De novo mutation in POLG leads to haplotype insufficiency and Alpers syndrome

Inherited mitochondrial genomic instability and chemical exposures

There are approximately 1500 proteins that are needed for mitochondrial structure and function, most of which are encoded in the nuclear genome (Calvo et al., 2006). Each mitochondrion has its own genome (mtDNA), which in humans encodes 13 polypeptides, 22 tRNAs and 2 rRNAs required for oxidative phosphorylation. The mitochondrial genome of humans and most vertebrates is approximately 16.5kbp, double-stranded, circular, with few non-coding bases. Thus, maintaining mtDNA stability, that is, the ability of the cell to maintain adequate levels of mtDNA template for oxidative phosphorylation is essential and can be impacted by the level of mtDNA mutation currently within the cell or mitochondrion, but also from errors made during normal mtDNA replication, defects in mitochondrial quality control mechanisms, and exacerbated by exposures to exogenous and/or endogenous genotoxic agents. In this review, we expand on the origins and consequences of mtDNA instability, the current state of research regarding the mechanisms by which mtDNA instability can be overcome by cellular and chemical interventions, and the future of research and treatments for mtDNA instability.

Yeast model analysis of novel polymerase gamma variants found in patients with autosomal recessive mitochondrial disease

Replication of the mitochondrial genome depends on the single DNA polymerase (pol gamma). Mutations in the POLG gene, encoding the catalytic subunit of the human polymerase gamma, have been linked to a wide variety of mitochondrial disorders that show remarkable heterogeneity, with more than 200 sequence variants, often very rare, found in patients. The pathogenicity and dominance status of many such mutations remain, however, unclear. Remarkable structural and functional conservation of human POLG and its S. cerevisiae ortholog (Mip1p) led to the development of many successful yeast models, enabling to study the phenotype of putative pathogenic mutations. In a group of patients with suspicion of mitochondrial pathology, we identified five novel POLG sequence variants, four of which (p.Arg869Ter, p.Gln968Glu, p.Thr1053Argfs*6, and p.Val1106Ala), together with one previously known but uncharacterised variant (p.Arg309Cys), were amenable to modelling in yeast. Familial analysis indicated causal relationship of these variants with disease, consistent with autosomal recessive inheritance. To investigate the effect of these sequence changes on mtDNA replication, we obtained the corresponding yeast mip1 alleles (Arg265Cys, Arg672Ter, Arg770Glu, Thr809Ter, and Val863Ala, respectively) and tested their effect on mitochondrial genome stability and replication fidelity. For three of them (Arg265Cys, Arg672Ter, and Thr809Ter), we observed a strong, partially dominant phenotype of a complete loss of functional mtDNA, whereas the remaining two led to partial mtDNA depletion and significant increase in point mutation frequencies. These results show good correlation with the severity of symptoms observed in patients and allow to establish these variants as pathogenic mutations.

MMS exposure promotes increased MtDNA mutagenesis in the presence of replication-defective disease-associated DNA polymerase γ variants

Mitochondrial DNA (mtDNA) encodes proteins essential for ATP production. Mutant variants of the mtDNA polymerase cause mutagenesis that contributes to aging, genetic diseases, and sensitivity to environmental agents. We interrogated mtDNA replication in Saccharomyces cerevisiae strains with disease-associated mutations affecting conserved regions of the mtDNA polymerase, Mip1, in the presence of the wild type Mip1. Mutant frequency arising from mtDNA base substitutions that confer erythromycin resistance and deletions between 21-nucleotide direct repeats was determined. Previously, increased mutagenesis was observed in strains encoding mutant variants that were insufficient to maintain mtDNA and that were not expected to reduce polymerase fidelity or exonuclease proofreading. Increased mutagenesis could be explained by mutant variants stalling the replication fork, thereby predisposing the template DNA to irreparable damage that is bypassed with poor fidelity. This hypothesis suggests that the exogenous base-alkylating agent, methyl methanesulfonate (MMS), would further increase mtDNA mutagenesis. Mitochondrial mutagenesis associated with MMS exposure was increased up to 30-fold in mip1 mutants containing disease-associated alterations that affect polymerase activity. Disrupting exonuclease activity of mutant variants was not associated with increased spontaneous mutagenesis compared with exonuclease-proficient alleles, suggesting that most or all of the mtDNA was replicated by wild type Mip1. A novel subset of C to G transversions was responsible for about half of the mutants arising after MMS exposure implicating error-prone bypass of methylated cytosines as the predominant mutational mechanism. Exposure to MMS does not disrupt exonuclease activity that suppresses deletions between 21-nucleotide direct repeats, suggesting the MMS-induce mutagenesis is not explained by inactivated exonuclease activity. Further, trace amounts of CdCl₂ inhibit mtDNA replication but suppresses MMS-induced mutagenesis. These results suggest a novel mechanism wherein mutations that lead to hypermutation by DNA base-damaging agents and associate with mitochondrial disease may contribute to previously unexplained phenomena, such as the wide variation of age of disease onset and acquired mitochondrial toxicities.

Thousands of mitochondrial DNA (mtDNA) per cell are necessary to maintain energy required for cellular survival in humans. Interfering with the mtDNA polymerase can result in mitochondrial diseases and mitochondrial toxicity. Therefore, it is important to explore new genetic and environmental mechanisms that alter the effectiveness and accuracy of mtDNA replication. This genetic study uses the budding yeast to demonstrate that heterozygous strains harboring disease-associated mutations in the mtDNA polymerase gene in the presence of a wild type copy of the mtDNA polymerase are associated with increased mtDNA point mutagenesis in the presence of methane methylsulfonate, a known base damaging agent. Further observations suggest that the inability of disease-associated variants to replicate mtDNA resulted in increased vulnerability to irreparable base damage that was likely to result in mutations when replicated. Also, this study showed that trace amounts of the environmental contaminant cadmium chloride impairs mtDNA replication but eliminates damage-induced mutagenesis in the remaining functional mitochondria. This interplay between disease-associated variant and wild type polymerase offers new insights on possible disease variation and implicates novel environmental consequences for compound heterozygous patients.

Mitochondriale Erkrankungen

Mitochondriale Erkrankungen sind – wie auch die übrigen Artikel dieses Schwerpunkthefts verdeutlichen – ein weites Feld in der klinischen Genetik. Aufgrund des bunten klinischen Bildes sowohl bei Kindern als auch bei Erwachsenen ergeben sich relativ häufig Konstellationen, in denen auch eine mitochondriale Erkrankung in das differenzialdiagnostische Spektrum mit einbezogen wird. In der genetischen Beratung stellt dies eine besondere Herausforderung dar, da unter dieser Verdachtsdiagnose grundsätzlich alle Erbgänge, inklusive einer maternalen Vererbung, möglich sind und gleichzeitig eine zielgerichtete Diagnostik zum molekulargenetischen Beleg oder auch Ausschluss der Diagnose durch die außerordentliche genetische Heterogenität erschwert ist. Im Folgenden erläutern wir ein rationales Vorgehen in der molekulargenetischen Diagnostik und besondere Aspekte der genetischen Beratung.

Complete Deletion of a POLG1 Allele in a Patient with Alpers Syndrome

Mutations in the gene encoding the catalytic subunit of polymerase γ (POLG1) are a major cause of human mitochondrial disease. More than 150 different point mutations in the gene have been reported to be disease causing, resulting in a large range of clinical symptoms. Depending on the mutation or combination of mutations, disease onset can occur in early infancy or late in adult life. Here, we describe the use of multiplex ligation-dependent probe amplification (MLPA) analysis to detect deletions within POLG1, which could otherwise go undetected by solely sequencing of the gene. We present a case where an entire POLG1 allele is deleted, with a known pathogenic mutation (W748S) on the remaining allele. The deletion was found in a boy with Alpers syndrome, presenting at 18 months of age with slightly retarded motor development, balance problems, and seizures. Administration of valproic acid (VPA) led to rapidly progressive fatal liver failure in our patient, and we would like to highlight the need to carry out complete POLG1 gene analysis before administration of VPA in cases of pediatric seizure disorders of unknown origin. Debut and severity of the disease in this patient was unique when compared to homozygous or heterozygous patients with the W748S mutation, leading to the conclusion that gene dosage plays a role in the clinical phenotype of this disease.

Drug-resistant epilepsia and fulminant valproate liver toxicity. Alpers-Huttenlocher syndrome in two children confirmed post mortem by identification of p.W748S mutation in POLG gene

Background

POLG (polymerase gamma) gene mutations lead to a variety of neurological disorders, including Alpers-Huttenlocher syndrome (AHS). The diagnostic triad of AHS is: resistant epilepsy, liver impairment triggered by sodium valproate (VA), and mitochondrial DNA depletion.

Material/Methods

A cohort of 28 children with mitochondrial encephalopathy and liver failure was qualified for retrospective study of mitochondrial DNA depletion and POLG mutations.

Results

The p.W748S POLG gene mutation was revealed in 2 children, the only ones in the cohort who fulfilled the AHS criteria. Depletion of mtDNA (16% of control value) was confirmed post mortem in available liver tissue and was not detected in the muscle. The disease started with drug-resistant seizures, failure to thrive and developmental regression at the ages of 7 and 18 months, respectively. Irreversible liver failure developed after VA administration. Co-existence of epilepsy, VA liver toxicity, lactic acidemia and muscle respiratory chain dysfunction led finally to the diagnosis of mitochondrial disorder (and AHS suspicion).

Conclusions

Our results confirm, for the first time, the occurrence of a pathology caused by POLG gene mutation(s) in the Polish population. POLG mutation screening and mtDNA depletion assessment should be included in differential diagnosis of drug-resistant epilepsy associated with a hepatopathy.