Heteroplasmy Levels Research Articles

High frequency of mitochondrial DNA rearrangements in the peripheral blood of adults with intellectual disability.

Mitochondrial DNA (mtDNA) rearrangements are recognised factors in mitochondrial disorders and ageing, but their involvement in neurodevelopmental disorders, particularly intellectual disability (ID) and autism spectrum disorder (ASD), remains poorly understood. Previous studies have reported mitochondrial dysfunction in individuals with both ID and ASD. The aim of this study was to investigate the prevalence of large-scale mtDNA rearrangements in ID and ID with comorbid ASD (ID-ASD). We used mtDNA-targeted next-generation sequencing and the MitoSAlt high-throughput computational pipeline in peripheral blood samples from 76 patients with ID (mean age 52.5years, 37% female), 59 patients with ID-ASD (mean age 41.3years, 46% female) and 32 healthy controls (mean age 42.4years, 47% female) from Catalonia. The study revealed a high frequency of mtDNA rearrangements in patients with ID, with 10/76 (13.2%) affected individuals. However, the prevalence was significantly lower in patients with ID-ASD 1/59 (1.7%) and in HC 1/32 (3.1%). Among the mtDNA rearrangements, six were identified as deletions (median size 6937bp and median heteroplasmy level 2.3%) and six as duplications (median size 10 455bp and median heteroplasmy level 1.9%). One of the duplications, MT-ATP6 m.8765-8793dup (29bp), was present in four individuals with ID with a median heteroplasmy level of 3.9%. Our results show that mtDNA rearrangements are frequent in patients with ID, but not in those with ID-ASD, when compared to HC. Additionally, MitoSAlt has demonstrated high sensitivity and accuracy in detecting mtDNA rearrangements, even at very low heteroplasmy levels in blood samples. While the high frequency of mtDNA rearrangements in ID is noteworthy, the role of these rearrangements is currently unclear and needs to be confirmed with further data, particularly in post-mitotic tissues and through age-matched control studies.

Endocrine disorders in Kearns-Sayre syndrome with different severity of symptoms: two case reports and a literature review.

Kearns-Sayre Syndrome (KSS) is a variant of mitochondrial disorder caused by a Mitochondrial Deoxyribonucleic Acid (mtDNA) deletion. Clinical manifestations of KSS can include different organ and system involvement. Different organ malfunctions, more often cardiac dysfunction, can lead to death. No effective treatment of this condition exists to date. Here, we report two patients with KSS. Female patient with a large-scale deletion of 7,020 base pairs (bp) suffered from hypogonadism, diabetes mellitus with fluctuating glucose levels, and had poor general health. A male patient with a common 4,977 bp deletion did not have diabetes mellitus but had impaired glucose tolerance. He also had a higher level of general health than our female patient. Both patients had reduced Bone Mineral Density (BMD). In female patients, calcium and vitamin D supplementation combined with metabolic therapy and nutritional drink supplements helped increase BMD (up to 32% in L1-L4). Comparing these two patients suggests that the larger the mtDNA deletion is, the more severe the course of the disease is. Not only does the size of the mtDNA deletion probably determine the severity of the disease, but also such factors as mtDNA heteroplasmy level, presence of mtDNA duplications, and pleioplasmy. Moreover, continuous nonconsecutive metabolic therapy and nutritional supplements are helpful in the prevention of deterioration of symptoms and general health.

Targeted nanopore sequencing using the Flongle device to identify mitochondrial DNA variants

Variants in mitochondrial genomes (mtDNA) can cause various neurological and mitochondrial diseases such as mitochondrial myopathy, encephalopathy, lactic acidosis, stroke-like episodes (MELAS). Given the 16 kb length of mtDNA, continuous sequencing is feasible using long-read sequencing (LRS). Herein, we aimed to show a simple and accessible method for comprehensive mtDNA sequencing with potential diagnostic applications for mitochondrial diseases using the compact and affordable LRS flow cell “Flongle.” Whole mtDNA amplification (WMA) was performed using genomic DNA samples derived from four patients with mitochondrial diseases, followed by LRS using Flongle. We compared these results to those obtained using Cas9 enrichment. Additionally, the accuracy of heteroplasmy rates was assessed by incorporating mtDNA variants at equimolar levels. Finally, mtDNA from 19 patients with Parkinson’s disease (PD) was sequenced using Flongle to identify disease risk-associated variants. mtDNA variants were detected in all four patients with mitochondrial diseases, with results comparable to those obtained from Cas9 enrichment. Heteroplasmy levels were accurately detected (r2 > 0.99) via WMA using Flongle. A reported variant was identified in three patients with PD. In conclusion, Flongle can simplify the traditionally cumbersome and expensive mtDNA sequencing process, offering a streamlined and accessible approach to diagnosing mitochondrial diseases.

Analysis of Mutational Burden of Mitochondrial Genome in Cells of Different Human Organs and Tissues.

Cells of different human organs and tissues contain different numbers of mitochondria. In these organelles, there are different copies of the mitochondrial genome, which is characteristic of a certain organ or tissue. The aim of the investigation was to analyze the results of scientific works dedicated to the analysis of heteroplasmy levels of mitochondrial genome mutations in a number of organs and tissues. Based on literature data, the level of heteroplasmy of mitochondrial genome mutations was analyzed in organs such as the liver, lungs, muscles, small intestine, large intestine, spleen, kidney, brain, heart, and hair. In addition, this parameter was studied in such tissues as leukocytes, buccal epithelium, and epithelial cells from urine. Significant differences in the mutational burden of the mitochondrial genome were found in various samples of organs and tissues. The highest heteroplasmy level for mtDNA mutations was in muscles; it was lower in buccal epithelium; and in human blood cells, the heteroplasmy level of mitochondrial mutations turned out to be significantly lower compared to other tissues. During the comparison of samples of patients with different diseases and healthy people, significant differences were found in the heteroplasmy level between some organs and tissues. The heteroplasmy level of mitochondrial genome mutations can significantly differ in the organs and tissues of individuals. In addition, in a number of literature sources, it is noted that there is a dependence on the mutational burden of the mitochondrial genome from the type of disease, sex, and age of a person.

Variability of Mitochondrial DNA Heteroplasmy: Association with Asymptomatic Carotid Atherosclerosis.

Background and Objectives: Atherosclerosis is one of the main reasons for cardiovascular disease development. This study aimed to analyze the association of mtDNA mutations and atherosclerotic plaques in carotid arteries of patients with atherosclerosis and conditionally healthy study participants from the Novosibirsk region. Methods: PCR fragments of DNA containing the regions of 10 investigated mtDNA mutations were pyrosequenced. The heteroplasmy levels of mtDNA mutations were analyzed using a quantitative method based on pyrosequencing technology developed by M. A. Sazonova and colleagues. Results: In the analysis of samples of patients with atherosclerotic plaques of the carotid arteries and conditionally healthy study participants from the Novosibirsk region, four proatherogenic mutations in the mitochondrial genome (m.5178C>A, m.652delG, m.12315G>A and m.3256C>T) and three antiatherogenic mutations in mtDNA (m.13513G>A, m.652insG, and m.14846G>A) were detected. A west-east gradient was found in the distribution of the mtDNA mutations m.5178C>A, m.3256C>T, m.652insG, and m.13513G>A. Conclusions: Therefore, four proatherogenic mutations in the mitochondrial genome (m.5178C>A, m.652delG, m.12315G>A, and m.3256C>T) and three antiatherogenic mutations in mtDNA (m.13513G>A, m.652insG, and m.14846G>A) were detected in patients with atherosclerotic plaques in their carotid arteries from the Novosibirsk region.

A de novo novel variant in the MT-TD gene is associated with prominent extra-neurologic manifestations.

Defects in the mitochondrial tRNA genes cause a group of highly clinically and genetically heterogeneous disorders, which poses a challenge for clinical identification and genetic diagnosis. Here, we present a pre-school boy with a novel MT-TD variant m.7560T>C at the heteroplasmy level of 76.53% in blood, 93.34% in urine sediments, and absent in the healthy mother's blood and urine. Besides convulsions, brain magnetic resonance imaging abnormalities and high plasma lactate, the boy presented with the prominent extra-neurologic phenotype including steroid-resistant nephrotic syndrome associated with focal segmental glomerulosclerosis characterized by abnormal mitochondria in podocytes, cortical blindness, and pancreatitis. To our knowledge, this is the unique case with MT-TD m.7560T>C-related multi-organ impairments, which expands the phenotypic and mutational spectrum of primary mitochondrial diseases.

Mitochondrial DNA mosaicism in normal human somatic cells

Somatic cells accumulate genomic alterations with age; however, our understanding of mitochondrial DNA (mtDNA) mosaicism remains limited. Here we investigated the genomes of 2,096 clones derived from three cell types across 31 donors, identifying 6,451 mtDNA variants with heteroplasmy levels of ≳0.3%. While the majority of these variants were unique to individual clones, suggesting stochastic acquisition with age, 409 variants (6%) were shared across multiple embryonic lineages, indicating their origin from heteroplasmy in fertilized eggs. The mutational spectrum exhibited replication-strand bias, implicating mtDNA replication as a major mutational process. We evaluated the mtDNA mutation rate (5.0 × 10−8 per base pair) and a turnover frequency of 10–20 per year, which are fundamental components shaping the landscape of mtDNA mosaicism over a lifetime. The expansion of mtDNA-truncating mutations toward homoplasmy was substantially suppressed. Our findings provide comprehensive insights into the origins, dynamics and functional consequences of mtDNA mosaicism in human somatic cells.

Assessment of Aminoglycoside-Induced Hearing Loss Risk in the Perinatal Period.

This study aimed to determine the prevalence and heteroplasmy level(s) of MT-RNR1 variants m.1555A > G and m.1494C > T, which are associated with aminoglycoside-induced hearing loss, in a general perinatal population. This study also aimed to characterize the association of these variants and their heteroplasmy levels with hearing loss outcomes with and without aminoglycoside exposure. Droplet digital polymerase chain reaction was performed on 479 maternal DNA samples from a general perinatal biobank at our institution to detect the presence and heteroplasmy levels of MT-RNR1 variants m.1555A > G and m.1494C > T. Testing of paired neonatal specimen(s) was planned for positive maternal tests. A retrospective chart review was performed to characterize the population, identify aminoglycoside exposures, and determine hearing outcomes. All maternal samples tested negative for MT-RNR1 variants m.1555A > G and m.1494C > T. Maternal and neonatal subjects had high rates of aminoglycoside exposure (15.9 and 13.9%, respectively). No subjects with sensorineural or mixed hearing loss had documented aminoglycoside exposure. This study demonstrated that a larger sample size is needed to establish the prevalence of these variants as no subjects tested positive. Determination of variant prevalence in the neonatal population, association of variant heteroplasmy levels with hearing outcomes, and reliability of maternal testing as a surrogate for neonatal testing are important next steps toward universal prenatal or newborn screening. · MT-RNR1 variants are associated with aminoglycoside-induced hearing loss.. · Prevalence of MT-RNR1 variants is uncertain.. · Universal screening for MT-RNR1 variants may be indicated..

O-275 Prenatal genetic screening to assess mtDNA disease occurrence in children

Abstract Study question Can prenatal genetic testing accurately predict mtDNA mutation load anddisease transmission to children for families affected by Leigh Syndrome? Summary answer Whole genome mtDNA sequencing for 13513G>A mutation in chorionic villi and amniotic fluid was similar to those measured in babies suggesting accuracy of disease prediction. What is known already Severity of mtDNA disease in children depends on heteroplasmy levels(proportion of mutant to wild-type mtDNA). There is a minimum threshold for the mutant mtDNA heteroplasmy (typically 60%) above which oxidative metabolism is impaired to cause disease. Predicting the disease based on the mutation load measured during embryonic or fetal development is critically needed. However, preimplantation genetics screening for many mtDNA mutations has limitations due to the potential increase in heteroplasmy levels after implantation. We hypothesized that prenatal screening of chorionic villi and/or amniotic fluid during the first trimester of pregnancy could provide more reliable diagnosis of disease occurrence in children. Study design, size, duration We evaluated mtDNA heteroplasmy in biopsies collected from chorionic villi and amniotic fluid at 10- and 16-weeks of gestation, respectively, for two consecutive, naturally conceived pregnancies for a carrier of 13513G>A mutation. Sequencing results were compared to mutations in the blood, skin, and urine of children after birth. Both children were also extensively monitored for a few years for disease occurrence. Participants/materials, setting, methods A family with maternally transmitted Leigh Syndrome including both parents and two existing children were enrolled during the initial phase. Whole mtDNA sequencing was used to confirm the maternal transmission of the mutation by analysis of blood, skin, and urine from asymptomatic parents and the older son and the severely affected younger son. Furthermore, prenatal diagnostics were performed for two consecutive pregnancies and children after birth. Main results and the role of chance The mother carried 13513G>A mutation in the skin (91% heteroplasmy), urine(39%), and blood (6.8%), while no mutation was detected in the father’s samples. The asymptomatic eldest child revealed a low mutation in the skin (14%), urine(23%), and blood (10%). While the younger son diagnosed with Leigh syndrome carried 56% mutation in blood, 86% in skin, and 97% in urine. Heteroplasmy ranging from 0.6% to 40% was also measured in 4 individual immature oocytes retrieved upon hormonal stimulation of the carrier. The family later naturally conceived 2 consecutive pregnancies and requested help with prenatal diagnostics. In the first pregnancy, mutation loads were 27.5% in chorionic villi and 29.5% in amniotic fluid. The family decided to keep the pregnancy which resulted in the birth of a healthy child with low mutations in blood (0.07%) and skin (14.5%). In the second pregnancy, prenatal diagnostics in CVS showed low mutation at 0.11%, resulting in the birth of an unaffected child with mutation loads of 1.4% in blood and 0% in skin. Limitations, reasons for caution Genetic counseling for mtDNA disease transmission is difficult due tocomplex inheritance of heteroplasmic variants for various pathogenicmutations. Inheritance and distribution of mtDNA mutations also influencedby individual family genetics. Therefore, prenatal diagnostic screeningshould be cautiously considered based on the specific circumstances for eachfamily. Wider implications of the findings Prenatal genetic diagnostics for families with mtDNA disease based on whole mtDNA sequencing by the qualified laboratory may accurately predict heteroplasmy levels and disease occurrence in children. However, careful analysis of family history and the likelihood of having low mutation load oocytes was critical for the success of our case. Trial registration number N/A

O-270 Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing

Abstract Study question Can a simple, and scalable assay be developed to concurrently perform all forms of preimplantation genetic testing (PGT), effectively addressing the increasing demand? Summary answer Whole genome sequencing-based haplarithmisis offers a single-assay solution for all forms of PGT, enhancing resolution and diagnosis in complex cases. What is known already State-of-the-art preimplantation genetic testing (PGT) methods, including genotyping-by-sequencing (GBS)-based haplotyping, enable PGT for monogenic disorders (PGT-M), structural rearrangements (PGT-SR), and aneuploidies (PGT-A) in a single assay. However, they are labour intensive, only partially cover the genome, require a close relative to determine meiotic and mitotic origin of aneuploidies, and are troublesome for consanguineous families and in complex genomic contexts. Furthermore, the prevailing PGT approach for mitochondrial DNA disorders (PGT-MT) involves a PCR-based method. This underscores the need to develop a universal PGT method that streamlines laboratory protocols and provides genome-wide coverage to address genetic disorders, even in complex genomic loci. Study design, size, duration In a retrospective pilot study, we compared whole genome sequencing (WGS) at 30-40X with GBS (6 embryos, 2 families, 3 indications). We carried out subsampling of WGS data and determined 10X as the optimal diagnostic depth-of-coverage. We clinically validated our approach by comparing WGS to GBS for PGT-M and PGT-SR (31 embryos, 16 families, 22 indications), to shallow sequencing for PGT-SR (10 embryos, 3 families) and to PCR-based PGT for PGT-MT (10 embryos, 2 families). Participants/materials, setting, methods DNA from parents and close relative(s) and whole genome amplified (WGAed) DNA from embryos, underwent WGS with subsequent haplarithmisis. Quality metrics, such as Mendelian inconsistency rates, number of informative SNPs, and haplotype concordance were assessed. Translocation breakpoints were identified utilizing aberrantly aligned paired sequencing reads. Additionally, single-nucleotide variants (SNVs), including mitochondrial DNA SNVs, were detected by allele counting. Finally, segregational origin was determined via a parents-only haplarithmisis approach that uses the embryo as phasing reference. Main results and the role of chance WGS-PGT alleviates technical limitations by decreasing WGA artifacts by 68.4%, increasing breadth of coverage by 4-fold, and decreasing wet-lab turnaround time by 2.5-fold. Owing to its inherent higher resolution and improved genomic coverage, 5 out of 13 – previously inconclusive – embryos with genetic disorders in complex genomic regions could be assigned a diagnosis. Furthermore, we show the ability to directly detect single- and few-base pair genetic variants in any region of interest. Importantly, we show trio-based PGT-A for aneuploidy origin, an approach we term PGT-AO that – using the parents-only genotype calls – can detect the segregational origin of aneuploidies without the need of a close relative as reference for phasing. The segregational origin detected by parents-only haplarithmisis was concordant with the segregational origin determined from haplarithmisis when using a close relative. Unbalanced translocations could be detected indirectly via haplotyping or directly at single base resolution using a structural variant caller. Mitochondrial heteroplasmy level calculation from WGS yielded comparable results to PCR-based methods, both in blastomere and trophectoderm biopsy samples. Limitations, reasons for caution Direct variant detection with an average coverage of 10X may occasionally be inadequate, as certain locations may lack sufficient coverage (<5 reads). Inherently to the limited sample size of PGT-MT families, WGS-PGT needs further validation. The need for invasive trophectoderm biopsies of preimplantation embryos remains the key limitation of WGS-PGT. Wider implications of the findings Our approach enables all forms of PGT in a single assay. Direct variant detection complements haplarithmisis, addressing inconclusive findings and aiding families with a de novo variant or lacking a close relative for phasing. Finally, PGT-AO facilitates research on the origin of aneuploidies in preimplantation embryos and their clinical outcome. Trial registration number not applicable

The establishment of a molecular diagnostic platform for mitochondrial diseases: from conventional to next-generation sequencing

BackgroundThe aim of this study was to create a molecular diagnostic platform and establish a diagnostic pipeline for patients highly suspected of mitochondrial disorders. The effectiveness of three methods, namely, traditional restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR), Sanger sequencing for hotspot detection and whole mitochondrial DNA (mtDNA), and third-generation (Nanopore) whole mtDNA sequencing, will be compared in diagnosing patients with suspected primary mitochondrial diseases (PMDs). The strengths and limitations of different methods are also discussed. Material and methodsA single-center prospective cohort study was conducted to validate the diagnostic pipeline for suspected mitochondrial diseases. In the first stage, a PCR-based method with five sets of primers was used to screen for eight hotspots (m.3243A>G, m.3460G>A, m.8344A>G, m.8993T>G, m.9185T>C, m.11778G>A, m.13513G>A, and m.4977deletion) using either RFLP or direct Sanger sequencing. Sanger sequencing was also used to confirm the RFLP-positive samples. In the second stage, for samples with negative screening results for the eight hotspots, mitochondrial whole-genome sequencing was performed using Sanger sequencing or third-generation nanopore sequencing. ResultsBetween June 2020 and May 2023, 30 patients from ages 0 to 63 with clinically suspected mitochondrial disease were enrolled. The positive yield for the diagnosis of PMDs was 8/30=26.7%, and the sensitivity of the heteroplasmy level for the RFLP-based method was approximately 5%. The remaining 22 patients who tested negative at the first stage were tested using Sanger sequencing or the third-generation sequencing Nanopore, and all tested negative for pathological mtDNA mutations. Compared to the Sanger sequencing method, the results of RFLP-PCR were compromised by the limitations of incomplete RFLP enzyme digestion. For whole-genome sequencing of mtDNA, Sanger sequencing, instead of nanopore sequencing, is preferred at our institution because of its cost-effectiveness. Conclusions: In our highly selective cohort, most tested positive in the first stage of the 8 hot spots screen. Sanger sequencing is a conventional and accurate method for mitochondrial disease screening, at least for the most common hot spots in the region. The results revealed that Sanger sequencing is an accurate method with the benefit of being more cost-effective. This integral platform of molecular diagnosis bears the advantages of being relatively low cost and having a shorter reporting time, facilitating crucial identification of patients with clinical evidence of such disorders. This diagnostic flowchart has also been translated into routine clinical use in the tertiary hospital.

Spectrum of rare and common mitochondrial DNA variations from 1029 whole genomes of self-declared healthy individuals from India

Mitochondrial disorders are a class of heterogeneous disorders caused by genetic variations in the mitochondrial genome (mtDNA) as well as the nuclear genome. The spectrum of mtDNA variants remains unexplored in the Indian population. In the present study, we have cataloged 2689 high confidence single nucleotide variants, small insertions and deletions in mtDNA in 1029 healthy Indian individuals. We found a major proportion (76.5 %) of the variants being rare (AF<=0.005) in the studied population. Intriguingly, we found two ‘confirmed’ pathogenic variants (m.1555 A>G and m.14484 T>C) with a frequency of ∼1 in 250 individuals in our dataset. The high carrier frequency underscores the need for screening of the mtDNA pathogenic mutations in newborns in India. Interestingly, our analysis also revealed 202 variants in our dataset which have been ‘reported’ in disease cases as per the MITOMAP database. Additionally, we found the frequency of haplogroup M (52.2 %) to be the highest among all the 18 top-level haplogroups found in our dataset. In comparison to the global population datasets, 20 unique mtDNA variants are found in the Indian population. We hope the whole genome sequencing based compendium of mtDNA variants along with their allele frequencies and heteroplasmy levels in the Indian population will drive additional genome scale studies for mtDNA. Furthermore, the identification of clinically relevant variants in our dataset will aid in better clinical interpretation of the variants in mitochondrial disorders.

Limited variation in microbial communities across populations of Macrosteles leafhoppers (Hemiptera: Cicadellidae).

Microbial symbionts play crucial roles in insect biology, yet their diversity, distribution, and temporal dynamics across host populations remain poorly understood. In this study, we investigated the spatio-temporal distribution of bacterial symbionts within the widely distributed and economically significant leafhopper genus Macrosteles, with a focus on Macrosteles laevis. Using host and symbiont marker gene amplicon sequencing, we explored the intricate relationships between these insects and their microbial partners. Our analysis of the cytochrome oxidase subunit I (COI) gene data revealed several intriguing findings. First, there was no strong genetic differentiation across M. laevis populations, suggesting gene flow among them. Second, we observed significant levels of heteroplasmy, indicating the presence of multiple mitochondrial haplotypes within individuals. Third, parasitoid infections were prevalent, highlighting the complex ecological interactions involving leafhoppers. The 16S rRNA data confirmed the universal presence of ancient nutritional endosymbionts-Sulcia and Nasuia-in M. laevis. Additionally, we found a high prevalence of Arsenophonus, another common symbiont. Interestingly, unlike most previously studied species, M. laevis exhibited only occasional cases of infection with known facultative endosymbionts and other bacteria. Notably, there was no significant variation in symbiont prevalence across different populations or among sampling years within the same population. Comparatively, facultative endosymbionts such as Rickettsia, Wolbachia, Cardinium and Lariskella were more common in other Macrosteles species. These findings underscore the importance of considering both host and symbiont dynamics when studying microbial associations. By simultaneously characterizing host and symbiont marker gene amplicons in large insect collections, we gain valuable insights into the intricate interplay between insects and their microbial partners. Understanding these dynamics contributes to our broader comprehension of host-microbe interactions in natural ecosystems.

Pharmacogénétique de l’ototoxicité des aminosides : état des connaissances et des pratiques – recommandations du Réseau francophone de pharmacogénétique (RNPGx)

The administration of aminoglycosides can induce nephrotoxicity or ototoxicity, which can be monitored through pharmacological therapeutic drug monitoring. However, there are cases of genetic predisposition to ototoxicity related to the MT-RNR1 gene, which may occur from the first administrations. Pharmacogenetic analysis recommendations have recently been proposed by the Clinical Pharmacogenetics Implementation Consortium (CPIC). The Francophone Pharmacogenetics Network (RNPGx) provides a bibliographic synthesis of this genetic predisposition, as well as professional recommendations. The MT-RNR1 gene codes for mitochondrial 12S rRNA, which constitutes the small subunit of the mitochondrial ribosome. Three variants can be identified: the variants m.1555A>G and m.1494C>T of the MT-RNR1 gene have a 'high' level of evidence regarding the risk of ototoxicity. The variant m.1095T>C has a 'moderate' level of evidence. The search for these variants can be performed in the laboratory if the administration of aminoglycosides can be delayed after obtaining the result. However, if the treatment is urgent, there is currently no rapid test available in France (a 'point-of-care' test is authorized in Great Britain). RNPGx considers: (1) the search for the m.1555A>G, m.1494C>T variants as 'highly recommended' and the m.1095T>C variant as 'moderately recommended' before the administration of an aminoglycoside (if compatible with the medical context). It should be noted that the level of heteroplasmy detected does not modify the recommendation; (2) pharmacogenetic analysis is currently not feasible in situations of short-term aminoglycoside administration, in the absence of an available analytical solution (rapid test to be evaluated in France); (3) the retrospective analysis in case of aminoglycoside-induced ototoxicity is 'recommended'; (4) analysis of relatives is 'recommended'. Through this summary, RNPGx proposes an updated review of the MT-RNR1-aminoglycoside gene-drug pair to serve as a basis for adapting practices regarding pharmacogenetic analysis related to aminoglycoside treatment.

Exploring mitochondrial heteroplasmy in neonates: implications for growth patterns and overweight in the first years of life.

Mitochondrial heteroplasmy reflects genetic diversity within individuals due to the presence of varying mitochondrial DNA (mtDNA) sequences, possibly affecting mitochondrial function and energy production in cells. Rapid growth during early childhood is a critical development with long-term implications for health and well-being. In this study, we investigated if cord blood mtDNA heteroplasmy is associated with rapid growth at 6 and 12 months and overweight in childhood at 4-6 years. This study included 200 mother-child pairs of the ENVIRONAGE birth cohort. Whole mitochondrial genome sequencing was performed to determine mtDNA heteroplasmy levels (in variant allele frequency; VAF) in cord blood. Rapid growth was defined for each child as the difference between WHO-SD scores of predicted weight at either 6 or 12 months and birth weight. Logistic regression models were used to determine the association of mitochondrial heteroplasmy with rapid growth and childhood overweight. Determinants of relevant cord blood mitochondrial heteroplasmies were identified using multiple linear regression models. One % increase in VAF of cord blood MT-D-Loop16362T > C heteroplasmy was associated with rapid growth at 6 months (OR = 1.03; 95% CI: 1.01-1.05; p = 0.001) and 12 months (OR = 1.02; 95% CI: 1.00-1.03; p = 0.02). Furthermore, this variant was associated with childhood overweight at 4-6 years (OR = 1.01; 95% CI 1.00-1.02; p = 0.05). Additionally, rapid growth at 6 months (OR = 3.00; 95% CI: 1.49-6.14; p = 0.002) and 12 months (OR = 4.05; 95% CI: 2.06-8.49; p < 0.001) was also associated with childhood overweight at 4-6 years. Furthermore, we identified maternal age, pre-pregnancy BMI, maternal education, parity, and gestational age as determinants of cord blood MT-D-Loop16362T > C heteroplasmy. Our findings, based on mitochondrial DNA genotyping, offer insights into the molecular machinery leading to rapid growth in early life, potentially explaining a working mechanism of the development toward childhood overweight.

A novel MT-ATP6 variant associated with complicated ataxia in two unrelated Italian patients: case report and functional studies

BackgroundMT-ATP6 is a mitochondrial gene which encodes for the intramembrane subunit 6 (or A) of the mitochondrial ATP synthase, also known asl complex V, which is involved in the last step of oxidative phosphorylation to produce cellular ATP through aerobic metabolism. Although classically associated with the NARP syndrome, recent evidence highlights an important role of MT-ATP6 pathogenic variants in complicated adult-onset ataxias.MethodsWe describe two unrelated patients with adult-onset cerebellar ataxia associated with severe optic atrophy and mild cognitive impairment. Whole mitochondrial DNA sequencing was performed in both patients. We employed patients’ primary fibroblasts and cytoplasmic hybrids (cybrids), generated from patients-derived cells, to assess the activity of respiratory chain complexes, oxygen consumption rate (OCR), ATP production and mitochondrial membrane potential.ResultsIn both patients, we identified the same novel m.8777 T > C variant in MT-ATP6 with variable heteroplasmy level in different tissues. We identifed an additional heteroplasmic novel variant in MT-ATP6, m.8879G > T, in the patients with the most severe phenotype. A significant reduction in complex V activity, OCR and ATP production was observed in cybrid clones homoplasmic for the m.8777 T > C variant, while no functional defect was detected in m.8879G > T homoplasmic clones. In addition, fibroblasts with high heteroplasmic levelsof m.8777 T > C variant showed hyperpolarization of mitochondrial membranes.ConclusionsWe describe a novel pathogenic mtDNA variant in MT-ATP6 associated with adult-onset ataxia, reinforcing the value of mtDNA screening within the diagnostic workflow of selected patients with late onset ataxias.

Single-cell analysis reveals context-dependent, cell-level selection of mtDNA.

Heteroplasmy occurs when wild-type and mutant mitochondrial DNA (mtDNA) molecules co-exist in single cells1. Heteroplasmy levels change dynamically in development, disease and ageing2,3, but it is unclear whether these shifts are caused by selection or drift, and whether they occur at the level of cells or intracellularly. Here we investigate heteroplasmy dynamics in dividing cells by combining precise mtDNA base editing (DdCBE)4 with a new method, SCI-LITE (single-cell combinatorial indexing leveraged to interrogate targeted expression), which tracks single-cell heteroplasmy with ultra-high throughput. We engineered cells to have synonymous or nonsynonymous complex I mtDNA mutations and found that cell populations in standard culture conditions purge nonsynonymous mtDNA variants, whereas synonymous variants are maintained. This suggests that selection dominates over simple drift in shaping population heteroplasmy. We simultaneously tracked single-cell mtDNA heteroplasmy and ancestry, and found that, although the population heteroplasmy shifts, the heteroplasmy of individual cell lineages remains stable, arguing that selection acts at the level of cell fitness in dividing cells. Using these insights, we show that we can force cells to accumulate high levels of truncating complex I mtDNA heteroplasmy by placing them in environments where loss of biochemical complex I activity has been reported to benefit cell fitness. We conclude that in dividing cells, a given nonsynonymous mtDNA heteroplasmy can be harmful, neutral or even beneficial to cell fitness, but that the 'sign' of the effect is wholly dependent on the environment.

Vitamin B12 status and folic acid supplementation influence mitochondrial heteroplasmy levels in mice.

One-carbon metabolism is a complex network of metabolic reactions that are essential for cellular function including DNA synthesis. Vitamin B12 and folate are micronutrients that are utilized in this pathway and their deficiency can result in the perturbation of one-carbon metabolism and subsequent perturbations in DNA replication and repair. This effect has been well characterized in nuclear DNA but to date, mitochondrial DNA (mtDNA) has not been investigated extensively. Mitochondrial variants have been associated with several inherited and age-related disease states; therefore, the study of factors that impact heteroplasmy are important for advancing our understanding of the mitochondrial genome's impact on human health. Heteroplasmy studies require robust and efficient mitochondrial DNA enrichment to carry out in-depth mtDNA sequencing. Many of the current methods for mtDNA enrichment can introduce biases and false-positive results. Here, we use a method that overcomes these limitations and have applied it to assess mitochondrial heteroplasmy in mouse models of altered one-carbon metabolism. Vitamin B12 deficiency was found to cause increased levels of mitochondrial DNA heteroplasmy across all tissues that were investigated. Folic acid supplementation also contributed to elevated mitochondrial DNA heteroplasmy across all mouse tissues investigated. Heteroplasmy analysis of human data from the Framingham Heart Study suggested a potential sex-specific effect of folate and vitamin B12 status on mitochondrial heteroplasmy. This is a novel relationship that may have broader consequences for our understanding of one-carbon metabolism, mitochondrial-related disease and the influence of nutrients on DNA mutation rates.

Clinical Characteristics of Diabetes in People with Mitochondrial DNA 3243A>G Mutation in Korea.

Maternally inherited diabetes and deafness (MIDD) is a rare mitochondrial disorder primarily resulting from m.3243A>G mutation. The clinical characteristics of MIDD exhibit significant heterogeneity. Our study aims to delineate these characteristics and determine the potential correlation with m.3243A>G heteroplasmy levels. This retrospective, descriptive study encompassed patients with confirmed m.3243A>G mutation and diabetes mellitus at Seoul National University Hospital. Our cohort comprises 40 patients with MIDD, with a mean age at study enrollment of 33.3±12.9 years and an average % of heteroplasmy of 30.0%± 14.6% in the peripheral blood. The most prevalent comorbidity was hearing loss (90%), followed by albuminuria (61%), seizure (38%), and stroke (33%). We observed a significant negative correlation between % of heteroplasmy and age at diabetes diagnosis. These clinical features can aid in the suspicion of MIDD and further consideration of genetic testing for m.3243A>G mutation.

Mitochondrial disorders in patients with familial form of MERRF syndrome

MERRF syndrome (myoclonic epilepsy ragged red fibres) belongs to the group of primary mitochondrial diseases and is characterized by a combination of myoclonic epilepsy and the phenomenon of ragged red fibres on muscle biopsy. The aim of this work is to study mitochondrial disorders in patients from a family with MERRF syndrome by determining the cytochemical activity of mitochondrial enzymes in peripheral blood lymphocytes and the level of lactate in the blood. Clinical cases of a 25-year-old sister and a 19-year-old brother with MERRF syndrome with the m.8344A&gt;G variant in MT-TK (tRNA (Lys)) with a blood heteroplasmy level of 50 % in the sister and homoplasmy in the brother are presented. Mitochondrial disorders were assessed by blood lactate levels and cytochemical studies of mitochondrial enzyme activity in peripheral blood lymphocytes. Pre-prandial blood lactate levels were elevated in both patients. After a carbohydrate load, it increased in the sister, and decreased in the brother. The sister had decreased activity of peripheral blood lymphocyte enzymes while taking levetiracetam, 100 mg of coenzyme Q10 and 100 mg of L-carnitine. The dose of energotropic drugs was increased, which led to an increase in the activity of mitochondrial enzymes. The brother had a compensatory increase in the level of succinate dehydrogenase and a decrease in the activity of other enzymes. The methods we used can be used in clinical practice to diagnose mitochondrial disorders and to adjust the dosage of energotropic drugs, which remain relevant due to the lack of effective gene therapy.