Recent advances in understanding the molecular genetic basis of mitochondrial disease

Abstract

Mitochondrial disease is hugely diverse with respect to associated clinical presentations and underlying genetic causes, with pathogenic variants in over 300 disease genes currently described. Approximately half of these have been discovered in the last decade due to the increasingly widespread application of next generation sequencing technologies, in particular unbiased, whole exome-and latterly, whole genome sequencing. These technologies allow more genetic data to be collected from patients with mitochondrial disorders, continually improving the diagnostic success rate in a clinical setting. Despite these significant advances, some patients still remain without a definitive genetic diagnosis. Large datasets containing many variants of unknown significance have become a major challenge with next generation sequencing strategies and these require significant functional validation to confirm pathogenicity. This interface between diagnostics and research is critical in continuing to expand the list of known pathogenic variants and concomitantly enhance our knowledge of mitochondrial biology. The increasing use of whole exome sequencing, whole genome sequencing and other "omics" techniques such as transcriptomics and proteomics will generate even more data and allow further interrogation and validation of genetic causes, including those outside of coding regions. This will improve diagnostic yields still further and emphasizes the integral role that functional assessment of variant causality plays in this process-the overarching focus of this review.

Keywords: diagnosis; mitochondrial disease; molecular mechanisms; next generation sequencing.

Figure 1

List of genes currently associated with mitochondrial disease sorted according to function. Some genes have more than one mitochondrial function, so we have used broad categories to ensure their most appropriate assignment. Our selection criteria necessitated causative genes have a primary or secondary impact on OXPHOS and does not include genes where variants have been described in cancer, but not a mitochondrial disorder (eg, SDHC). Over 150 genes linked to mitochondrial disease have been discovered since the implementation of next generation sequencing (NGS) in 2010. Today, pathogenic variants in 36/37 mitochondrial‐encoded genes and 295 nuclear‐encoded mitochondrial genes have been shown to affect mitochondrial energy metabolism, highlighting the impact NGS has had in the identification of causative genes that are associated with a wide range of mitochondrial functions

Figure 2

An overview of the workflow utilized to identify and validate variants associated with mitochondrial disease. First, clinical information is vital to inform appropriate genetic testing. If no mitochondrial DNA (mtDNA) or syndrome‐associated nuclear variants are identified, we advocate the use of trio whole‐exome (WES) or whole‐genome (WGS) sequencing. For each of the outcomes of WES/WGS, different levels of investigation are required to prove pathogenicity. Then, we have outlined some of the basic techniques that can be used to investigate the impact of those variants on OXPHOS metabolism using patient tissue or cells. In cases where disease mechanisms are poorly understood, these materials alongside cell and animal models can aid investigations. There is a plethora of techniques available, and instead of providing an exhaustive list we have highlighted those most commonly used, as well as gene function‐specific investigations, some of which are expanded upon in the text. Abbreviations: Co‐IP (co‐immunoprecipitation); EMSA (electrophoretic mobility shift assay); FRET (fluorescence resonance energy transfer); iPSC (induced pluripotent stem cells); MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke‐like episodes); MIDD (maternally inherited diabetes and deafness); OXPHOS (oxidative phosphorylation); SBF‐SEM (serial block‐face scanning electron microscopy); STED (stimulated emission depletion); TAP (transporter associated with antigen processing); TEM (transmission electron microscopy); WES (whole‐exome sequencing); WGS (whole‐genome sequencing); Y2H (yeast two‐hybrid)