Dataset Information

VSX1 and SOD1 Mutation Screening in Patients with Keratoconus in the South of Iran.

ABSTRACT: PURPOSE:To investigate mutations of visual system homeobox 1 (VSX1) and superoxide dismutase 1 (SOD1) in 20 patients with keratoconus in the south of Iran. METHODS:Twenty patients with keratoconus who had a positive familial history were enrolled in this study and gave informed consent for DNA analysis. Genomic DNA was extracted from peripheral blood lymphocytes. Polymerase chain reaction (PCR) was carried out to amplify exon 2 of SOD1 and its exon-intron boundary for the detection of a seven-base deletion in intron 2 of SOD1, and also all five exons of VSX1 and their exon-intron boundaries. Amplified samples were then subjected to direct DNA sequencing. RESULTS:Sequencing data were compared against reference sequences using NCBI basic local alignment search tool (BLAST), which revealed that our patients had no mutations in SOD1 and VSX1. Two single-nucleotide polymorphisms (SNPs), namely in VSX1(rs58752432 and rs59089167) were found in six patients. CONCLUSION:Mutations in VSX1 and SOD1 genes associated with keratoconus were not identified in our patients. Therefore, it will be necessary to investigate other chromosomal loci for potential causal mutations of keratoconus using next generation sequencing (NGS) methods in our population.

SUBMITTER: Nejabat M

PROVIDER: S-EPMC5423365 | biostudies-literature | 2017 Apr-Jun

REPOSITORIES: biostudies-literature

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<i>VSX1</i> and <i>SOD1</i> Mutation Screening in Patients with Keratoconus in the South of Iran.

Nejabat Mahmood M Naghash Payam P Dastsooz Hassan H Mohammadi Sanaz S Alipour Mohsen M Fardaei Majid M

Journal of ophthalmic & vision research 20170401 2

<h4>Purpose</h4>To investigate mutations of visual system homeobox 1 (<i>VSX1</i>) and superoxide dismutase 1 (<i>SOD1</i>) in 20 patients with keratoconus in the south of Iran.<h4>Methods</h4>Twenty patients with keratoconus who had a positive familial history were enrolled in this study and gave informed consent for DNA analysis. Genomic DNA was extracted from peripheral blood lymphocytes. Polymerase chain reaction (PCR) was carried out to amplify exon 2 of <i>SOD1</i> and its exon-intron boun ...[more]

PMID: 28540003

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Project description:Purpose:To investigate the presence of the variants of lysyl oxygenase (LOX) and superoxide dismutase 1 (SOD1) genes in Brazilian patients with advanced keratoconus. Methods:Donor genomic DNA extracted from blood samples was screened for 5'UTR, exonic LOX, and SOD1 variants in a subset of 26 patients presenting with advanced keratoconus (KISA > 1000% and I-S > 2.0) by Sanger sequencing. The impact of non-synonymous amino acid changes was evaluated by SIFT, PMUT, and PolyPhen algorithms. The Mutation Taster tool was used to evaluate the potential impact of formation of new donor and acceptor splice sites in the promoter region of affected volunteers carrying sequence variants. A 7-base SOD1 deletion (IVS2 + 50del7bp) previously associated with keratoconus was screened in 140 patients presenting classical keratoconus by gel fragment analysis, and positive samples were sequenced for confirmation. Results:We found an unreported missense variant in LOX exon 6 in one heterozygous patient, leading to substitution of proline with threonine at residue 392 (p. Thr392Pro) of LOX protein sequence. This mutation was predicted to be potentially damaging to LOX protein. Another LOX variant, Arg158Gln, was also detected in another patient but predicted to be non-pathogenic. Two additional new polymorphisms in LOX 5'UTR region (-116C > T and -58C > T) were found in two patients presenting with advanced keratoconus and were predicted to modulate or create donor/acceptor splice sites in LOX transcripts. Additionally, SOD1 deletion was detected in one patient presenting with severe keratoconus, not in control samples. Conclusion:We described three novel LOX polymorphisms identified for the first time in Brazilian patients with advanced keratoconus, as well as a previously described SOD1 deletion strongly associated with keratoconus. A possible role of these variants in modulating transcript levels in the cornea of affected individual requires further investigation.

Project description:BackgroundKeratoconus normally presents as a sporadic disease. Although different studies have found sequence variants of the visual system homeobox 1 (VSX1) gene associated with keratoconus in humans, no research has detected such variants in sporadic keratoconus patients from China. To investigate the possibility of VSX1 being a candidate susceptibility gene for Chinese patients with sporadic keratoconus, we performed sequence screening of this gene in such patients.MethodsWhole DNA was obtained from the leukocytes in the peripheral venous blood of 50 patients with sporadic keratoconus and 50 control subjects without this ocular disorder. Polymerase chain reaction single-strand conformation polymorphism analysis and direct DNA sequencing technology were used to detect sequence variation in the five exons and splicing regions of the introns of the VSX1 gene. The sequencing results were analyzed using DNAstar software.ResultsOne novel missense heterozygous sequence variant (p.Arg131Pro) was found in the first exon of the VSX1 gene in one keratoconus patient. Another heterozygous sequence variant (p.Gly160Val) in the second exon was found in two keratoconus patients. These variants were not detected in the control subjects. In the third intron of the VSX1 gene, c.8326G > A nucleotide substitution (including heterozygous and homozygous change) was also discovered. The frequency of this variation did not differ significantly between patients and controls, it should belong to single-nucleotide polymorphism of the VSX1 gene. Bioinformatic analysis also predicted that one missense sequence variation (p.Arg131Pro) may not cause a pathogenic change.ConclusionsIn this study, we added one novel missense sequence variation (p.Arg131Pro) in the coding region of the VSX1 gene to the range of VSX1 coding region variations observed in patients with sporadic keratoconus from China. Our work suggests that VSX1 sequence variants might be involved in the pathogenesis of sporadic keratoconus, but their precise role in disease causation requires further investigation.

Dataset Information

VSX1 and SOD1 Mutation Screening in Patients with Keratoconus in the South of Iran.

Publications

<i>VSX1</i> and <i>SOD1</i> Mutation Screening in Patients with Keratoconus in the South of Iran.

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