Expanding the landscape of tRNA pathogenic variants in mitochondrial DNA

We present a comprehensive molecular and histopathological characterization of nine patients with mitochondrial myopathy, predominantly manifesting progressive external ophthalmoplegia (PEO), associated with heteroplasmic variants in mitochondrial tRNA genes (mt-tRNA). Among the ten variants identified, four were novel and previously unreported in MITOMAP. Using laser capture microdissection and deep next-generation sequencing, we quantified heteroplasmy at the single-muscle-fibre level, demonstrating that cytochrome c oxidase (COX)-deficient fibres consistently reached near-homoplasmic mutant loads, whereas COX-positive fibres remained heteroplasmic with lower variant fractions. These findings firmly support the pathogenic role of all variants. Furthermore, digital droplet PCR revealed an increased mitochondrial DNA (mtDNA) content in COX-deficient fibres, indicating compensatory mitochondrial biogenesis. Of particular note, one patient harboured two novel heteroplasmic variants, m.10009G > A and m.15961G > A, for which long-read sequencing identified mitogenomes carrying both variants also in cis, suggesting the occurrence of mtDNA recombination in human tissue. By applying refined American College of Medical Genetics and Genomics (ACMG) criteria specific for mt-tRNA, we reclassified several variants as pathogenic or likely pathogenic, including three previously deemed of uncertain significance. Overall, our integrative approach-combining single-fibre molecular dissection, mtDNA quantification, and long-read sequencing-broadens the mutational spectrum of pathogenic mt-tRNA variants, highlights the diagnostic value of single-fibre analyses in confirming pathogenicity, and provides new insights into mitochondrial genome dynamics and compensatory responses in mitochondrial disease.