|
1
|
Garcia CAB, Zubair M, Santos MV, Lee SH, Graham IA, Stanley V, George RD, Gleeson JG, Machado HR, Yang X. Identification of Novel Mosaic Variants in Focal Epilepsy-Associated Patients' Brain Lesions. Genes (Basel) 2025; 16:421. [PMID: 40282380 PMCID: PMC12026736 DOI: 10.3390/genes16040421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2025] [Revised: 03/27/2025] [Accepted: 03/28/2025] [Indexed: 04/29/2025] Open
Abstract
Focal cortical dysplasia type III (FCDIII) is a rare and complex condition associated with drug-resistant epilepsy and often characterized by cortical lamination abnormalities, along with a variety of neoplasms and vascular abnormalities. OBJECTIVES This study aimed to elucidate the genetic architecture underlying FCDIII through the use of whole-exome sequencing (WES) of brain and peripheral blood samples from 19 patients who had been diagnosed with FCDIII. METHODS Variants were identified through a series of machine-learning-based detection and functional prediction methods and were not previously associated with FCDIII. Mosaic fraction scores of these variants validated the variants' pathogenicity, and in silico and gene ontology enrichment analyses demonstrated that these variants had severe destabilizing effects on protein structure. RESULTS We reported ten novel pathogenic somatic missense and loss of function variants across eight genes, including CNTNAP2, ACY1, SERAC1, and BRAF. Genetic alterations were linked to clinical manifestations, such as encephalopathies and intellectual disabilities, thereby emphasizing their role as molecular drivers of FCDIII. CONCLUSIONS We demonstrated that next-generation sequencing-based mosaic variant-calling pipelines are useful for the genetic diagnosis of FCDIII, opening up avenues for targeted therapies, yet further research is required to validate these findings and examine their therapeutic implications.
Collapse
Affiliation(s)
- Camila Araújo Bernardino Garcia
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirao Preto 14049-900, SP, Brazil; (C.A.B.G.); (M.V.S.)
| | - Muhammad Zubair
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; (M.Z.); (S.H.L.); (I.A.G.)
| | - Marcelo Volpon Santos
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirao Preto 14049-900, SP, Brazil; (C.A.B.G.); (M.V.S.)
| | - Sang Hyun Lee
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; (M.Z.); (S.H.L.); (I.A.G.)
| | - Ian Alfred Graham
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; (M.Z.); (S.H.L.); (I.A.G.)
| | - Valentina Stanley
- Department of Neuroscience, University of California, San Diego, CA 92093, USA; (V.S.); (R.D.G.); (J.G.G.)
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Renee D. George
- Department of Neuroscience, University of California, San Diego, CA 92093, USA; (V.S.); (R.D.G.); (J.G.G.)
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Joseph G. Gleeson
- Department of Neuroscience, University of California, San Diego, CA 92093, USA; (V.S.); (R.D.G.); (J.G.G.)
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Hélio Rubens Machado
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirao Preto 14049-900, SP, Brazil; (C.A.B.G.); (M.V.S.)
| | - Xiaoxu Yang
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; (M.Z.); (S.H.L.); (I.A.G.)
| |
Collapse
|