Santin Aurora, Pianigiani Giulia, Gialluisi Alessandro, Pecori Alessandro, Spedicati Beatrice, Costanzo Simona, Persichillo Mariarosaria, Bracone Francesca, Nardone Giuseppe Giovanni, Tesolin Paola, Lenarduzzi Stefania, Morgan Anna, De Curtis Amalia, van der Valk Wouter, Rousset Francis, Roccio Marta, Locher Heiko, Iacoviello Licia, Concas Maria Pina, Girotto Giorgia
Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.
Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy.
Front Genet. 2025 May 19;16:1522338. doi: 10.3389/fgene.2025.1522338. eCollection 2025.
Deepening the genetic mechanisms underlying Normal Hearing Function (NHF) has proven challenging, despite extensive efforts through Genome-Wide Association Studies (GWAS).
NHF was described as a set of nine quantitative traits (i.e., hearing thresholds at 0.25, 0.5, 1, 2, 4, and 8 kHz, and three pure-tone averages of thresholds at low, medium, and high frequencies). For each trait, GWAS analyses were performed on the Moli-sani cohort (n = 1,209); then, replication analyses were conducted on Carlantino (CAR, n = 261) and Val Borbera (VBI, n = 425) cohorts. Expression levels of the most significantly associated genes were assessed employing single-nucleus RNA sequencing data (snRNA-seq) on human fetal and adult inner ear tissues. Finally, for all nine NHF traits, Transcriptome-Wide Association Studies (TWAS) were performed, combining GWAS summary statistics and pre-computed gene expression weights in 12 brain tissues.
GWAS on the Discovery cohort allowed the detection of 667 SNPs spanning 327 protein coding genes at a < 10, across the nine NHF traits. Two loci with a p < 5 × 10 were replicated: 1. rs112501869 within gene, encoding a brain high-affinity glutamate transporter, reached = 6.21 × 10 in the 0.25 kHz trait. 2. rs73519456 within gene, encoding the Astrotactin protein 2, reached genome-wide significance in three NHF traits: 0.5 kHz ( = 1.86 × 10), PTAL ( = 9.40 × 10), and PTAM ( = 3.64 × 10). SnRNA-seq data analyses revealed a peculiar expression of the gene in the neuronal and dark cells populations, while for no significant expression was detected. TWAS analyses detected that the gene (eQTL: rs1584327) was statistically significant ( = 4.49 × 10) in the hippocampal tissue for the 0.25 kHz trait.
This study took advantage of three Italian cohorts, deeply characterized from a genetic and audiological point of view. Bioinformatics and biostatistics analyses allowed the identification of three novel candidate genes, namely, and . Functional studies and replication in larger and independent cohorts will be essential to confirm the biological role of these genes in regulating hearing function; however, these results confirm GWAS and TWAS as powerful methods for novel gene discovery, thus paving the way for a deeper understanding of the entangled genetic landscape underlying the auditory system.
尽管通过全基因组关联研究（GWAS）付出了巨大努力，但深入了解正常听力功能（NHF）背后的遗传机制仍具有挑战性。
NHF被描述为一组九个定量性状（即0.25、0.5、1、2、4和8kHz处的听力阈值，以及低频、中频和高频阈值的三个纯音平均值）。对Moli-sani队列（n = 1209）中的每个性状进行GWAS分析；然后，在Carlantino（CAR，n = 261）和Val Borbera（VBI，n = 425）队列中进行重复分析。使用人类胎儿和成人内耳组织的单核RNA测序数据（snRNA-seq）评估最显著相关基因的表达水平。最后，针对所有九个NHF性状，结合GWAS汇总统计数据和12种脑组织中预先计算的基因表达权重，进行全转录组关联研究（TWAS）。
在发现队列上进行的GWAS允许在九个NHF性状中检测到跨越３２７个蛋白质编码基因的667个单核苷酸多态性（SNP），其p < 10。复制了两个p < 5×10的位点：1. 基因内的rs112501869，编码一种脑高亲和力谷氨酸转运体，在0.25kHz性状中达到p = 6.21×10。2. 基因内的rs73519456，编码Astrotactin蛋白2，在三个NHF性状中达到全基因组显著性：0.5kHz（p = 1.86×１０）、PTAL（p = 9.40×10）和PTAM（p = 3.64×10）。SnRNA-seq数据分析揭示了该基因在神经元和暗细胞群体中的特殊表达，而对于该基因未检测到显著表达。TWAS分析检测到该基因（eQTL：rs1584327）在海马组织中对于0.25kHz性状具有统计学显著性（p = 4.49×10）。
本研究利用了三个意大利队列，从遗传和听力学角度进行了深入表征。生物信息学和生物统计学分析允许鉴定出三个新的候选基因，即和。在更大且独立的队列中进行功能研究和重复验证对于确认这些基因在调节听力功能中的生物学作用至关重要；然而，这些结果证实了GWAS和TWAS作为发现新基因的强大方法，从而为更深入理解听觉系统背后错综复杂的遗传景观铺平了道路。
