Identifying new genes in mitochondrial disease

Abstract

Mendelian mitochondrial disease presents vast clinical and genetic heterogeneity, which provides challenges in attaining genetic diagnoses for affected patients. With approximately 1,200 proteins encoded by the nuclear genome that tightly coordinate mitochondrial function, targeted screening of a subset of genes provides a low diagnostic yield. Clinicians and researchers have increasingly turned to whole exome sequencing (WES), a targeted next-generation sequencing technology for the identification of all variants in the exons (coding regions) of all known genes for variant discovery and prioritisation, constituting approximately 1% of the human genome. WES was utilised to provide genetic diagnoses in two patients cohorts with clinically well-defined, genetically undetermined mitochondrial disease: (i) adult-onset progressive external ophthalmoplegia (PEO) (n=19), a mitochondrial DNA (mtDNA) maintenance disorder characterised by extraocular paresis and skeletal muscle restricted multiple mtDNA deletions, with broad phenotypes ranging from indolent PEO and fatal multisystem PEO-plus; (ii) early-onset mitochondrial respiratory chain complex (RC) deficiency (n=20), typically affecting patients in the first decade of life and are associated with heterogeneous phenotypes. Pathogenic mtDNA mutations were previously excluded in all patients. Adult-onset PEO with multiple mtDNA deletions patients were recruited following negative genetic testing of commonly associated nuclear genes, while early-onset RC deficiency patients were negative genetic testing in a small selection of nuclear genes. Using custom variant filtering strategies for each cohort, confirmed diagnoses were attained in 10% of adult-onset PEO with multiple mtDNA deletions patients and 35% of early-onset RC deficiency patients. This was comprised of known mitochondrial disease associated genes in both cohorts (AARS2, EARS2, MRPS22, PDHA1, SCO1, TK2, TRMU, TWNK), while novel candidate genes involved in mitochondrial translation, mtDNA replication, nucleotide metabolism and mitochondrial dynamics were also proposed. The pathological mechanism of a novel heterozygous GMPR1 variant was characterised as a potential new candidate gene associated with late-onset PEO due to impaired nucleotide balance for mtDNA maintenance. GTPBP3 was identified as a novel locus causing defective tRNA modification with multiple RC deficiency and the clinical, molecular and genetic features of AARS2, EARS2 and YARS2 mutations were expanded. Finally, this research highlights the potential significance of de novo and somatic mosaic variants in WES variant discovery and prioritisation.