MethyLYZR permits tumor class prediction on sparse knowledge with out mannequin retraining. Credit score: Nature Medication (2025). DOI: 10.1038/s41591-024-03435-3
A staff of researchers on the College Medical Heart Schleswig-Holstein (UKSH), Kiel Campus, the Kiel College, and the Max Planck Institute for Molecular Genetics, Berlin, have developed an modern methodology for real-time molecular genetic classification of mind tumors throughout surgical procedure. This strategy combines DNA methylation evaluation with superior machine studying applied sciences to offer detailed details about the tumor sort throughout surgical procedure.
For the primary time, neurosurgery could be tailor-made not solely to the placement and proximity of a tumor to vital mind capabilities but in addition to its particular molecular traits. This allows a focused strategy to tumor elimination, which is a decisive benefit for sufferers, particularly in complicated instances. The findings have been printed on 28 February 2025 in Nature Medication.
“Only through close collaboration between basic research scientists and physicians working in translational medicine was it possible to develop a method that surpasses all previous similar approaches in terms of precision and speed,” says Prof. Dr. Franz-Josef Müller, deputy Director of the Division of Psychiatry and Psychotherapy on the UKSH, Kiel Campus, and Professor within the medical school of the CAU.
He led the interdisciplinary staff along with Prof. Dr. Helene Kretzmer, former group chief “Computational Genomics” on the MPIMG, Dr. Alena van Bömmel, former postdoc on the MPIMG, Ph.D. scholar Mara Steiger, MPIMG, and Ph.D. scholar Björn Brändl, Heart for Integrative Psychiatry, Campus Kiel.
The research was carried out in collaboration with the Division of Neurosurgery at UKSH, Campus Kiel. “Whereas previous advances in neurosurgery have refined methods for tumor elimination, this disease-centered strategy revolutionizes your complete process. As an alternative of merely specializing in the tumor’s location, intraoperative identification of the tumor sort opens up new potentialities for real-time changes within the surgical technique based mostly on the tumor’s particular biology.
“This approach directly links precision medicine with neurosurgery, elevating treatment from a technique-driven procedure to a personalized, disease-centered therapy. Surgery, in this way, becomes a custom-tailored therapy,” says Dr. Carolin Kubelt-Kwamin, senior doctor on the Clinic for Neurosurgery.
DNA methylation, an epigenetic marker, serves as a “fingerprint” that displays a tumor’s origin. Various kinds of tumors exhibit distinct methylation patterns, which could be analyzed through sequencing. The brand new methodology employs nanopore sequencing to determine these patterns with outstanding velocity and accuracy.
“However, because this sequencing must occur within the narrow timeframe of surgery, it can realistically only capture a fraction of the tumor’s methylation patterns,” explains Dr. Kretzmer. To handle this limitation, the researchers utilized a mathematical strategy from chance idea generally known as Bayes’ theorem.
“By using this method, we trained a machine learning model that, in combination with specialized software, processes the sequencing data in real time and enables tumor classification in less than an hour using less than 0.1% of the genetic data,” says Mara Steiger. This represents a major development over earlier strategies, which took hours to weeks.
The research demonstrates that the outcomes from this new methodology align with these of a whole neuropathological examination. The researchers spotlight that the strategy can precisely classify even diagnostically difficult tumors, the place conventional histopathological methods usually fall brief. This innovation presents a major benefit for sufferers, significantly in complicated instances, by enabling a extra focused and exact strategy to tumor elimination.
Trendy molecular and epigenetic analyses have revealed that many tumors beforehand regarded as one sort of most cancers are, actually, extremely numerous. For instance, tumors of the central nervous system at the moment are categorized into practically 90 distinct classes. These variations demand totally different therapeutic methods. Whereas some tumors could be handled with radiation or medicine, others require intensive surgical procedure.
Till now, nevertheless, tumor tissue was solely analyzed postoperatively, leaving surgeons unsure concerning the tumor’s classification throughout surgical procedure and forcing them to make choices that threat damaging wholesome mind tissue. Intraoperative DNA methylation evaluation, mixed with nanopore sequencing, now offers vital data that surgeons can use in actual time to make extra knowledgeable choices, supporting customized precision surgical procedure.
Extra data:
Björn Brändl et al, Speedy mind tumor classification from sparse epigenomic knowledge, Nature Medication (2025). DOI: 10.1038/s41591-024-03435-3
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