Single-nucleus RNA sequencing reveals ferroptosis as a potential contributor to the pathogenesis of focal cortical dysplasia.

Overview

1. Epilepsy Center and Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
2. Shenzhen Pediatrics Institute, Shantou University Medical College, Shenzhen, Guangdong, China

Abstract

Objective: Focal cortical dysplasia (FCD) is a leading cause of drug‐resistant epilepsy, whereas its molecular and cellular mechanisms remain poorly understood. This study aimed to characterize the cellular heterogeneity of FCD and investigate the function of ferroptosis in FCD pathogenesis.

Methods: Single‐nucleus RNA sequencing was carried out on epileptogenic cortical tissues from 18 patients with FCD and 6 perilesional control samples with normal histology. Data were analysed using uniform manifold approximation and projection for dimensionality reduction and visualization. Differentially expressed genes (DEGs) were identified and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. UCell scoring and gene set enrichment analysis (GSEA) were applied to assess pathway activity. Expression levels of ferroptosis‐related genes (FRGs) were validated by immunofluorescence, and biochemical assays quantified the levels of superoxide dismutase (SOD), glutathione (GSH), malondialdehyde (MDA) and lipid peroxides (LPO).

Results: A total of 170 747 nuclei were profiled, resolving five major cell types, including inhibitory neurons, excitatory neurons, astrocytes, microglia and oligodendrocytes. DEGs across these populations were significantly enriched in ferroptosis and oxidative stress–associated pathways. UCell and GSEA highlighted remarkable alterations in ferroptosis, apoptosis and oxidative stress, particularly in inhibitory neurons and astrocytes. Immunofluorescence confirmed upregulation of key FRGs, including ferritin light chain, ferritin heavy chain 1, poly rC binding protein 1, microtubule‐associated protein 1 light chain 3B and prion protein‐encoding gene, in FCD tissues. Concordantly, biochemical assays demonstrated reduced SOD and GSH levels, alongside elevated MDA and LPO levels, confirming the transcriptional and histological findings.

Conclusions: The results indicated that ferroptosis may play a notable role or act as a concurrent mechanism in the pathogenesis of FCD, potentially contributing to the neuronal and glial dysfunction and epileptogenesis. Integrating transcriptomic, histological and biochemical data, this study demonstrated that targeting ferroptosis‐related pathways may hold promise as a potential therapeutic strategy for FCD, providing new insights into the molecular mechanisms underlying this condition.

Highlights: This study pioneers the first single‐nucleus transcriptomic atlas for Focal Cortical Dysplasia (FCD) types I and II, deciphering the cellular heterogeneity across five major brain cell types within the epileptogenic cortex.

Through integrated multi‐omics analysis, it reveals for the first time a significant association between the ferroptosis pathway and FCD pathogenesis.

We identify and validate ferroptosis‐related genes (e.g., FTH1, FTL, PCBP1) as potential biomarkers and therapeutic targets, supported by congruent biochemical evidence of oxidative stress in this drug‐resistant epilepsy.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Data

Datasets cited

• bioproject:PRJNA1336443 — at NCBI BioProject; found in “DATA AVAILABILITY STATEMENT”
• figshare:30988093 — at figshare; found in “DATA AVAILABILITY STATEMENT”

Data availability statement

The raw single‐nucleus RNA sequencing data generated in this study have been deposited in the NCBI Sequence Read Archive (SRA) under the accession number of PRJNA1336443 and are publicly accessible at https://www.ncbi.nlm.nih.gov/sra/PRJNA1336443. All processed and structured analysis datasets supporting the findings of this study and used to generate the figures and conclusions have been curated and deposited in the public repository Figshare (https://figshare.com/) under the permanent DOI: https://doi.org/10.6084/m9.figshare.30988093.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 7 keywords, 7 MeSH terms, 2 funders, 54 references.

Cite

This paper

Zeng, Q., Zhu, F., Cao, D., Sun, Y., Li, L., Tan, Z., Li, C., Ren, X., Liu, Y., Lin, Z., & Zou, D. (2026). Single-nucleus RNA sequencing reveals ferroptosis as a potential contributor to the pathogenesis of focal cortical dysplasia. Clinical and translational medicine, 16(5), e70668. https://doi.org/10.1002/ctm2.70668

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