Investigating gene mutations in a South African paediatric cohort diagnosed with mitochondrial disease

Abstract

Mitochondrial diseases (MD) are a clinically heterogenous group of genetic disorders that affect the neuromuscular system, the central nervous system (collectively known as encephalomyopathies), and other high-energy demanding organs, often with multi-system involvement. This involvement, whether single- or multi-system, can have extensive phenotypical features which could make the diagnosis of MD a daunting task. Over recent years, substantial progress has been made towards a better understanding of the most common mitochondrial encephalomyopathies including their clinical manifestation and underlying genetic cause. This progress has been made in mainly non-African patient populations. For these well-studied populations, routine clinical, biochemical, and genetic diagnostic approaches have consequently been established, improving diagnosis of MD in paediatric and adult patients alike. The limited diagnostic capacity in developing countries such as South Africa with its ethnically diverse populations, has hindered the advancement of diagnostic procedures for MDs in these countries. As a result, there is limited information available on clinical manifestations and genetic causation for the most common MDs in these understudied patient populations. However, over the last decade the following progress has been made towards an understanding of the underlying genetic cause of MD in South African patients: Firstly, since 1998 paediatric clinical referrals and assessments have been performed on paediatric patients with mitochondrial-disease-like signs and symptoms at the Steve Biko Academic Hospital, Pretoria (forming the cohort for this investigation). Secondly, biochemical analyses also commenced shortly afterwards and were performed for every patient who has been clinically diagnosed with an MD, which at the time of this investigation was 212. Thirdly, genetic investigations followed, starting with a small number of patients (n = 71) for whom whole mitochondrial genome next-generation sequencing was performed. This number has been expanded throughout recent years, and to date there are whole mitochondrial DNA sequencing data for 123 patients. Results from this initial mtDNA sequencing approach revealed relatively few pathogenic mutations. For the majority of these cases, a clear MD aetiology could not be established. It was collaboratively decided to perform targeted gene panel sequencing on nuclear-encoded genes associated with MD. Three panels were designed and used in this study, each consisting of genes directly involved with the mitochondrion. An inhouse bioinformatics pipeline was developed during this study to analyse the sequence data. The results for the nuclear gene investigations revealed that a clear genotype-phenotype correlation could be established in only two of the 85 selected cases. One of these patients was extensively investigated and later published as a case-report. Due to the disappointingly low diagnostic yield of panel sequencing, whole exome sequencing was performed on a small number of African patients to probe the outcome of this approach. These initial results were promising as six of the eight sequenced cases presented with a pathogenic or likely pathogenic variant. Additional screening for two putative African-population-specific gene mutations was also performed on all of the African cases. Combined, from the results, the aetiology could be determined in ten cases; eight cases using next-generation sequencing, and two cases using selected gene mutation screening. In conclusion, this study was the first in size and scope to investigate the molecular genetics of MD in an understudied ethnically diverse population, providing new knowledge on these patients and insight into future strategies. Diagnosis of MD remains a daunting task in South Africa and will only improve once diagnostic capacity has been significantly enhanced