Whole exome sequencing, in silico and functional studies confirm the association of the GJB2 mutation p.Cys169Tyr with deafness and suggest a role for the TMEM59 gene in the hearing process

Mona Mahfood; Jihen Chouchen; Walaa Kamal Eddine Ahmad Mohamed; Abdullah Al Mutery; Rania Harati; Abdelaziz Tlili

doi:10.1016/j.sjbs.2021.04.036

Whole exome sequencing, in silico and functional studies confirm the association of the GJB2 mutation p.Cys169Tyr with deafness and suggest a role for the TMEM59 gene in the hearing process

Saudi J Biol Sci. 2021 Aug;28(8):4421-4429. doi: 10.1016/j.sjbs.2021.04.036. Epub 2021 Apr 20.

Authors

Mona Mahfood¹, Jihen Chouchen², Walaa Kamal Eddine Ahmad Mohamed², Abdullah Al Mutery^{1

2}, Rania Harati³, Abdelaziz Tlili^{1

2}

Affiliations

¹ Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates.
² Human Genetics and Stem Cell Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates.
³ Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.

Abstract

The development of next generation sequencing techniques has facilitated the detection of mutations at an unprecedented rate. These efficient tools have been particularly beneficial for extremely heterogeneous disorders such as autosomal recessive non-syndromic hearing loss, the most common form of genetic deafness. GJB2 mutations are the most common cause of hereditary hearing loss. Amongst them the NM_004004.5: c.506G > A (p.Cys169Tyr) mutation has been associated with varying severity of hearing loss with unclear segregation patterns. In this study, we report a large consanguineous Emirati family with severe to profound hearing loss fully segregating the GJB2 missense mutation p.Cys169Tyr. Whole exome sequencing (WES), in silico, splicing and expression analyses ruled out the implication of any other variants and confirmed the implication of the p.Cys169Tyr mutation in this deafness family. We also show preliminary murine expression analysis that suggests a link between the TMEM59 gene and the hearing process. The present study improves our understanding of the molecular pathogenesis of hearing loss. It also emphasizes the significance of combining next generation sequencing approaches and segregation analyses especially in the diagnosis of disorders characterized by complex genetic heterogeneity.

Keywords: ARNSHL, autosomal recessive non-syndromic hearing loss; Actb, Actin beta; BAM, Binary Alignment Map; BWA, Burrows-Wheeler Aligner; C1QTNF9, C1q and TNF related 9; Cx26, Connexin 26; ESRRAP2, Estrogen-Related Receptor Alpha Pseudogene 2; GJB2 gene; GJB2, Gap Junction Protein Beta 2; HHLA1, HERV-H LTR-Associating 1; HL, Hearing loss; KCNQ3, Potassium Voltage-Gated Channel Subfamily Q Member 3; Missense mutation; NGS, next generation sequencing; NSHL, Non-syndromic hearing loss; Non-syndromic hearing loss; PROVEAN, Protein Variation Effect Analyzer; PolyPhen-2, Polymorphism Phenotyping v2; RFLP, restriction fragment length polymorphism; ROH, runs of homozygosity; RT-PCR, reverse transcription PCR; RT-qPCR, quantitative reverse transcription PCR; SAM, Sequence Alignment/Map; SIFT, Sorting Intolerant From Tolerant; SJL, Swiss Jim Lambert; SPATA13, Spermatogenesis Associated 13; ST3GAL1, ST3 Beta-Galactoside Alpha-2,3-Sialyltransferase 1; TMEM59, Transmembrane Protein 59; UAE, United Arab Emirates; VariMAT, Variation and Mutation Annotation Toolkit; WES, Whole exome sequencing; Whole exome sequencing; dpSNP, Single Nucleotide Polymorphism Database; gEAR, gene Expression Analysis Resource; gnomAD, genome aggregation database; qPCR, quantitative PCR.