requires data input that is generated in a tedious, lengthy and costly manner. This limits its global implementation due to unavailability of resources and the time- consuming nature of the protocol, which ultimately hampers patient care.
With DC2M-TAEC, we will leverage a rapid and more accessible platform to simultaneously generate methylation and sequencing results: long-read, or so called nanopore sequencing – a PCR-free, single-molecule sequencing approach. We will paradigmatically establish this method in a large center in which molecular profiling is so far not regularly available due to the aforementioned hurdles.
Within this consortium, experts from Heidelberg, Oslo, Istanbul, and Toronto join forces. The Heidelberg group will focus on the bioinformatics behind methylation-based classification and adapting their algorithm to accept various data types as input – including nanopore data. This classification tool will then be optimized and tested for analysis of single-cell DNA nanopore data, to examine epigenetic changes in the tumor and its microenvironment over time. The sample processing and sequencing will be optimized for intra-operative classification in Oslo, which will then be implemented with the adapted Heidelberg classifier in Istanbul. Lastly, to complete the full circle of diagnostic potential, Nanopore sequencing will be devised for analyzing liquid biopsy samples in Toronto, e.g. for pre-operative usage or disease monitoring.
Ultimately, the resulting diagnostic workflow, demonstrated to be globally feasible, will allow individualized and risk-adapted care for patients with brain tumors. This tremendous translational impact is emphasized by the fact that the approaches will span early detection, surgery planning, intra-operative surgery guidance, treatment monitoring, and biological insight by detection of resistance mechanisms. This project can serve as a proof of concept to further establish nanopore sequencing beyond the field of neuro-oncology in the future.