Peculiar combinations of individually non-pathogenic missense mitochondrial DNA variants cause low penetrance Leber's hereditary optic neuropathy

We here report on the existence of Leber’s hereditary optic neuropathy (LHON) associated with peculiar combinations of individually non-pathogenic missense mitochondrial DNA (mtDNA) variants, affecting the MT-ND4, MT-ND4L and MT-ND6 subunit genes of Complex I. The pathogenic potential of these mtDNA haplotypes is supported by multiple evidences: first, the LHON phenotype is strictly inherited along the maternal line in one very large family; second, the combinations of mtDNA variants are unique to the two maternal lineages that are characterized by recurrence of LHON; third, the Complex I-dependent respiratory and oxidative phosphorylation defect is co-transferred from the proband’s fibroblasts into the cybrid cell model. Finally, all but one of these missense mtDNA variants cluster along the same predicted fourth E-channel deputed to proton translocation within the transmembrane domain of Complex I, involving the ND1, ND4L and ND6 subunits. Hence, the definition of the pathogenic role of a specific mtDNA mutation becomes blurrier than ever and only an accurate evaluation of mitogenome sequence variation data from the general population, combined with functional analyses using the cybrid cell model, may lead to final validation. Our study conclusively shows that even in the absence of a clearly established LHON primary mutation, unprecedented combinations of missense mtDNA variants, individually known as polymorphisms, may lead to reduced OXPHOS efficiency sufficient to trigger LHON. In this context, we introduce a new diagnostic perspective that implies the complete sequence analysis of mitogenomes in LHON as mandatory gold standard diagnostic approach.
Author summary Leber’s hereditary optic neuropathy (LHON) is a common cause of maternally inherited vision loss. In the large majority of cases LHON is due to mitochondrial DNA (mtDNA) point mutations, clearly distinct from common polymorphisms normally found in the general population, affecting the mitochondrial function, thus defined as pathogenic. For the first time, we here demonstrate, on the genetic and functional ground, that unusual combinations of otherwise polymorphic and non-pathogenic mtDNA variants are sufficient for causing low-penetrance maternally inherited optic neuropathy in pedigrees fitting the LHON clinical diagnosis. Our findings bridge the blurry border between “pathogenic” and “neutral” mutations in an overall continuum that truly depends on the specific and sometime unique combination of variants characterizing each mitogenome. As a result, we conclude that, for an accurate diagnosis of LHON and possibly of other mitochondrial diseases, the only approach that can disclose all possible causative sources is complete mitogenome sequencing.