Novel Pathogenic Sequence Variation m.5789T>C Causes NARP Syndrome and Promotes Formation of Deletions of the Mitochondrial Genome

Marius Hippen; Gábor Zsurka; Viktoriya Peeva; Judith Machts; Kati Schwiecker; Grazyna Debska-Vielhaber; Rudolf J Wiesner; Stefan Vielhaber; Wolfram S Kunz

doi:10.1212/NXG.0000000000000660

Novel Pathogenic Sequence Variation m.5789T>C Causes NARP Syndrome and Promotes Formation of Deletions of the Mitochondrial Genome

Neurol Genet. 2021 Mar 3;8(2):e660. doi: 10.1212/NXG.0000000000000660. eCollection 2022 Apr.

Authors

Marius Hippen¹, Gábor Zsurka¹, Viktoriya Peeva¹, Judith Machts¹, Kati Schwiecker¹, Grazyna Debska-Vielhaber¹, Rudolf J Wiesner¹, Stefan Vielhaber¹, Wolfram S Kunz¹

Affiliation

¹ Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany.

Abstract

Background and objectives: We report the pathogenic sequence variant m.5789T>C in the anticodon stem of the mitochondrial tRNA for cysteine as a novel cause of neuropathy, ataxia, and retinitis pigmentosa (NARP), which is usually associated with pathogenic variants in the MT-ATP6 gene.

Methods: To address the correlation of oxidative phosphorylation deficiency with mutation loads, we performed genotyping on single laser-dissected skeletal muscle fibers. Stability of the mitochondrial tRNA^Cys was investigated by Northern blotting. Accompanying deletions of the mitochondrial genome were detected by long-range PCR and their breakpoints were determined by sequencing of single-molecule amplicons.

Results: The sequence variant m.5789T>C, originating from the patient's mother, decreases the stability of the mitochondrial tRNA for cysteine by disrupting the anticodon stem, which subsequently leads to a combined oxidative phosphorylation deficiency. In parallel, we observed a prominent cluster of low-abundance somatic deletions with breakpoints in the immediate vicinity of the m.5789T>C variant. Strikingly, all deletion-carrying mitochondrial DNA (mtDNA) species, in which the corresponding nucleotide position was not removed, harbored the mutant allele, and none carried the wild-type allele.

Discussion: In addition to providing evidence for the novel association of a tRNA sequence alteration with NARP syndrome, our observations support the hypothesis that single nucleotide changes can lead to increased occurrence of site-specific mtDNA deletions through the formation of an imperfect repeat. This finding might be relevant for understanding mechanisms of deletion generation in the human mitochondrial genome.