A novel method for obtaining epileptic brain tissue for omic analyses using electrodes from a clinical stereoelectroencephalography study

Ehrnrooth, N.; Kangas, S. M.; Malyutina, A.; Wilenius, J.; Tuhkala, A.; Keskitalo, S. E.; Salokas, K.; Varjosalo, M.; Lindgren, H.; Mäkelä, A.; Tynninen, O.; Karppinen, A.; Lauronen, L.; Vanhanen, J.; Nevalainen, P.; Peltola, M.; Uusimaa, J.; Hinttala, R.; Metsähonkala, E.-L.; Ignatius, E.

doi:10.64898/2026.09.01.747265

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bioRxiv · 10.64898/2026.09.01.747265

A novel method for obtaining epileptic brain tissue for omic analyses using electrodes from a clinical stereoelectroencephalography study

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Abstract

Abstract Purpose: Developing a valid and practical method for obtaining brain tissue samples for transcriptomic and proteomic analyses using tissue adhered to stereoelectroencephalography (SEEG) electrodes, to enable investigation of the molecular mechanisms underlying chronic epilepsy. Method: Brain tissue samples adhered to SEEG electrodes were collected from six patients with drug-resistant epilepsy and preprocessed in a hospital environment after electrode removal. RNA extraction was initiated immediately, and proteomics samples were snap-frozen until subsequent analysis. The samples were categorized into three groups according to their electrophysiological profile: epileptogenic zone, propagation zone, and least-involved zone. The omic findings between these zones and anatomical brain areas were compared. Results: High-quality RNA and protein samples were obtained from tissue adhered to SEEG electrodes. Neuron- and brain-specific gene expression patterns and proteins were identified. Signs of activation of inflammatory mechanisms were most pronounced in the epileptogenic zone. Transcriptomic and proteomic findings demonstrated concordance. Conclusion: SEEG electrodes are a useful source for obtaining brain tissue for molecular characterization of chronic epilepsy. This method will enable the identification of shared and distinct molecular mechanisms in patients with varying etiologies of epilepsy.

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Ehrnrooth, N., Kangas, S. M., Malyutina, A., Wilenius, J., Tuhkala, A., Keskitalo, S. E., Salokas, K., Varjosalo, M., Lindgren, H., Mäkelä, A., Tynninen, O., Karppinen, A., Lauronen, L., Vanhanen, J., Nevalainen, P., Peltola, M., Uusimaa, J., Hinttala, R., Metsähonkala, E.-L., Ignatius, E.. 2026-09-04. A novel method for obtaining epileptic brain tissue for omic analyses using electrodes from a clinical stereoelectroencephalography study. https://doi.org/10.64898/2026.09.01.747265

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