{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T23:47:58Z","timestamp":1788997678114,"version":"build-2803163510"},"reference-count":45,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T00:00:00Z","timestamp":1764633600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001592","name":"Higher Education Authority Ireland","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001592","id-type":"DOI","asserted-by":"crossref"}]},{"name":"FutureNeuro","award":["16\/RC\/3948"],"award-info":[{"award-number":["16\/RC\/3948"]}]},{"name":"FutureNeuro","award":["21\/RC\/10294_P2"],"award-info":[{"award-number":["21\/RC\/10294_P2"]}]},{"DOI":"10.13039\/501100000780","name":"European Union Horizon 2020","doi-asserted-by":"publisher","award":["964712"],"award-info":[{"award-number":["964712"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["3110103"],"award-info":[{"award-number":["3110103"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF177"],"award-info":[{"award-number":["DNRF177"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"name":"StAR MD programme at RCSI in collaboration with Blackrock Clinic, Dublin"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Background: Our understanding of the pathomechanisms of epilepsy has improved through techniques that access the living human brain. We recently reported that explanted stereo-electroencephalography (SEEG) electrodes from patients with epilepsy carry residual biomolecules and cells, which may be utilised for transcriptome and DNA methylation profiling. Methods: Here, we applied bioinformatic and other analyses to explore the transcriptomes (RNA sequencing-based) of those SEEG cases to better understand the types of recovered transcripts in terms of representation of genes expressed by different cell types, brain structures, and the extent to which the signal may reflect local epileptiform activity. Results: Electrodes from all clinical cases retained protein-coding transcripts which reflected the local molecular microenvironment as well as epileptiform activity. Expression of genes involved in housekeeping functions, as well as markers of neuronal activity, was consistent between patients and between the electrode locations within the brain. We detected transcripts representing various cell types and subtypes, including excitatory and inhibitory neurons, all major classes of glia, and endothelial cells, as well as transcripts enriched in specific brain regions. Several genes showed a gradient of expression depending on the electrode position within the brain. We found examples of gene expression that correlated with epileptiform activity as recorded by SEEG. Conclusions: These findings extend the evidence that SEEG electrodes reflect the molecular microenvironments of brain activity in patients with epilepsy, both at sites of seizure onset and within the wider seizure network. The approach has potential applications in intraoperative surgical decision-making, as well as to identify molecular biomarkers or therapeutic targets for the drug-resistant epilepsies.<\/jats:p>","DOI":"10.3390\/biom15121684","type":"journal-article","created":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T12:39:43Z","timestamp":1764679183000},"page":"1684","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Transcriptomic Profiles from Stereo-EEGs May Reflect the Local Brain Cell Microenvironment in Human Epilepsy"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-6317-179X","authenticated-orcid":false,"given":"Julian","family":"Larkin","sequence":"first","affiliation":[{"name":"Department of Neurology and Clinical Neurophysiology, Beaumont Hospital, D09 V2N0 Dublin, Ireland"},{"name":"Strategic Academic Recruitment Doctor of Medicine Programme, RCSI University of Medicine and Health Sciences in Collaboration with Blackrock Clinic, D02 YN77 Dublin, Ireland"},{"name":"FutureNeuro Research Ireland Centre, RCSI University of Medicine & Health Sciences, 123 St. Stephen\u2019s Green, D02 YN77 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anuj Kumar","family":"Dwivedi","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine, University of Southern Denmark, 5230 Odense M, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arun","family":"Mahesh","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine, University of Southern Denmark, 5230 Odense M, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert","family":"Sanfeliu","sequence":"additional","affiliation":[{"name":"FutureNeuro Research Ireland Centre, RCSI University of Medicine & Health Sciences, 123 St. Stephen\u2019s Green, D02 YN77 Dublin, Ireland"},{"name":"Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, D02 YN77 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kieron J.","family":"Sweeney","sequence":"additional","affiliation":[{"name":"FutureNeuro Research Ireland Centre, RCSI University of Medicine & Health Sciences, 123 St. Stephen\u2019s Green, D02 YN77 Dublin, Ireland"},{"name":"Department of Neurosurgery, Beaumont Hospital, D09 V2N0 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donncha F.","family":"O\u2019Brien","sequence":"additional","affiliation":[{"name":"FutureNeuro Research Ireland Centre, RCSI University of Medicine & Health Sciences, 123 St. Stephen\u2019s Green, D02 YN77 Dublin, Ireland"},{"name":"Department of Neurosurgery, Beaumont Hospital, D09 V2N0 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijay K.","family":"Tiwari","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine, University of Southern Denmark, 5230 Odense M, Denmark"},{"name":"Danish Institute for Advanced Study (DIAS), 5230 Odense M, Denmark"},{"name":"Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark"},{"name":"Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry, and Biomedical Science, Queens University Belfast, Belfast BT9 7BL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Widdess-Walsh","sequence":"additional","affiliation":[{"name":"Department of Neurology and Clinical Neurophysiology, Beaumont Hospital, D09 V2N0 Dublin, Ireland"},{"name":"FutureNeuro Research Ireland Centre, RCSI University of Medicine & Health Sciences, 123 St. Stephen\u2019s Green, D02 YN77 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6237-9632","authenticated-orcid":false,"given":"David C.","family":"Henshall","sequence":"additional","affiliation":[{"name":"FutureNeuro Research Ireland Centre, RCSI University of Medicine & Health Sciences, 123 St. Stephen\u2019s Green, D02 YN77 Dublin, Ireland"},{"name":"Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, D02 YN77 Dublin, Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"107757","DOI":"10.1016\/j.neuropharm.2019.107757","article-title":"Identifying targets for preventing epilepsy using systems biology of the human brain","volume":"168","author":"Kirchner","year":"2020","journal-title":"Neuropharmacology"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1111\/epi.13791","article-title":"Defining epileptogenic networks: Contribution of SEEG and signal 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