Identification of SETX Gene Mutations Using Whole Exome Sequencing in Amyotrophic Lateral Sclerosis in a Khuzestan Family

Document Type : Original Article (s)

Authors

1 Student, Department of Biology, Dez.C., Islamic Azad University, Dezful, Iran

2 Assistant Professor, Department of Biology, Dez.C., Islamic Azad University, Dezful, Iran.

10.48305/jims.v43.i834.1276

Abstract

Background: Amyotrophic lateral sclerosis (ALS) is a complex neurological disorder characterized by rapid and progressive paralysis, eventually leading to respiratory failure. Approximately 10% of ALS cases are familial, stemming from specific genetic mutations that follow Mendelian inheritance patterns. Amyotrophic lateral sclerosis type 4 (ALS4) is a juvenile-onset form of familial ALS caused by mutations in the senataxin (SETX) gene. Advanced genomic technologies expedite the diagnosis of genetic disorders and enhance the quality of genetic support for patients and their families.
Methods: In this research, the detection of mutations in the SETX gene was performed through whole-exome sequencing (WES). The Polymerase Chain Reaction (PCR) technique was subsequently employed to validate the variant, followed by Sanger sequencing, and the resulting sequences were analyzed using Chromas Pro software.
Findings: The whole-exome sequencing results revealed a homozygous mutation in the gene (NM_015046:exon19:c.C6461T:p.T2154M) in the exome sequences of the affected offspring in the family.
Conclusion: This study highlights the advantage of utilizing WES for the genetic diagnosis of ALS. By investigating the genetic cause of ALS4, we can achieve a better understanding of the molecular biology of this disease.

Highlights

Zohreh Valizadeh: Google Scholar

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Main Subjects


  1. Ziff OJ, Neeves J, Mitchell J, Tyzack G, Martinez-Ruiz C, Luisier R, et al. Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology. Nat Commun 2023; 14(1): 2176.
  2. Morello G, La Cognata V, Guarnaccia M, La Bella V, Conforti FL, Cavallaro S. A Diagnostic Gene-Expression Signature in Fibroblasts of Amyotrophic Lateral Sclerosis. Cells 2023; 12(14): 1884.
  3. Bennett CL, Dastidar S, Arnold FJ, McKinstry SU, Stockford C, Freibaum BD, et al. Senataxin helicase, the causal gene defect in ALS4, is a significant modifier of C9orf72 ALS G4C2 and arginine-containing dipeptide repeat toxicity. Acta Neuropathol Commun 2023; 11(1): 164.
  4. Wang JC, Ramaswami G, Geschwind DH. Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility. Sci Rep 2021; 11(1): 5748.
  5. Edgar S, Ellis M, Abdul-Aziz NA, Goh K-J, Shahrizaila N, Kennerson ML, et al. Mutation analysis of SOD1, C9orf72, TARDBP and FUS genes in ethnically-diverse Malaysian patients with amyotrophic lateral sclerosis (ALS). Neurobiol Aging 2021; 108: 200-6.
  6. Richard P, Feng S, Tsai Y-L, Li W, Rinchetti P, Muhith U, et al. SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation. Autophagy 2021; 17(8): 1889-906.
  7. Nanetti L, Cavalieri S, Pensato V, Erbetta A, Pareyson D, Panzeri M, et al. SETX mutations are a frequent genetic cause of juvenile and adult onset cerebellar ataxia with neuropathy and elevated serum alpha-fetoprotein. Orphanet J Rare Dis 2013; 8: 123.
  8. Gaaib JN, Nassief AF, Al-Assi AH. Simple salting-out method for genomic DNA extraction from whole blood. Tikrit J Pure Sci 2011; 16(2): 1813-662.
  9. BioLabs NE. Guidelines for PCR Optimization with Taq DNA Polymerase. Accessed 2015; Available from: https://www.neb.com/en/tools-and-resources/usage-guidelines/guidelines-for-pcr-optimization-with-taq-dna-polymerase?srsltid=AfmBOopyzjdJqqVye1p7cODLnpfXF9rACGsx0HpaYjmDM9a50Uuna8fa.
  10. Masrori P, van Damme P. Amyotrophic lateral sclerosis: a clinical review. Eur J Neurol 2020; 27(10): 1918-29.
  11. Longinetti E, Fang F. Epidemiology of amyotrophic lateral sclerosis: an update of recent literature. Curr Opin Neurol 2019; 32(5): 771-6.
  12. Sajjadi M, Etemadifar M, Nemati A, Ghazavi H, Basiri K, Khoundabi B, et al. Epidemiology of amyotrophic lateral sclerosis in Isfahan, Iran. Eur J Neurol 2010; 17(7): 984-9.
  13. Mehta PR, Jones AR, Opie-Martin S, Shatunov A, Iacoangeli A, Al Khleifat A, et al. Younger age of onset in familial amyotrophic lateral sclerosis is a result of pathogenic gene variants, rather than ascertainment bias. J Neurol Neurosurg Psychiatry 2019; 90(3): 268-71.
  14. Chen Y-Z, Bennett CL, Huynh HM, Blair IP, Puls I, Irobi J, et al. DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). Am J Hum Genet 2004; 74(6): 1128-35.
  15. Bennett CL, Dastidar SG, Ling S-C, Malik B, Ashe T, Wadhwa M, et al. Senataxin mutations elicit motor neuron degeneration phenotypes and yield TDP-43 mislocalization in ALS4 mice and human patients. Acta Neuropathol 2018; 136(3): 425-43.
  16. Grunseich C, Patankar A, Amaya J, Watts JA, Li D, Ramirez P, et al. Clinical and molecular aspects of senataxin mutations in amyotrophic lateral sclerosis 4. Ann Neurol 2020; 87(4): 547-55.