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EpilepsiaPathologyPeer-reviewed journal article

Synaptic Ultrastructural Alterations in Human Focal Cortical Dysplasia: Insights from Volume Electron Microscopy

Gyu Hyun KimiD, Na‐Young SeoiD, Seung‐Ki KimiD, Jae‐Kyung WoniD, Yang Hoon HuhiD, Ji Yeoun LeeiD, Kea Joo LeeiD

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In-depth summary

Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 1 (6 Mar 2025) · CC BY 4.0

Volume EM of one focal cortical dysplasia type I patient shows fewer somatic inhibitory and dendritic excitatory synapses, oversized vesicle-rich excitatory synapses, and thicker myelin.

Excitation-inhibition imbalance underlies seizures in focal cortical dysplasia, a leading cause of drug-resistant epilepsy, but earlier light and electron microscopy studies disagree on how excitatory synapses change. This work measures synapse density, size, spacing and organelles in 3D, comparing an epileptic focus with adjacent histologically normal cortex from the same patient.

Key results

  1. ShownIn this patient's dysplastic layer III, distal pyramidal dendrites carried far fewer spines and asymmetric (excitatory) synapses, while symmetric (inhibitory) synapse density was unchanged. As a result, the upper half of inhibitory-to-nearest-excitatory distances was longer.

    SB-SEM, n = 10 dendrites per condition: asymmetric synapses/10 μm 9.7 ± 1.04 control vs 4.4 ± 0.30 epileptogenic (p = 0.0001); total spines/10 μm 11.8 ± 1.09 vs 4.3 ± 0.31 (p < 0.0001); symmetric 0.7 ± 0.26 vs 0.7 ± 0.20 (p = 0.86); top 50% inhibitory-excitatory distance 1.23 ± 0.15 vs 2.07 ± 0.29 μm (p = 0.027), overall p = 0.34. · Ultrastructural Synaptic Analysis of in Cortical…; Spatial Distribution of Excitatory and…; Figure legends

  2. SuggestedSymmetric (inhibitory) synapses on pyramidal neuron cell bodies were less dense in the epileptogenic region than in adjacent control cortex, which fits with weaker perisomatic inhibition.

    ATUM-SEM with twelve segmented neurons per group: inhibitory synapses per 100 μm^3 were 1.86 ± 0.32 in control vs 0.94 ± 0.24 in epileptogenic tissue (p = 0.029). · ATUM-SEM imaging and Analysis; Ultrastructural Synaptic Analysis of in Cortical…

  3. ShownOn average, remaining spines in dysplastic cortex were larger, with a subset notably enlarged. Among the largest 20% of spines, postsynaptic densities were bigger, and necks widened more than heads, lowering the head-to-neck ratio. The authors propose this may weaken electrochemical compartmentalization.

    Spine volume 0.15 ± 0.01 vs 0.35 ± 0.05 μm^3 (p = 0.048); top 20% PSD area 0.91 ± 0.06 vs 1.40 ± 0.24 μm^2 (p = 0.013); neck diameter 0.15 ± 0.01 vs 0.30 ± 0.02 μm and head-to-neck ratio 3.92 ± 0.16 vs 2.61 ± 0.21 (both p < 0.0001; control n = 156, epilepsy n = 79); spine length unchanged (p = 0.26). · Ultrastructural Synaptic Analysis of in Cortical…; Figure legends

  4. SuggestedElectron tomography showed larger presynaptic boutons and spine heads in the epileptogenic region. Boutons held a larger total vesicle pool, but the number of docked vesicles did not differ.

    HVEM tomography of 26 boutons (12 control, 14 epileptogenic): total SVs/bouton 173.8 ± 23.2 vs 361.5 ± 67.5 (p = 0.042); docked SVs 16.3 ± 1.9 vs 23.1 ± 4.2 (p = 0.38); bouton volume 0.15 ± 0.02 vs 0.24 ± 0.03 μm^3 (p = 0.034); spine head volume 0.06 ± 0.01 vs 0.12 ± 0.03 μm^3 (p = 0.031). · Electron Tomography; Intrasynaptic Organelle Analysis (Vesicles…

  5. SuggestedIn the dysplastic region, fewer boutons contained mitochondria, but those that did had more and larger mitochondria. Only a minority of synaptic protrusions had a spine apparatus, and myelin sheaths were thicker (lower G-ratio).

    Mitochondria-containing boutons/10 μm 6.6 ± 0.41 vs 3.3 ± 0.31 (p < 0.0001); mitochondria per bouton 1.2 ± 0.06 vs 1.7 ± 0.15 (p = 0.03); volume 0.08 ± 0.01 vs 0.15 ± 0.01 μm^3 (p < 0.0001); synaptic protrusions with SA 84.6 ± 6.0% vs 24.0 ± 8.4% (p < 0.0001); G-ratio 0.731 ± 0.012 vs 0.691 ± 0.013 (p = 0.028, n = 40 per group). · Intrasynaptic Organelle Analysis (Vesicles…; Myelination Changes in the Epileptogenic Cortex; Figure legends

Methods, data and reproducibility

Within-patient comparison of immersion-fixed layer III temporal cortex from one focal cortical dysplasia (FCD) type I patient, epileptic focus versus adjacent normal-appearing tissue, using serial block-face SEM (SB-SEM) dendrite reconstruction, tape-collected serial-section SEM (ATUM-SEM) for somata and myelin, and high-voltage EM tomography of synapses.

  • Resected left medial temporal cortex from a 16-year-old male with FCD type I and intractable epilepsy: the epileptic focus plus a nearby control area · human · n = single patient (within-patient comparison)
  • SB-SEM stacks of layer III (200 serial images, 20,250 μm³ each) from control and epileptogenic regions, with manually reconstructed spiny dendrite segments · human · n = 20 dendrites (10 per condition)
  • ATUM-SEM serial 50 nm sections of layer III, used for symmetric synapses on pyramidal somata and for myelin G-ratio · human · n = Twelve neurons per group; 40 per group for G-ratio
  • HVEM tilt-series tomograms (61 tilt images each) of excitatory synapses in 250 nm sections · human · n = 26 boutons (12 control, 14 epileptogenic)
  • H&E and anti-NeuN stained biopsy sections for FCD typing and layer III cell density (550–900 μm below the pia) · human
Methods & tools
Merlin 3View serial block-face SEM (Carl Zeiss), ATUMtome with Gemini 300 SEM (Carl Zeiss), Atlas 5 (Fibics) large-area imaging, JEM-1000BEF high-voltage EM at 1,000 kV (JEOL), TEM Recorder (JEOL), Composer and Visualizer-Kai tomogram reconstruction, ImageJ / Fiji, TrakEM2 image alignment, Synapseweb open-source reconstruction software, GraphPad Prism, H&E staining and anti-NeuN immunohistochemistry, Leica VT 1000S vibratome
Reproducibility gaps
Data are available only from the corresponding author on reasonable request. No image stacks, reconstructions or analysis scripts are deposited, and the listed URLs point to third-party tools, not the authors' own code.
Limitations (6)
  • All 3D EM data come from a single case, so the authors caution that the findings may not extend to the wider population of FCD patients with epilepsy; whether they hold across cases is untested. · stated by the authors
  • Tissue was immersion-fixed rather than perfusion-fixed. The authors acknowledge this as a potential limitation, although they report excellent ultrastructural preservation. · stated by the authors
  • Some changes in the epileptogenic cortex may be compensatory or secondary responses to ongoing epilepsy rather than primary FCD pathology. · stated by the authors
  • Functional effects such as weaker shunting inhibition are inferred from structure alone. Electrophysiological recordings, computational modelling, and cell-type, circuit and glial analyses are still needed. · stated by the authors
  • The statistics treat dendrites, spines, boutons and axons from one patient as independent observations, so the p-values describe variability within this tissue, not differences between patients. The spacing difference was significant only in the top 50% subset (overall p = 0.34). · noted in this summary
  • The control was adjacent cortex from the same epileptic brain. Dysplastic layer III was defined by depth because lamination was indistinct, so mismatched layers or seizure effects reaching the control tissue could contribute to the differences. · noted in this summary

Read this if you study epileptogenic human cortex or synapse ultrastructure and want quantitative volume EM data on excitatory, inhibitory, organelle and myelin changes in FCD type I.

Citations
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Abstract

Focal cortical dysplasia (FCD) is a developmental disorder of the cerebral cortex and a leading cause of drug-resistant epilepsy in children and young adults. A disrupted excitation-inhibition (E-I) balance is a hallmark of neuronal hyperexcitability in FCD, yet the underlying synaptic ultrastructural alterations remain poorly understood. Using volume electron microscopy, we performed a detailed morphological assessment of synaptic density, size, and organelle distribution within synapses in the temporal cortical layer III of an FCD patient. Our quantitation revealed a reduced density of inhibitory (symmetric) synapses on pyramidal neuron cell bodies. Notably, the dysplastic region displayed a lower density of excitatory (asymmetric) synapses but contained extra-large excitatory synapses, which contained an increased number of synaptic vesicles. Additionally, inhibitory synapses were located further away from the nearest excitatory synapses along distal dendrites, possibly weakening the effectiveness of shunting inhibition in the dysplastic area. There was also a decrease in presynaptic boutons housing mitochondria and in postsynaptic protrusions containing a spine apparatus, pointing to potential deficits in intracellular calcium handling and synaptic plasticity in the epileptogenic area. Moreover, maladaptive myelination was a prominent feature in the dysplastic region. These findings collectively indicate that synaptic architectural modifications may contribute to the neuronal hyperexcitability associated with epilepsy in FCD.

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