Variants in WFS1 and Other Mendelian Deafness Genes Are Associated with Cisplatin-Associated Ototoxicity

Abstract

Purpose: Cisplatin is one of the most commonly used chemotherapy drugs worldwide and one of the most ototoxic. We sought to identify genetic variants that modulate cisplatin-associated ototoxicity (CAO).Experimental Design: We performed a genome-wide association study (GWAS) of CAO using quantitative audiometry (4-12 kHz) in 511 testicular cancer survivors of European genetic ancestry. We performed polygenic modeling and functional analyses using a variety of publicly available databases. We used an electronic health record cohort to replicate our top mechanistic finding.Results: One SNP, rs62283056, in the first intron of Mendelian deafness gene WFS1 (wolframin ER transmembrane glycoprotein) and an expression quantitative trait locus (eQTL) for WFS1 met genome-wide significance for association with CAO (P = 1.4 × 10^-8). A significant interaction between cumulative cisplatin dose and rs62283056 genotype was evident, indicating that higher cisplatin doses exacerbate hearing loss in patients with the minor allele (P = 0.035). The association between decreased WFS1 expression and hearing loss was replicated in an independent BioVU cohort (n = 18,620 patients, Bonferroni adjusted P < 0.05). Beyond this top signal, we show CAO is a polygenic trait and that SNPs in and near 84 known Mendelian deafness genes are significantly enriched for low P values in the GWAS (P = 0.048).Conclusions: We show for the first time the role of WFS1 in CAO and document a statistically significant interaction between increasing cumulative cisplatin dose and rs62283056 genotype. Our clinical translational results demonstrate that pretherapy patient genotyping to minimize ototoxicity could be useful when deciding between cisplatin-based chemotherapy regimens of comparable efficacy with different cumulative doses. Clin Cancer Res; 23(13); 3325-33. ©2016 AACR.

Figure 1. GWAS of cisplatin-associated ototoxicity (CAO)

(A) The association of SNP genotype and CAO in 511 testicular cancer survivors was tested for significance via linear regression. −log₁₀ P-values are plotted against the respective chromosomal position of each SNP. The red line indicates the genome-wide significance threshold (P = 5 × 10⁻⁸). (B) The top GWAS signal rs62283056 is in the first intron of WFS1 (wolframin ER transmembrane glycoprotein). The color of each dot represents the SNP’s linkage disequilibrium r² with rs62283056 in the 1000 Genomes European populations. (C) For individuals with the CG and CC genotypes at rs62283056, the absolute value of median hearing threshold increases by 6 dB and 20 dB over those with the GG genotype, respectively. Hearing loss begins at thresholds below the red line (< −20 dB). Boxes define the inter-quartile range (IQR) and the middle horizontal line represents the median. The upper whisker extends from the third quartile to the highest value that is within 1.5 × IQR. The lower whisker extends from the first quartile to the lowest value within 1.5 × IQR.

Figure 2. Enrichment of top GWAS SNPs in Mendelian deafness genes

(A) Quantile-quantile plot showing the distribution of P-values from all SNPs in the GWAS compared to the SNPs within 50kb of 84 Mendelian deafness genes (23,24). (B) Distribution of the number of top SNPs (P < 0.01) in Mendelian deafness genes based on 500 permutations of the GWAS phenotype-genotype connections. The black dot is the number of observed GWAS SNPs with P < 0.01 that are within 50kb of Mendelian deafness genes, a significant enrichment (empirical P = 0.048).

Figure 3. Lower expression of WFS1 associates with increased cellular sensitivity to cisplatin

WFS1 gene expression data from the Cancer Cell Line Encyclopedia are plotted against cellular sensitivity (log₂ IC₅₀) of CNS tumor cell lines (27 glioma and 3 medulloblastoma) to (A) cisplatin, (B) cytarabine, (C) docetaxel, or (D) vinblastine from the Genomics of Drug Sensitivity in Cancer database. Spearman’s rho (r) and P-values are shown. Only cisplatin IC₅₀ significantly associated with WFS1 expression (P = 0.036).

Figure 4. Interaction between rs62283056 genotype and cisplatin dose

Hearing threshold (CAO phenotype) is plotted against rs62283056 genotype dichotomized by cumulative dose group (≤ 300 mg/m² or > 300 mg/m² cisplatin). We found a significant interaction between rs62283056 genotype and cumulative cisplatin dose (P = 0.035), indicating higher doses exacerbate the hearing loss effect in patients carrying the minor (C) allele. Boxes define the inter-quartile range (IQR) and the middle horizontal line represents the median. The upper whisker extends from the third quartile to the highest value that is within 1.5 × IQR. The lower whisker extends from the first quartile to the lowest value within 1.5 × IQR.