{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:55:40Z","timestamp":1785426940393,"version":"3.56.0"},"posted":{"date-parts":[[2026,3,5]]},"group-title":"Neuroscience","reference-count":56,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T00:00:00Z","timestamp":1772668800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["Neuroscience Research Training Scholarship"],"award-info":[{"award-number":["Neuroscience Research Training Scholarship"]}],"id":[{"id":"https:\/\/ror.org\/00mv9dj85","id-type":"ROR","asserted-by":"publisher"}]},{"award":["K08 NS123509"],"award-info":[{"award-number":["K08 NS123509"]}],"id":[{"id":"https:\/\/ror.org\/01s5ya894","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Recovery Fund Recovery and Resilience Facility","award":["RRF-2.3.1-21-2022-00001"],"award-info":[{"award-number":["RRF-2.3.1-21-2022-00001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Mesial temporal lobe epilepsy (TLE) is the most common form of acquired epilepsy involving the hippocampus and is a frequent sequelae of head trauma. TLE is associated with refractory seizures and significant cognitive deficits. Yet, the gene expression patterns and cell types driving epileptogenesis and the associated cognitive deficits are poorly understood. To address this, we performed single nucleus RNA sequencing on hippocampal tissue from mice at 3 and 6 weeks following pilocarpine-induced status epilepticus, a robust model of TLE. At these early timepoints, epilepsy samples showed reductions in specific Cck and Lamp5-Lhx6 interneuron subclusters, alongside increases in Cajal-Retzius cells, dentate granule (DG) cell precursors, and a mature DG cell subcluster. Among glia, an astrocyte subcluster and a markedly expanded microglia sublcuster were increased. We term this microglia population epilepsy-associated microglia (EAM). The transcriptomic profile of EAM partially overlaps with microglia described in models of Alzheimer\u2019s disease and traumatic brain injury, with enrichment of genes including\n                  <jats:italic>Myo1e<\/jats:italic>\n                  and\n                  <jats:italic>Igf1<\/jats:italic>\n                  . EAM display amoeboid morphology, can be found in dense clumps around pyramidal and granule cell body layers, and exhibit enlarged vesicles and mitochondria on electron microscopy. Cell-cell interaction analysis predict that DG cells are the main interaction partners of EAM. This dataset recapitulates known cellular alterations in TLE while defining their underlying transcriptomic programs, enabling mechanistic dissection of the key processes driving epileptogenesis.\n                <\/jats:p>","DOI":"10.64898\/2026.03.04.709339","type":"posted-content","created":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T08:50:15Z","timestamp":1772787015000},"source":"Crossref","is-referenced-by-count":0,"title":["Single-Nucleus Transcriptomics Reveals Cell Type-Specific Remodeling and Epilepsy-Associated Microglia"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4159-1356","authenticated-orcid":false,"given":"Victoria","family":"Ho","sequence":"first","affiliation":[{"name":"Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA"},{"name":"Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Tjondropurnomo","sequence":"additional","affiliation":[{"name":"Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA"},{"name":"Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eszter","family":"Balk\u00f3","sequence":"additional","affiliation":[{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha","family":"Depew","sequence":"additional","affiliation":[{"name":"Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xing","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Radhika","family":"Singh","sequence":"additional","affiliation":[{"name":"Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA"},{"name":"Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1798-3210","authenticated-orcid":false,"given":"J Edward","family":"Van Veen","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1933-5332","authenticated-orcid":false,"given":"Bence","family":"R\u00e1cz","sequence":"additional","affiliation":[{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5406-7695","authenticated-orcid":false,"given":"Peyman","family":"Golshani","sequence":"additional","affiliation":[{"name":"Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA"},{"name":"Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA"},{"name":"Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026031005400805000_2026.03.04.709339v1.1","doi-asserted-by":"crossref","unstructured":"Engel, J. & Pitk\u00e4nen, A . 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