Pathogenic Bi-allelic Mutations in NDUFAF8 Cause Leigh Syndrome with an Isolated Complex I Deficiency

Charlotte L Alston,Sila Hopton,Andrew Y Sung,Alexander Broomfield,Julija Pavaine,Joseph T Alaimo,Jullianne Diaz,Lucie S Taylor,Philipp Wolf,Holger Prokisch,Juliana Heidler,Robert Mcfarland,David J Pagliarini,Saskia B Wortmann,Robert W Taylor,Penelope E Bonnen,Ilka Wittig,Mike T Veling,Eyby Leon,Langping He

doi:10.1016/j.ajhg.2019.12.001

Abstract

Leigh syndrome is one of the most common neurological phenotypes observed in pediatric mitochondrial disease presentations. It is characterized by symmetrical lesions found on neuroimaging in the basal ganglia, thalamus, and brainstem and by a loss of motor skills and delayed developmental milestones. Genetic diagnosis of Leigh syndrome is complicated on account of the vast genetic heterogeneity with >75 candidate disease-associated genes having been reported to date. Candidate genes are still emerging, being identified when “omics” tools (genomics, proteomics, and transcriptomics) are applied to manipulated cell lines and cohorts of clinically characterized individuals who lack a genetic diagnosis. NDUFAF8 is one such protein; it has been found to interact with the well-characterized complex I (CI) assembly factor NDUFAF5 in a large-scale protein-protein interaction screen. Diagnostic next-generation sequencing has identified three unrelated pediatric subjects, each with a clinical diagnosis of Leigh syndrome, who harbor bi-allelic pathogenic variants in NDUFAF8. These variants include a recurrent splicing variant that was initially overlooked due to its deep-intronic location. Subject fibroblasts were found to express a complex I deficiency, and lentiviral transduction with wild-type NDUFAF8-cDNA ameliorated both the assembly defect and the biochemical deficiency. Complexome profiling of subject fibroblasts demonstrated a complex I assembly defect, and the stalled assembly intermediates corroborate the role of NDUFAF8 in early complex I assembly. This report serves to expand the genetic heterogeneity associated with Leigh syndrome and to validate the clinical utility of orphan protein characterization. We also highlight the importance of evaluating intronic sequence when a single, definitively pathogenic variant is identified during diagnostic testing.

Highlights

Leigh syndrome is one of the most common neurological phenotypes observed in pediatric mitochondrial disease presentations
Causative pathogenic variants have been identified in both the nuclear genome and the mitochondrial genome, and these variants affect various aspects of mitochondrial function including structural subunits and assembly factors of respiratory chain complexes (e.g., NDUFS2 [MIM: 602985]5 and SURF1 [MIM: 185620]6), Krebs cycle components (e.g., PDHA1 [MIM: 300502]7), mitochondrial protein translation (e.g., MTFMT [MIM 611766]8), and valine metabolism (e.g., ECHS1 [MIM 602292]9)
Evolving from the 100,000 Genomes Project in the UK, the newly established National Health Service (NHS) Genomic Medicine Service promises to revolutionize the genetic diagnosis of heterogeneous conditions such as Leigh syndrome through clinical whole-genome sequencing,[10] with similar programs occurring elsewhere including the Bavarian Genome Project in Germany and at the Victorian Clinical Genetics Services (VCGS) in Melbourne, Australia

Summary

Introduction

Leigh syndrome is one of the most common neurological phenotypes observed in pediatric mitochondrial disease presentations. This report serves to expand the genetic heterogeneity associated with Leigh syndrome and validates the clinical utility of orphan protein characterization; we highlight the importance of evaluating intronic sequence when a single, definitively pathogenic variant is identified during diagnostic testing.

Results

Conclusion