Three rare pathogenic mtDNA substitutions in LHON patients with low heteroplasmy

Impact of the m.13513G>A Variant on the Functions of the OXPHOS System and Cell Retrograde Signaling

Mitochondria are involved in many vital functions in living cells, including the synthesis of ATP by oxidative phosphorylation (OXPHOS) and regulation of nuclear gene expression through retrograde signaling. Leigh syndrome is a heterogeneous neurological disorder resulting from an isolated complex I deficiency that causes damage to mitochondrial energy production. The pathogenic mitochondrial DNA (mtDNA) variant m.13513G>A has been associated with Leigh syndrome. The present study investigated the effects of this mtDNA variant on the OXPHOS system and cell retrograde signaling. Transmitochondrial cytoplasmic hybrid (cybrid) cell lines harboring 50% and 70% of the m.13513G>A variant were generated and tested along with wild-type (WT) cells. The functionality of the OXPHOS system was evaluated by spectrophotometric assessment of enzyme activity and high-resolution respirometry. Nuclear gene expression was investigated by RNA sequencing and droplet digital PCR. Increasing levels of heteroplasmy were associated with reduced OXPHOS system complex I, IV, and I + III activities, and high-resolution respirometry also showed a complex I defect. Profound changes in transcription levels of nuclear genes were observed in the cell lines harboring the pathogenic mtDNA variant, indicating the physiological processes associated with defective mitochondria.

Mitochondrial Lipid Peroxidation Is Responsible for Ferroptosis

Ferroptosis induced by erastin (an inhibitor of cystine transport) and butionine sulfoximine (an inhibitor of glutathione biosynthesis) was prevented by the mitochondria-targeted antioxidants SkQ1 and MitoTEMPO. These effects correlate with the prevention of mitochondrial lipid peroxidation, which precedes cell death. Methylene blue, a redox agent that inhibits the production of reactive oxygen species (ROS) in complex I of the mitochondrial electron transport chain, also inhibits ferroptosis and mitochondrial lipid peroxidation. Activation of ROS production in complex I with rotenone in the presence of ferrous iron stimulates lipid peroxidation in isolated mitochondria, while ROS produced by complex III are ineffective. SkQ1 and methylene blue inhibit lipid peroxidation. We suggest that ROS formed in complex I promote mitochondrial lipid peroxidation and ferroptosis.

[Optic neuropathies as an interdisciplinary subject of research]

Despite the wide range of clinical, instrumental and laboratory methods used in modern ophthalmology, the problem of diagnosing optic neuropathy and identifying its etiology remains relevant. A complex multidisciplinary approach involving various specialists is required in the differential diagnosis of immune-mediated optic neuritis, for example in multiple sclerosis, neuromyelitis optica spectrum disorder, and MOG-associated diseases. Of special interest is differential diagnosis of optic neuropathy in demyelinating diseases of the central nervous system, hereditary optic neuropathies and ischemic optic neuropathy. The article presents a summary of scientific and practical results of differential diagnosis of optic neuropathies with various etiologies. Timely diagnosis and early therapy start reduces the degree of disability in patients with optic neuropathies of different etiologies.

[Hereditary optic neuropathy associated with demyelinating diseases of the central nervous system]

Demyelinating optic neuritis and hereditary optic neuropathy (HON) take a leading place among the diseases, the leading clinical syndrome of which is bilateral optic neuropathy with a simultaneous or sequential significant decrease in visual acuity. Optic neuritis can occur at the onset or be one of the syndromes within multiple sclerosis (MS), neuromyelitis optica spectrum disorders (NMOSD), and myelin oligodendrocyte glycoprotein (MOG) antibody disease (MOGAD). HON are a group of neurodegenerative diseases, among which the most common variants are Leber's hereditary optic neuropathy (LHON), associated with mitochondrial DNA (mtDNA) mutations, and autosomal recessive optic neuropathy (ARON), caused by nuclear DNA (nDNA) mutations in DNAJC30. There are phenotypes of LHON «plus», one of which is the association of HON and CNS demyelination in the same patient. In such cases, the diagnosis of each of these diseases causes significant difficulties, due to the fact that in some cases there are clinical and radiological coincidences between demyelinating and hereditary mitochondrial diseases.

[Rare pathogenic nucleotide variants of mitochondrial DNA associated with Leber's hereditary optic neuropathy]

Patients with Leber Hereditary Optic Neuropathy (LHON) in most cases have one of the three most common mutations: m.11778G>A in the ND4 gene, m.3460G>A in the ND1 gene, or m.14484T>C in the ND6 gene. According to the international Mitomap database, in addition to these three most common mutations, there are 16 other primary mutations that are even more rare. There are nucleotide substitutions that are classified as candidate or conditionally pathogenic mutations. Their involvement in the disease development is not proven due to insufficient research. Moreover, in many publications, the authors describe new primary and potential mitochondrial DNA mutations associated with LHON, which are not yet included in the genetic data bases. This makes it possible to expand the diagnostic spectrum during genetic testing in the future. The advancements in genetic diagnostic technologies allow confirmation of the clinical diagnosis of LHON. The importance of genetic verification of the disease is determined by the existing problem of differential diagnosis of hereditary optic neuropathies with optic neuropathies of a different origin.

Clinical outcomes of treatment with idebenone in Leber's hereditary optic neuropathy in the Netherlands: A national cohort study

PURPOSE

The purpose of the study was to present results from a national Dutch cohort of patients with Leber's Hereditary Optic Neuropathy (LHON) treated with idebenone.

METHODS

The multicentre, open-label, retrospective evaluation of the long-term outcome of idebenone treatment of Dutch LHON patients on visual function and on thickness of the retinal ganglion cell layer. Patients included in the analysis had a confirmed mutation in their mitochondrial DNA encoding either of the seven subunits of complex I, had a reported loss of vision in at least one eye and had a follow-up of more than 6 months after their treatment was started. Control visits involved routine clinical examinations of visual function and retinal structure at (1) the start of treatment, (2) nadir (time of lowest visual acuity), (3) the time of recovery (if any), (4) the time of termination of treatment and (5) more than 6 months after termination of the treatment.

RESULTS

Data from 72 patients were analysed. Treatment duration was 23.8 ± 14.4 (mean ± SD) months. A positive response, that is either a clinically relevant recovery (CRR) or a clinically relevant stabilization (CRS), occurred in 53% and 11% of the patients, respectively. The magnitude of CRR was 0.41 ± 1.54 logMAR. CRR of visual acuity is associated with recovery of colour discrimination. The thickness of both the ganglion cell complex (GCC) and the retinal nerve fibre layer (RNFL) is irreversibly reduced.

CONCLUSION

Our results confirm that idebenone may help to restore or maintain visual function. Whether this effect will persist is still unknown. Thinning of retinal neural tissue appears to be permanent.

Clinical Reasoning: A 31-Year-Old Man With Sequential Vision Loss

A 31-year-old healthy White man experienced painless sequential vision loss. Brain imaging and laboratory investigations for infectious, inflammatory, and nutritional conditions, in addition to targeted genetic testing for Leber hereditary optic neuropathy (LHON), were all normal or negative. Despite systemic corticosteroid therapy and plasma exchange, vision continued to worsen. Eventually, mitochondrial whole-genome sequencing was performed, which demonstrated a mutation at the 13513G>A position confirming the diagnosis of LHON. The three primary mutations (11778G>A, 14484T>C, and 3460G>A) account for 90% of LHON cases; therefore, it is important to consider whole-genome mitochondrial sequencing in cases with a high index of clinical suspicion and negative primary mutation screening testing.

Management of biobanking for medical genetics research

Biobanking is one of the most important elements of the modern infrastructure for biomedical research. Organization of a biobank on the basis of the N. P. Bochkov Medical Genetics Research Center provides a centralized infrastructure for preparing biomaterial for research. Biobank has the format of a research equipment sharing center and works with two types of unique biomaterials from patients with genetic diseases: blood/blood components and vital cells of various tissue origin. The storage facility of the Biobank is equipped with low-temperature (-80° C) and cryostorage (-196° C) systems. Identification and search of samples is carried out using a bar-coding system and is implemented through the information interface of the biobank, which is integrated into the general database of patients at the Medical Genetics Research Center. Information on biomaterial samples is presented in periodically updated catalogs on the page of equipment sharing center “Biobank”. Biobank collection is available to internal and external users.

[Leber's hereditary optic neuropathy clinical features in patients with mitochondrial DNA m.13513G>A candidate mutation]

Leber's hereditary optic neuropathy (LHON) is caused by primary mtDNA by both primary mtDNA mutations and new mtDNA mutations. The last ones, when detected in several independent LHON families, receive candidate status. The description of new LHON-associated mtDNA mutation is relevant.

PURPOSE

To determine the LHON clinical features in patients with the m.13513G>A mutation and to estimate the patients' proportion with this pathogenic variant in the LHON patients' sample.

MATERIAL AND METHODS

The study included 5 LHON patients, associated with m.13513G>A mutation in the ND5 gene in the heteroplasmic state. A standard examination was performed, including color blindness test, visual fields test, spectral optical coherence tomography.

RESULTS

LHON, associated with m.13513G>A in the heteroplasmic state in the range of 25-60%, is characterized by visual impairment without additional neurological or other extraocular symptoms. Visual recovery to 0.3-1.0 presents in all patients; the visual recovery onset occurs between 12 and 20 months from the disease manifestation. The decrease of the central scotoma size and its density and the color vision improvement are also observed as well as the average retinal nerve fibers layer and ganglion cell complex thickness decrease. The m.13513G>A mutation frequency is 5% in 100 LHON patients' sample and 22.5% in 22 LHON patients with rare and candidate mtDNA mutations.

CONCLUSION

The m.13513G>A mutation can be considered as primary LHON mutation. The list of pathogenic variants recommended for testing LHON can include this mutation. The m.13513 G>A mutation determines the mild LHON course and good visual functions prognosis in these patients.

[Inherited retinal dystrophy: first results of RPE65 gene replacement therapy in Russia]

PURPOSE

To present the main aspects of interdisciplinary diagnostics of patients with hereditary retinal diseases and the first results of the follow-up of patients with inherited retinal dystrophies (IRD) caused by biallelic mutations in the gene RPE65 after gene replacement therapy in Russia.

MATERIAL AND METHODS

The cohort of patients consisted of six children (5-15 years old) with the diagnosis of Leber amaurosis type 2. All patients underwent a multi-disciplinary examination using conventional clinical, instrumental and molecular-genetic methods. Genetic diagnosis was established based on the results of two-stage DNA diagnostics using high-performance parallel sequencing of a custom panel and family segregation analysis by Sanger sequencing.

RESULTS

In the Research Centre for Medical Genetics the first group of Russian patients with an orphan inherited retinal disease was verified, they underwent subretinal injection of the gene replacement drug Voretigene neparvovec (12 eyes) in the Helmholtz National Medical Research Center of Eye Diseases. According to the regulated terms of monitoring gene therapy patients, they were examined in the Research Centre for Medical Genetics after 1, 3, 6 and 12 months, and then once per year. Thus, the available data allows us to analyze the first results 3 months after the treatment.

CONCLUSION

The presented data on inherited retinal dystrophies caused by biallelic mutations in the RPE65 gene emphasize the need to change the diagnostic algorithm in the ophthalmic practice. The use of clinical instrumental and molecular genetic diagnostic methods makes it possible to apply etiotropic treatment to patients with a disabling disease that was previously considered untreatable. The gene replacement drug Voretigene neparvovec registered in Russia showed irrefutable first positive results in all targeted patients.

Leber's Hereditary Optic Neuropathy: A Report on Novel mtDNA Pathogenic Variants

Leber's hereditary optic neuropathy (LHON) is due to missense point mutations affecting mitochondrial DNA (mtDNA); 90% of cases harbor the m.3460G>A, m.11778G>A, and m.14484T>C primary mutations. Here, we report and discuss five families with patients affected by symptomatic LHON, in which we found five novel mtDNA variants. Remarkably, these mtDNA variants are located in complex I genes, though without strong deleterious effect on respiration in cellular models: this finding is likely linked to the tissue specificity of LHON. This study observes that in the case of a strong clinical suspicion of LHON, it is recommended to analyze the whole mtDNA sequence, since new rare mtDNA pathogenic variants causing LHON are increasingly identified.

A high mutation load of m.14597A>G in MT-ND6 causes Leigh syndrome

Leigh syndrome (LS) is an early-onset progressive neurodegenerative disorder associated with mitochondrial deficiency. m.14597A>G (p.Ile26Thr) in the MT-ND6 gene was reported to cause Leberʼs hereditary optic neuropathy (LHON) or dementia/dysarthria. In previous reports, less than 90% heteroplasmy was shown to result in adult-onset disease. Here, by whole mitochondrial sequencing, we identified m.14597A>G mutation of a patient with LS. PCR–RFLP analysis on fibroblasts from the patient revealed a high mutation load (> 90% heteroplasmy). We performed functional assays using cybrid cell models generated by fusing mtDNA-less rho0 HeLa cells with enucleated cells from patient fibroblasts carrying the m.14597A>G variant. Cybrid cell lines bearing the m.14597A>G variant exhibited severe effects on mitochondrial complex I activity. Additionally, impairment of cell proliferation, decreased ATP production and reduced oxygen consumption rate were observed in the cybrid cell lines bearing the m.14597A>G variant when the cells were metabolically stressed in medium containing galactose, indicating mitochondrial respiratory chain defects. These results suggest that a high mutation load of m.14597A>G leads to LS via a mitochondrial complex I defect, rather than LHON or dementia/dysarthria.

[New possibilities in diagnosis of hereditary optic neuropathies]

The study analyses data from clinical and genetic examination of 114 patients, as well as examination of cytological skin fibroblasts of 20 patients with hereditary optic neuropathy (HON). The clinical examination revealed HON symptoms in all study patients, primary damage of the retinal ganglion cells accompanied by swelling of the peripapillary retinal nerve fiber layer (RNFL) in the acute stage of the disease was observed in 47% of cases. MtDNA mutations that cause the development of Leber hereditary optic neuropathy (LHON) were detected in 73% of cases, including three frequent mutations in 59% of cases, rare and candidate mutations - in 14% of cases; nDNA mutations associated with autosomal dominant optic neuropathy (ADON) - in 6.1% of cases; mutations in the DNAJC30 nDNA gene that caused autosomal recessive optic neuropathy (ARON) - in 21% of cases. Among patients with a clinical picture of LHON, mtDNA mutations were found in 77.6% of cases, while mutations of the DNAJC30 gene of nDNA - in 22.4% of cases. Cytological studies using high-resolution respirometry confirmed the presence of mitochondrial dysfunction not only in the cells of patients harboring pathogenic mutations, but also of those harboring candidate mutations. An algorithm for clinical and genetic verification of HON together with a set of cytological studies allows identification of the mitochondrial genesis of the disease and is indispensable in confirming the pathogenicity of new or candidate mutations.

In silico model of mtDNA mutations effect on secondary and 3D structure of mitochondrial rRNA and tRNA in Leber's hereditary optic neuropathy

The Leber's hereditary optic neuropathy (LHON) is a rare disease caused by mitochondrial DNA (mtDNA) mutations. Beside primary mutations, the effect of secondary mtDNA mutations in still unclear. We examined the effect of secondary mtDNA mutations on secondary structure of different mitochondrial RNAs. Whole mitochondrial genome sequence of LHON patients has been obtained from in six non related pedigrees by Sanger sequencing method. The effect of mutations located in mitochondrial RNA genes was examined by creating in silico models of RNA secondary and regional 3D structure, accompanied by sequence conservation analysis. All three primary LHON mutations (m.3460G>A, m.11778G>A and m.14484 T>C) were revealed in study families. Four mutations in MT-RNR1 gene (m.750A>G, m.956delC, m.1438A>G and m.1555A>G) were identified and only an m.1555A>G causes significant changes of secondary structure of mitochondrial 12S ribosomal RNA (rRNA), while it is the only mutation which does not alter its 3D structure. Five mutations (m.1811A>G, m.2706A>G, m.2831G>A, m.3010G>A and m.3197T>C) were discovered in MT-RNR2 gene and all of them induced substantial alterations of mitochondrial 16S rRNA secondary structure. Significant changes of mitochondrial 16S rRNA 3D structure are caused by m.1811A>G, m.2706A>G, m.3010G>A and m.3197T>C. A single insertion variant (m.15986insG) has been found in the MT-TP gene which encodes mitochondrial transfer RNA for Proline (tRNA Pro). This mutation does not cause substantial changes of tRNA for Proline secondary structure, while the 3D geometry remains without major changes. Most of the mutation loci exhibited high level of sequence conservation. Presence of multiple mutations in a single family appears to cause more extensive changes in mitochondrial 12S and 16S rRNA, then their individual influence. The effect of discovered mutations on in silico modelled RNA structure is in a significant correlation with the present knowledge about the potential of these mutation to participate in the pathophysiology of LHON and other human diseases. The presence of certain multiple mitochondrial RNA mutations could be a possible explanation of LHON clinical presentation in some families. All revealed mutations have been evaluated for the first time in terms of in silico structural modelling. The application of bioinformatics tools such as secondary and 3D RNA structure prediction can have a great advantage in better understanding of the molecular standpoint of the LHON pathophysiology and clinical phenotype.

Whole Mitochondrial Genome Analysis in Serbian Cases of Leber's Hereditary Optic Neuropathy

Leber’s hereditary optic neuropathy (LHON) is a maternally inherited disorder that affects central vision in young adults and is typically associated with mitochondrial DNA (mtDNA) mutations. This study is based on a mutational screening of entire mtDNA in eight Serbian probands clinically and genetically diagnosed with LHON and four of their family members, who are asymptomatic mutation carriers. All obtained sequence variants were compared to human mtDNA databases, and their potential pathogenic characteristics were assessed by bioinformatics tools. Mitochondrial haplogroup analysis was performed by MITOMASTER. Our study revealed two well-known primary LHON mutations, m.11778G>A and m.3460G>A, and one rare LHON mutation, m.8836A>G. Various secondary mutations were detected in association with the primary mutations. MITOMASTER analysis showed that the two well-known primary mutations belong to the R haplogroup, while the rare LHON m.8836A>G was detected within the N1b haplogroup. Our results support the need for further studies of genetic background and its role in the penetrance and severity of LHON.