Assigning pathogenicity to mitochondrial tRNA mutations: when ‘definitely maybe’ is not good enough

doi:10.1016/j.tig.2004.09.014

Trends in Genetics

Volume 20, Issue 12, December 2004, Pages 591-596

https://doi.org/10.1016/j.tig.2004.09.014 Get rights and content

Some mutations in mitochondrial tRNA (mt-tRNA) genes cause devastating disease, whereas others have no clinical consequences. We understand little of the factors determining the pathogenicity of specific mt-tRNA mutations, making prediction of clinical outcome extremely difficult. Using extensive sequence databases, we compared the characteristics of neutral variations with those of pathogenic mutations. We recommend that the location of the proposed mutation within the secondary structure of the mt-tRNA molecule and the disruption it causes to Watson-Crick base pairing should be considered when assessing the pathological significance of a novel mt-tRNA mutation.

Section snippets

mt-tRNA mutations

In total, 91 different mt-tRNA mutations were listed as pathogenic on MITOMAP, but 66 (73%) of these were listed as ‘provisional’. The pathogenic status of four mutations was listed as ‘unclear,’ whereas another four mutations were not clearly described as either pathogenic or polymorphic. A dual entry on both the list of pathogenic mutations and the list of polymorphic variants occurred on six occasions, whereas two mutations that were provisionally identified as pathogenic also have a

Unsubstantiated claims

Although the canonical criteria of DiMauro and Schon are now generally accepted, they have been neither rigorously nor uniformly applied to suspected novel pathogenic mt-tRNA mutations before publication. Several mt-tRNA mutations were reported before the precepts of the canonical criteria were conceived but others, published more recently, simply lack the required evidence. In our study, 26% of the ‘pathogenic’ mt-tRNA mutations listed on MITOMAP fulfilled three or fewer basic criteria that

Concluding remarks

Our analysis of the published mt-tRNA mutations listed on MITOMAP indicates that, at present, there is insufficient evidence to classify a large proportion of the reported mutations as pathogenic. Furthermore, through our analysis we have been able to arrive at the following conclusions: (i) ∼73% of pathogenic mutations occur in the stems of mt-tRNA secondary structure; (ii) ‘hotspots’ for pathogenic mutations occur in both the acceptor and anticodon stems; (iii) the disruption of Watson–Crick

Acknowledgements

The research reported here was supported in part by the Wellcome Trust (D.M.T), The Newcastle upon Tyne Hospitals NHS Trust (R.W.T) and the National Science Foundation (N.H). R.M. and J.L.E. are supported by an MRC (UK) Clinician Scientist Fellowship and an MRC (UK) Bioinformatics Training Fellowship, respectively.

References (19)

Y. Goto
A new mtDNA mutation associated with mitochondrial myopathy, encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS)
Biochim. Biophys. Acta
(1991)
J.M. Shoffner
Myoclonic epilepsy and ragged-red fiber disease (MERRF) is associated with a mitochondrial DNA tRNA^Lys mutation
Cell
(1990)
R.W. Taylor
A homoplasmic mitochondrial transfer ribonucleic acid mutation as a cause of maternally inherited hypertrophic cardiomyopathy
J. Am. Coll. Cardiol.
(2003)
L.M. Wittenhagen et al.
Impact of disease-related mitochondrial mutations on tRNA structure and function
Trends Biochem. Sci.
(2003)
R. McFarland
A novel sporadic mutation in cytochrome c oxidase subunit II as a cause of rhabdomyolysis
Neuromuscul Disord.
(2004)
S. Shanske
Identical mitochondrial DNA deletion in a woman with ocular myopathy and in her son with Pearson syndrome
Am. J. Hum. Genet.
(2002)
B. Sohm
Towards understanding human mitochondrial leucine aminoacylation identity
J. Mol. Biol.
(2003)
D.E. Draper
Strategies for RNA folding
Trends Biochem. Sci.
(1996)
MITOMAP: A Human Mitochondrial Genome Database. http://www.mitomap.org,...

There are more references available in the full text version of this article.

Cited by (144)

A novel, pathogenic dinucleotide deletion in the mitochondrial MT-TY gene causing myasthenia-like features
2020, Neuromuscular Disorders
Mitochondrial DNA (mtDNA)-related diseases often pose a diagnostic challenge and require rigorous clinical and laboratory investigation. Pathogenic variants in the mitochondrial tRNA gene MT-TY, which encodes the tRNA^Tyr, are a rare cause of mitochondrial disease. Here we describe a novel m.5860delTA anticodon variant in the MT-TY gene in a patient who initially presented with features akin to a childhood onset myasthenic syndrome. Using histochemical, immunohistochemical and protein studies we demonstrate that this mutation leads to severe biochemical defects of mitochondrial translation, which is reflected in the early onset and progressive phenotype. This case highlights the clinical overlap between mtDNA-related diseases and other neuromuscular disorders, and demonstrates the potential pitfalls in analysis of next generation sequencing results, given whole exome sequencing of a blood DNA sample failed to make a genetics diagnosis. Muscle biopsy remains an important requirement in the diagnosis of mitochondrial disease and in establishing the pathogenicity of novel mtDNA variants.
Bioinformatics resources, databases, and tools for human mtDNA
2020, The Human Mitochondrial Genome: From Basic Biology to Disease
The topic of this chapter owes a lot to the work of Sanger first, and Maxam and Gilbert, thereafter. They designed and implemented the techniques that allow us to produce the sequence of nucleotides that make up any piece of DNA. With the advent of sequencing technologies, it was immediately clear that the explosion of data that would be produced would require the design and implementation of databases in which to store data, as well as the setting up of systems for querying sequences, extracting, and analyzing them. In this scenario, the first nucleus of nucleotide sequences produced and stored in public nucleotide databases also included the first complete human mitochondrial genome, sequenced in 1981: the so called “Cambridge Reference Sequence” then revised as rCRS and since then universally adopted as a reference sequence for both population and clinical studies. In more recent times, a virtual sequence has been produced with the aim of better simulating the process of generations of world populations namely the “Reconstructed Sapiens Reference Sequence”. Overall, a great number of complete human mitochondrial genomes or fragments regarding the major control region D-loop have been sequenced since then starting from the representative samples of different populations within mtDNA phylogeny studies as well as samples collected within forensic analyses and clinical research. Because of the range of mtDNA variants with potential clinical and evolutionary relevance, difficulties can be encountered in deciding whether or not a particular mtDNA variant is relevant for either clinical or evolutionary arguments. This choice is guided by the four generally accepted canonical criteria, that is (1) knowledge about the neutral nature of a polymorphism, (2) the functional effect in a conserved site, (3) the heteroplasmic level, and (4) the association of this latter to the severity of clinical symptoms observed. Bioinformatics resources and tools have been developed to manage and analyze this enormous volume of information, with the aim of annotating and classifying genomes and variants. In this chapter, we provide a comprehensive overview of the concepts underlying the criteria to assess mitochondrial variant pathogenicity, as well as bioinformatics databases and tools.
Methods for the identification of mitochondrial DNA variants
2020, The Human Mitochondrial Genome: From Basic Biology to Disease
Detection of human mitochondrial DNA variants and quantification of heteroplasmy have quickly evolved since the discovery of the mitochondrial genome in the early 1960s. Traditionally, mitochondrial variants were studied through a combination of molecular biology techniques, often limited to the analysis of single variants. The development of Sanger sequencing led to a paradigm shift in mitochondrial studies, which enabled to perform a comprehensive screening of the entire genome. Progress in robotics and nanotechnologies led to the development of high-throughput detection techniques, like modern DNA microarrays and next-generation sequencing. In this chapter, we provide a compendium of the most widely used techniques to identify mitochondrial variants, from PCR-based methods to third-generation sequencing, and also address the challenges posed by detection and heteroplasmy quantification. Likewise, we provide a description of the most up-to-date bioinformatic tools available to the scientific community to perform mitochondrial genome analysis as well as guidelines for variant detection in high-throughput sequencing data
A novel variant m.641A>T in the mitochondrial MT-TF gene is associated with epileptic encephalopathy in adolescent
2019, Mitochondrion
Citation Excerpt :
This case supports the heterogeneity of mitochondrial disorders and confirms the necessity of the whole mtDNA genome analysis to become a part of the routine diagnostics for patients with suspected mitochondrial diseases, presenting complex neurological manifestations. Despite the use of different scoring systems, it remains a great challenge to determine whether the given mtDNA substitution affects the mitochondrial function and is pathogenic (McFarland, 2004). The capability to predict whether the mtDNA mutation is responsible for the disease onset is of great importance for accurate and appropriate genetic counselling.
We present a 14-year-old girl with loss of motor functions, tetraplegia, epilepsy and nystagmus, caused by a novel heteroplasmic m.641A>T transition in an evolutionary conserved region of mitochondrial genome, affecting the aminoacyl stem of mitochondrial tRNA-Phe. In silico prediction, respirometry, Western blot and enzymatic analyses in skin fibroblasts support the pathogenicity of the m.641A>T substitution.
This is the 18th MT-TF point mutation associated with a mitochondrial disorder. The onset and the severity of the disease, however, is unique in this case and broadens the clinical picture related to mutations of mitochondrial tRNA-Phe.
Panel-Based Nuclear and Mitochondrial Next-Generation Sequencing Outcomes of an Ethnically Diverse Pediatric Patient Cohort with Mitochondrial Disease
2019, Journal of Molecular Diagnostics
Mitochondrial disease (MD) is a group of rare inherited disorders with clinical heterogeneous phenotypes. Recent advances in next-generation sequencing (NGS) allow for rapid genetic diagnostics in patients who experience MD, resulting in significant strides in determining its etiology. This, however, has not been the case in many patient populations. We report on a molecular diagnostic study using mitochondrial DNA and targeted nuclear DNA (nDNA) NGS of an extensive cohort of predominantly sub-Saharan African pediatric patients with clinical and biochemically defined MD. Patients in this novel cohort presented mostly with muscle involvement (73%). Of the original 212 patients, a muscle respiratory chain deficiency was identified in 127 cases. Genetic analyses were conducted for these 127 cases based on biochemical deficiencies, for both mitochondrial (n = 123) and nDNA using panel-based NGS (n = 86). As a pilot investigation, whole-exome sequencing was performed in a subset of African patients (n = 8). These analyses resulted in the identification of a previously reported pathogenic mitochondrial DNA variant and seven pathogenic or likely pathogenic nDNA variants (ETFDH, SURF1, COQ6, RYR1, STAC3, ALAS2, and TRIOBP), most of which were identified via whole-exome sequencing. This study contributes to knowledge of MD etiology in an understudied, ethnically diverse population; highlights inconsistencies in genotype-phenotype correlations; and proposes future directions for diagnostic approaches in such patient populations.
CPEO – Like mitochondrial myopathy associated with m.8340G>A mutation
2019, Mitochondrion
Two patients with an m.8340G>A mitochondrial DNA variant have been reported with one patient showing ptosis, ophthalmoparesis and myopathy at 53% heteroplasmy and another with pigmentary retinopathy, cataracts and sensory neural deafness and slightly higher heteroplasmy (65%). Here we report that higher muscle mutant heteroplasmy (93%) for m.8340G>A is associated with ptosis, ophthalmoparesis and mitochondrial myopathy, thus confirming the initial phenotypic association and showing that heteroplasmy per se does not explain the phenotypic spectrum of disease associated with the m.8340G>A mutation.

View all citing articles on Scopus

View full text

Trends in Genetics

Genome AnalysisAssigning pathogenicity to mitochondrial tRNA mutations: when ‘definitely maybe’ is not good enough

Section snippets

mt-tRNA mutations

Unsubstantiated claims

Concluding remarks

Acknowledgements

Biochim. Biophys. Acta

Cell

J. Am. Coll. Cardiol.

Trends Biochem. Sci.

Neuromuscul Disord.

Am. J. Hum. Genet.

J. Mol. Biol.

Trends Biochem. Sci.

Genome Analysis
Assigning pathogenicity to mitochondrial tRNA mutations: when ‘definitely maybe’ is not good enough