Modifier variant of METTL13 suppresses human GAB1–associated profound deafness
Rizwan Yousaf, … , Thomas B. Friedman, Saima Riazuddin
Rizwan Yousaf, … , Thomas B. Friedman, Saima Riazuddin
Published February 6, 2018
Citation Information: J Clin Invest. 2018;128(4):1509-1522. https://doi.org/10.1172/JCI97350.
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Research Article Genetics Otology

Modifier variant of METTL13 suppresses human GAB1–associated profound deafness

Abstract

A modifier variant can abrogate the risk of a monogenic disorder. DFNM1 is a locus on chromosome 1 encoding a dominant suppressor of human DFNB26 recessive, profound deafness. Here, we report that DFNB26 is associated with a substitution (p.Gly116Glu) in the pleckstrin homology domain of GRB2-associated binding protein 1 (GAB1), an essential scaffold in the MET proto-oncogene, receptor tyrosine kinase/HGF (MET/HGF) pathway. A dominant substitution (p.Arg544Gln) of METTL13, encoding a predicted methyltransferase, is the DFNM1 suppressor of GAB1-associated deafness. In zebrafish, human METTL13 mRNA harboring the modifier allele rescued the GAB1-associated morphant phenotype. In mice, GAB1 and METTL13 colocalized in auditory sensory neurons, and METTL13 coimmunoprecipitated with GAB1 and SPRY2, indicating at least a tripartite complex. Expression of MET-signaling genes in human lymphoblastoid cells of individuals homozygous for p.Gly116Glu GAB1 revealed dysregulation of HGF, MET, SHP2, and SPRY2, all of which have reported variants associated with deafness. However, SPRY2 was not dysregulated in normal-hearing humans homozygous for both the GAB1 DFNB26 deafness variant and the dominant METTL13 deafness suppressor, indicating a plausible mechanism of suppression. Identification of METTL13-based modification of MET signaling offers a potential therapeutic strategy for a wide range of associated hearing disorders. Furthermore, MET signaling is essential for diverse functions in many tissues including the inner ear. Therefore, identification of the modifier of MET signaling is likely to have broad clinical implications.

Authors

Rizwan Yousaf, Zubair M. Ahmed, Arnaud P.J. Giese, Robert J. Morell, Ayala Lagziel, Alain Dabdoub, Edward R. Wilcox, Sheikh Riazuddin, Thomas B. Friedman, Saima Riazuddin

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Figure 1

Variants of GAB1 and METTL13 associated with DFNB26 deafness and the unlinked DFNM1 dominant suppressor of DFNB26 deafness, respectively.

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Variants of GAB1 and METTL13 associated with DFNB26 deafness and the unl...
(A) PK-2 family segregating DFNB26-linked hearing loss and the DFNM1 modifier gene. Black symbols indicate affected individuals homozygous for the GAB1 variant. Green symbols indicate normal-hearing (nonpenetrant) individuals homozygous for the GAB1 variant and the METTL13 dominant modifier allele. The 7 genomic DNA samples used for WES are indicated by red numbers. (B) Nucleotide sequence chromatograms of exon 2 of GAB1 showing the WT sequence of a normal-hearing individual, while the affected and nonpenetrant individuals are homozygous for c.347G>A allele. Also shown are the nucleotide sequence chromatograms of exon 6 of METTL13 from a normal-hearing individual, an affected individual who is homozygous for the WT allele, and a nonpenetrant individual who is heterozygous for c.1647G>A allele of METTL13. (C) The longest transcript of human GAB1 has 10 exons. The c.347G>A variant is located in constitutive exon 2. The GAB1 protein has a PH domain, which harbors the p.Gly116Glu substitution. The position of tyrosine phosphorylation sites (Y) and 2 proline-rich regions (P) are shown along with the peptides (blue bar) used for antibody generation for each protein. (D) The glycine residue at amino acid position 116 of human GAB1 is conserved. (E) The longest transcript of human METTL13 has 8 exons. The c.1631G>A modifier variant is in exon 6. METTL13 protein is predicted to have methyltransferase and spermine/spermidine synthase domains. The antigen used for producing polyclonal antibodies is indicated by a blue bar below the METTL13 structure. (F) METTL13 arginine 544 is conserved in a wide variety of species.