Muscle-specific allelic imbalance reveals a novel IARS1 disease mechanism

Congenital myopathies are diagnostically challenging and genetically heterogeneous disorders. We investigated a familial case affecting three siblings with congenital myopathy, born to unaffected parents. Clinical features included generalized hypotonia, and muscle biopsies showed fiber atrophy with centralized nuclei. A combination of whole-exome and muscle RNA sequencing identified a muscle-specific allelic imbalance in the isoleucyl-tRNA synthetase (IARS1) gene. Genetic analysis revealed a compound heterozygous inheritance pattern in IARS1. The asymptomatic heterozygous mother carried a missense variant (p.R661H), while whole-genome sequencing of the father identified an intronic variant near exon 25 of IARS1 within a region of known methylation. In the affected children, transcriptomics revealed a muscle-specific allelic imbalance with near-exclusive expression of the maternal mutant allele suggesting a muscle-specific silencing of the paternal allele. The resulting pseudo-homozygous state of the pathogenic maternal variant could explain the myopathy in the children and the asymptomatic carrier status of the mother. To validate IARS1's role in muscle function, we showed that muscle-specific knockdown of its ortholog in C. elegans causes progressive sarcomeric disorganization. To dissect the cellular consequences of the variants, we established human models for mechanistic studies, including IARS1-knockout myoblasts and myotubes transdifferentiated from patient fibroblasts. We performed functional assays to determine the downstream effects of impaired IARS1 function, including cellular metabolism (WST-1), proliferation (IncuCyte), and enzyme kinetics (aminoacylation). This work highlights a potential novel muscle-specific, epigenetically modulated compound heterozygous inheritance mechanism for an AARS-related myopathy and provides insights into how disruptions in protein synthesis could lead to a specific muscle pathology.