Calpain 7 as a novel candidate gene in genetic generalized epilepsy

Document Type : Original Article

Authors

1 Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

2 Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran

3 Department of Neurology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

4 Academic Center for Education, Culture, and Research (ACECR)-Khorasan Razavi, Mashhad, Iran

5 Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany

6 Institut Für Humangenetik, Technische Universität München, School of Medicine and Health, Munich, Germany

7 Munich Cluster for Systems Neurology, SyNergy, Munich, Germany

8 Institute for Advanced Study, Technical University of Munich, Garching, Germany

10.22038/ijbms.2025.88053.19021

Abstract

Objective(s): Genetic generalized epilepsy (GGE) is a common subtype of epilepsy characterized by generalized seizure types, with an unclear etiology and recognized genetic contribution to its susceptibility. Although genetic factors play a significant role, the precise mechanisms and causative variants underlying GGE remain poorly understood. This study aimed to identify the genetic basis of GGE.
Materials and Methods: Whole exome sequencing (WES) was performed in eight consanguineous GGE families. Sanger sequencing was conducted to validate the WES findings and confirm variant segregation within the families. RNA-seq data (GSE185632) and in silico analyses were used to assess gene expression and variant pathogenicity.
Results: A rare nonsense variant in exon 13 of Calpain 7 (CAPN7, NM_014296.3: c.1454G>A; p.Trp485Ter) was identified and determined to be pathogenic according to the American College of Medical Genetics and Genomics (ACMG) criteria (PVS1, PM2, PP4, and PP1). The variant co-segregated with the disease in the family. RNA-seq analysis of epilepsy transcriptomes revealed significant down-regulation of this gene (log2FC= -0.84, padj = 0.016). Complementary computational analyses demonstrated strong evolutionary constraint and pathogenic signatures, further supporting its disease association. CAPN7 negatively perturbate endometrial stromal cell decidualization in epithelial–mesenchymal transition via AKT pathway. The proteolytic activity of CAPN7 is associated with degradation of EGFR. 
Conclusion: This study provides novel insight on the association of CAPN7 in GGE, highlighting its potential contribution to epilepsy pathogenesis. Further research is required to gather additional evidence and elucidate the molecular mechanisms underlying the clinical manifestations associated with CAPN7 variants.

Keywords

Main Subjects

References

1. Hirsch E, French J, Scheffer IE, Bogacz A, Alsaadi T, Sperling MR, et al. ILAE definition of the idiopathic generalized epilepsy syndromes: Position statement by the ILAE task force on nosology and definitions. Epilepsia 2022; 63: 1475-1499.
2. Silva Alves A, Rigoni I, Mégevand P, Lagarde S, Picard F, Seeck M, et al. High-density electroencephalographic functional networks in genetic generalized epilepsy: Preserved whole-brain topology hides local reorganization. Epilepsia 2024; 65: 961-973.
3. Perucca P, Bahlo M, Berkovic SF. The genetics of epilepsy. Annu Rev Genomics Hum Genet 2020; 21: 205-230.
4. Berg AT, Berkovic SF, Brodie MJ, Buchhalter J, Cross JH, van Emde Boas W, et al. Revised terminology and concepts for organization of seizures and epilepsies: Report of the ILAE Commission on Classification and Terminology, 2005-2009. Epilepsia 2010; 51: 676-685.
5. Scheffer IE, French J, Hirsch E, Jain S, Mathern GW, Moshé SL, et al. Classification of the epilepsies: New concepts for discussion and debate-special report of the ILAE classification task force of the commission for classification and terminology. Epilepsia Open 2016; 1: 37-44.
6. Vorderwülbecke BJ, Wandschneider B, Weber Y, Holtkamp M. Genetic generalized epilepsies in adults - challenging assumptions and dogmas. Nat Rev Neurol 2022; 18: 71-83.
7. Jallon P, Latour P. Epidemiology of idiopathic generalized epilepsies. Epilepsia 2005; 46: 10-14.
8. Gesche J, Christensen J, Hjalgrim H, Rubboli G, Beier CP. Epidemiology and outcome of idiopathic generalized epilepsy in adults. Eur J Neurol 2020; 27: 676-684.
9. Mullen SA, Berkovic SF. Genetic generalized epilepsies. Epilepsia 2018; 59: 1148-1153.
10. Weber YG, Lerche H. Genetic mechanisms in idiopathic epilepsies. Dev Med Child Neurol 2008; 50: 648-654.
11. DiFrancesco JC, Barbuti A, Milanesi R, Coco S, Bucchi A, Bottelli G, et al. Recessive loss-of-function mutation in the pacemaker HCN2 channel causing increased neuronal excitability in a patient with idiopathic generalized epilepsy. J Neurosci 2011; 31: 17327-17337.
12. Striano P, Weber YG, Toliat MR, Schubert J, Leu C, Chaimana R, et al. GLUT1 mutations are a rare cause of familial idiopathic generalized epilepsy. Neurology 2012; 78: 557-562.
13. Kahle KT, Merner ND, Friedel P, Silayeva L, Liang B, Khanna A, et al. Genetically encoded impairment of neuronal KCC2 cotransporter function in human idiopathic generalized epilepsy. EMBO Rep 2014; 15: 766-774.
14. Rudolf G, Lesca G, Mehrjouy MM, Labalme A, Salmi M, Bache I, et al. Loss of function of the retinoid-related nuclear receptor (RORB) gene and epilepsy. Eur J Hum Genet 2016; 24: 1761-1770.
15. Santolini I, Celli R, Cannella M, Imbriglio T, Guiducci M, Parisi P, et al. Alterations in the α2δ ligand, thrombospondin-1, in a rat model of spontaneous absence epilepsy and in patients with idiopathic/genetic generalized epilepsies. Epilepsia 2017; 58: 1993-2001.
16. Li M, Maljevic S, Phillips AM, Petrovski S, Hildebrand MS, Burgess R, et al. Gain-of-function HCN2 variants in genetic epilepsy. Hum Mutat 2018; 39: 202-209.
17. Wang Y, Yu H, Chen Y, Li G, Lei Y, Zhao J. Derivation of induced pluripotent stem cells TUSMi006 from an 87-year old Chinese Han Alzheimer’s disease patient carrying GRINB and SORL1 mutations. Stem Cell Res 2018; 31: 127-130.
18. Yap SM, Smyth S. Ryanodine receptor 2 (RYR2) mutation: A potentially novel neurocardiac calcium channelopathy manifesting as primary generalised epilepsy. Seizure 2019; 67: 11-14.
19. Liu X-R, Ye T-T, Zhang W-J, Guo X, Wang J, Huang S-P, et al. CHD4 variants are associated with childhood idiopathic epilepsy with sinus arrhythmia. CNS Neurosci Ther 2021; 27: 1146-1156.
20. Liu X-R, Xu X-X, Lin S-M, Fan C-Y, Ye T-T, Tang B, et al. GRIN2A variants associated with idiopathic generalized epilepsies. Front Mol Neurosci 2021; 14: 720984-720999.
21. Zech M, Jech R, Boesch S, Škorvánek M, Weber S, Wagner M, et al. Monogenic variants in dystonia: An exome-wide sequencing study. Lancet Neurol 2020; 19: 908-918.
22. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American college of medical genetics and genomics and the association for molecular pathology. Genet Med 2015; 17: 405-423.
23. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15: 1-21.
24. Roy A, Kucukural A, Zhang Y. I-TASSER: A unified platform for automated protein structure and function prediction. Nat Protoc 2010; 5: 725-738.
25. Lill MA, Danielson ML. Computer-aided drug design platform using PyMOL. J Comput Aided Mol Des 2011; 25: 13-19.
26. Ben Chorin A, Masrati G, Kessel A, Narunsky A, Sprinzak J, Lahav S, et al. ConSurf‐DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. Protein Sci 2020; 29: 258-267.
27. Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat 2019; 40: 1030-1038.
28. López-Ferrando V, Gazzo A, De La Cruz X, Orozco M, Gelpí JL. PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update. Nucleic Acids Res 2017; 45: W222-W228.
29. Nixon RA. The calpains in aging and aging-related diseases. Ageing Res Rev 2003; 2: 407-418.
30. Goll DE, Thompson VF, Li H, Wei W, Cong J. The calpain system. Physiol Rev 2003; 83: 731-801.
31. Ono Y, Saido TC, Sorimachi H. Calpain research for drug discovery: Challenges and potential. Nat Rev Drug Discov 2016; 15: 854-876.
32. Ono Y, Sorimachi H. Calpains: An elaborate proteolytic system. Biochim Biophys Acta 2012; 1824: 224-236.
33. Sorimachi H, Hata S, Ono Y. Impact of genetic insights into calpain biology. J Biochem 2011; 150: 23-37.
34. Futai E, Kubo T, Sorimachi H, Suzuki K, Maeda T. Molecular cloning of PalBH, a mammalian homologue of the Aspergillus atypical calpain PalB1. Biochim Biophys Acta (BBA) 2001; 1517: 316-319.
35. Kang N, Shan H, Wang J, Mei J, Jiang Y, Zhou J, et al. Calpain7 negatively regulates human endometrial stromal cell decidualization in EMs by promoting FoxO1 nuclear exclusion via hydrolyzing AKT1. Biol Reprod 2022; 106: 1112-1125.
36. Maemoto Y, Ono Y, Kiso S, Shibata H, Takahara T, Sorimachi H, et al. Involvement of calpain‐7 in epidermal growth factor receptor degradation via the endosomal sorting pathway. FEBS J 2014; 281: 3642-3655.
37. Wang Y, Liu Y, Yahya E, Quach D, Bi X, Baudry M. Calpain-2 activation in mouse hippocampus plays a critical role in seizure-induced neuropathology. Neurobiol Dis 2021; 147:105149.
38. Lam PM, González MI. Calpain activation and neuronal death during early epileptogenesis. Neurobiol Dis 2019; 124: 141-151.
39. Pizzanelli C, Mancuso M, Galli R, Choub A, Fanin M, Nascimbeni AC, et al. Epilepsy and limb girdle muscular dystrophy type 2A: double trouble, serendipitous finding or new phenotype? Neurol Sci 2006; 27: 134-136.
40. Viloria-Alebesque A, Bellosta-Diago E, Santos-Lasaosa S, Mauri-Llerda J. Familial association of genetic generalised epilepsy with limb-girdle muscular dystrophy through a mutation in CAPN3. Epilepsy Behav Case Rep 2019; 11: 122-124.
41. Bisceglia L, Zoccolella S, Torraco A, Piemontese MR, Dell’Aglio R, Amati A, et al. A new locus on 3p23-p25 for an autosomal-dominant limb-girdle muscular dystrophy, LGMD1H. Eur J Hum Genet 2010; 18: 636-641.
42. Maemoto Y, Ono Y, Kiso S, Shibata H, Takahara T, Sorimachi H, et al. Involvement of calpain-7 in epidermal growth factor receptor degradation via the endosomal sorting pathway. FEBS J 2014; 281: 3642-3655.
Iranian Journal of Basic Medical Sciences
Volume 28, Issue 10
October 2025
Pages 1328-1334

Files

Share

How to cite

Statistics