Mitochondrial Variation Research Articles

Association of LONP1 gene with epilepsy and the sub-regional effect

The LONP1 gene encodes Lon protease, which is responsible for degrading damaged or misfolded proteins and binding mitochondrial DNA. Previously, LONP1 variants have been identified in patients with cerebral, ocular, dental, auricular, and skeletal anomalies (CODAS syndrome) and mitochondrial diseases. Seizures were occasionally observed. However, the association between LONP1 and epilepsy remains elusive. In this study, we performed trio-based whole-exome sequencing in a cohort of 450 patients with unexplained epilepsy and identified four pairs of compound heterozygous LONP1 variants in four unrelated cases. All patients exhibited good responses to anti-seizure medications and demonstrated no developmental delay or intellectual disabilities. The variant allele frequencies observed in this study were absent or low in the general population and were significantly lower than those of benign variants. At least one variant in each biallelic pair affected hydrogen bonding and/or altered protein stability. The CODAS syndrome-associated variants were concentrated in the AAA+ module, especially the α domain. Four of the five mitochondrial disease-associated variants were located in the AAA + domain and the NTD5H and NTD3H subdomains. In contrast, each of the biallelic variants from the patients with pure epilepsy had one variant located in the linker domain, and the other variant located in the mitochondrial targeting sequence or P domain. This study suggested that LONP1 gene is potentially a novel candidate gene for pure epilepsy. The phenotypic variation is associated with the sub-regional effects of variants.

Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear

Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears’ mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.

MitoSort: Robust Demultiplexing of Pooled Single-cell Genomics Data Using Endogenous Mitochondrial Variants.

Multiplexing across donors has emerged as a popular strategy to increase throughput, reduce costs, overcome technical batch effects, and improve doublet detection in single-cell genomic studies. To eliminate additional experimental steps, endogenous nuclear genome variants are used for demultiplexing pooled single-cell RNA sequencing (scRNA-seq) data by several computational tools. However, these tools have limitations when applied to single-cell sequencing methods that do not cover nuclear genomic regions well, such as single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq). Here, we demonstrate that mitochondrial germline variants are an alternative, robust, and computationally efficient endogenous barcode for sample demultiplexing. We propose MitoSort, a tool that uses mitochondrial germline variants to assign cells to their donor of origin and identify cross-genotype doublets in single-cell genomics datasets. We evaluate its performance by using in silico pooled mitochondrial scATAC-seq (mtscATAC-seq) libraries and experimentally multiplexed data with cell hashtags. MitoSort achieves high accuracy and efficiency in genotype clustering and doublet detection for mtscATAC-seq data, addressing the limitations of current computational techniques tailored for scRNA-seq data. Moreover, MitoSort exhibits versatility and can be applied to various single-cell sequencing approaches beyond mtscATAC-seq, provided the mitochondrial variants are reliably detected. Furthermore, we demonstrate the application of MitoSort in a case study where B cells from eight donors were pooled and assayed by single-cell multi-omics sequencing. Altogether, our results demonstrate the accuracy and efficiency of MitoSort, which enables reliable sample demultiplexing in various single-cell genomic applications. MitoSort is available at https://github.com/tangzhj/MitoSort.

Neonatal Hemochromatosis Secondary to an Inborn Error of Metabolism (Mitochondrial Disorder): Post- mortem Diagnosis in the Fetus of a Young Primipara

Abstract Introduction/Objective Neonatal hemochromatosis (NH), an extremely rare congenital phenotype of acute hepatic failure with hepatic and extrahepatic siderosis, is primarily (98%) caused by gestational alloimmune liver disease (GALD) and, rarely (2%), by infection, metabolic disorders, bile acid defects, and mitochondrial hepatopathy. This report presents an extremely rare case of NH caused by an inborn error of metabolism (suspected mitochondrial dysfunction). This low-birth-weight female was born with acute liver failure, metabolic acidosis, multisystem failure, and progressive lactate acidosis, and expired on day 7. On autopsy, liver was less than 50% of normal size and without nodularity. Microscopic architecture was preserved with erythropoiesis, canalicular bile plugs, microvesicular steatosis (oil red O stain) and abundant coarsely granular siderosis (iron stain). GALD was unlikely because of the absence of the typical hepatocytic injury, fibrosis or biliary destruction, and the negative immunohistochemistry for MAC (C5b-C9). Extrahepatic siderosis was demonstrated in thyroid follicles, thymic Hassall corpuscles, myocardium, and adenohypophysis. Sanger sequencing and deletion testing of mitochondrial genome on a maternal buccal biopsy identified a homoplasmic variant (m.15482 T>C p.(S246P) in maternal MT-CYB gene but without molecular diagnosis of a mitochondrial DNA disorder. Infant plasma had increased C6DC, C5, C12-OH acylcarnitine, alanine, and proline. Urine contained elevated organic acids (lactate/pyruvate, 2-ketoacids, 3-methylglutarate, 3-methylglutaconate), concerning acute mitochondrial respiratory chain dysfunction. Methods/Case Report: Case Study Results (if a Case Study enter NA) NA Conclusion Diagnosis of NH warrants exclusion of the most common etiology, GALD. Mitochondrial genetic mutations are the most difficult to diagnosis because of heterogeneity and typically undiagnosed maternal defects. This is the first report of NH with a homoplasmic maternal variant of uncertain significance. Neonatal lactic acidosis is the strongest clinical clue for mitochondrial dysfunction and should trigger phenotyping, maternal mitochondrial genetic variants (mtDNA, nuDNA), functional, biochemical, and genetic studies.

Characterization of Nuclear Mitochondrial Insertions in Canine Genome Assemblies

Background: The presence of mitochondrial sequences in the nuclear genome (Numts) confounds analyses of mitochondrial sequence variation, and is a potential source of false positives in disease studies. To improve the analysis of mitochondrial variation in canines, we completed a systematic assessment of Numt content across genome assemblies, canine populations and the carnivore lineage. Results: Centering our analysis on the UU_Cfam_GSD_1.0/canFam4/Mischka assembly, a commonly used reference in dog genetic variation studies, we found a total of 321 Numts located throughout the nuclear genome and encompassing the entire sequence of the mitochondria. A comparison with 14 canine genome assemblies identified 63 Numts with presence–absence dimorphism among dogs, wolves, and a coyote. Furthermore, a subset of Numts were maintained across carnivore evolutionary time (arctic fox, polar bear, cat), with eight sequences likely more than 10 million years old, and shared with the domestic cat. On a population level, using structural variant data from the Dog10K Consortium for 1879 dogs and wolves, we identified 11 Numts that are absent in at least one sample, as well as 53 Numts that are absent from the Mischka assembly. Conclusions: We highlight scenarios where the presence of Numts is a potentially confounding factor and provide an annotation of these sequences in canine genome assemblies. This resource will aid the identification and interpretation of polymorphisms in both somatic and germline mitochondrial studies in canines.

Widespread Wolbachia infection is correlated with increased mtDNA diversity in native bees across the Fijian archipelago

AbstractInsects have a complex coevolutionary history with bacterial symbionts, among which Wolbachia pipientis stands out for its prevalence and role in reproductive manipulation. Wolbachia can induce cytoplasmic incompatibility, feminisation, male killing, and parthenogenesis, greatly influence the population genetics of their hosts and are potential drivers of invertebrate speciation. We might then assume that Wolbachia could act synergistically with other factors, such as niche conservation and isolation by distance, to drive speciation in hyper-diverse invertebrate taxa. The Fijian archipelago hosts a remarkable and recently diverged clade of Lasioglossum (Homalictus) bees. Some of these Lasioglossum have highly unusual species-level sex ratios and mitochondrial diversities, which can be hallmarks of infection by a bacterial reproductive manipulator. To examine the role of Wolbachia in Fijian Lasioglossum speciation, we screened the endemic Fijian bees for Wolbachia using the Wolbachia surface protein gene (wsp). We compare the distribution of Wolbachia infection across species with host mitochondrial haplotype diversity and conducted phylogenetic analyses to determine the relationship of host relatedness and symbiont infection status. We found that Wolbachia haplotypes probably span across supergroups A and B. In addition, we found multiple haplotypes were highly similar, with the most abundant group of wsp haplotypes being closely related with the drosophila Wolbachia strain wHa. We found evidence of mostly horizontal and limited vertical transmission, and little evidence for Wolbachia-host cospeciation. We show that, contrary to general patterns, Wolbachia-infected Lasioglossum species have higher mitochondrial diversity. Finally, we present evidence for the potential of multiple modes of host manipulation in this clade.

Mitochondrial genetic variations in leukemia: a comprehensive overview.

Leukemias are a group of heterogeneous hematological malignancies driven by diverse genetic variations, and the advent of genomic sequencing technologies facilitates the investigation of genetic abnormalities in leukemia. However, these sequencing-based studies mainly focus on nuclear DNAs. Increasing evidence indicates that mitochondrial dysfunction is an important mechanism of leukemia pathogenesis, which is closely related to the mitochondrial genome variations. Here, we provide an overview of current research progress concerning mitochondrial genetic variations in leukemia, encompassing gene mutations and copy number variations. We also summarize currently accessible mitochondrial DNA (mtDNA) sequencing methods. Notably, somatic mtDNA mutations may serve as natural genetic barcodes for lineage tracing and longitudinal assessment of clonal dynamics. Collectively, these findings enhance our understanding of leukemia pathogenesis and foster the identification of novel therapeutic targets and interventions.

Assembly and comparative analysis of the mitochondrial genome in diploid potatoes.

We report the mitochondrial genome of 39 diploid potatoes and identify a candidate ORF potentially linked to cytoplasmic male sterility in potatoes. Potato (Solanum tuberosum L.) holds a critical position as the foremost non-grain food crop, playing a pivotal role in ensuring global food security. Diploid potatoes constitute a vital genetic resource pool, harboring the potential to revolutionize modern potato breeding. Nevertheless, diploid potatoes are relatively understudied, and mitochondrial DNA can provide valuable insights into key potato breeding traits such as CMS. In this study, we examine and assemble the mitochondrial genome evolution and diversity of 39 accessions of diploid potatoes using high-fidelity (HiFi) sequencing. We annotated 54 genes for all the investigated accessions, comprising 34 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. Our analyses revealed differences in repeats sequences between wild and cultivated landraces. To understand the evolution of diploid maternal lineage inheritance, we conducted phylogenetic analysis, which clearly distinguished mitochondrial from nuclear gene trees, further supporting the evidence-based of clustering between wild and cultivated landraces accessions. Our study discovers new candidate ORFs associated with CMS in potatoes, including ORF137, which is homologous to other CMS in Solanaceae. Ultimately, this work bridges the gap in mitochondrial genome research for diploid potatoes, providing a steppingstone into evolutionary studies and potato breeding.

The biogeographic patterns of the olive fly and its primary symbiont Candidatus Erwinia dacicola across the distribution area of the olive tree.

The olive fly, Bactrocera oleae (Rossi, 1790), is the major insect pest of olives attacking both cultivated and wild olive. Bactrocera oleae carries a primary and vertically transmitted symbiont, the bacterium Candidatus Erwinia dacicola. As any primary symbiont, it plays an important role in the reproduction and lifespan of the fly. The genetic 16S rRNA diversity of the primary symbiont and the mitochondrial haplotype variation of the insect host were simultaneously examined in 54 olive fly populations. The aim was to unravel the biogeographic patterns of this economically relevant host-bacteria interaction across a wide distribution area. Three symbiont haplotypes were identified. The primary symbiont showed a lower haplotype diversity than that of its host, a characteristic indicative of a long-term interaction. A significant genetic and geographic association between host and primary symbiont was observed, with an East-West genetic differentiation pattern in the Mediterranean basin, coinciding with the historical genetic distribution of the olive tree. The study shows promise, informing and aiding the development of future tools for the control of the olive fly.

Abstract C169: Investigating the effects of ancestry in KRAS mediated lung adenocarcinoma: Exploring intratumoral heterogeneity and mitochondrial dynamics

Abstract Demonstrating a combination of high prevalence, late detection, and low survival, Lung cancer is the leading cause of cancer related deaths worldwide (Sainz de Aja J, 2021) and Lung Adenocarcinoma (LUAD) is its most prevalent pathologic subtype (Zhou, 2021). Emerging from within the distal alveolar epithelium, LUAD presents with vast heterogeneity in histology, mutational spectra, and epigenomic dysregulation (Sainz de Aja J, 2021) (Zhou, 2021). Additionally, LUAD’s considerable intratumoral heterogeneity manifests vast genomic and phenotypic diversity across tumor cells and cellular components of the tumor microenvironment (TME) within the same tumor tissue. LUAD also reveals significant racial disparities in incidence, survival and mortality rates between White and Black men in the United States. The occurrence of LUAD is approximately 68.3 per capita for Black men and 61.5 per capita for White men, reflecting an 11% higher rate in the former. Further, survival outcomes indicate that Black men generally exhibit lower 5-year relative survival rates compared to White men, highlighting greater mortality risk and conspicuously poorer prognosis (Siegel RL et al., 2023). While addressing the social determinants of health is vital for the mitigation of health disparities, understanding the genetic and molecular foundations that underly racial health inequities is essential for developing comprehensive interventions and advancing more precise therapeutic modalities for more diverse patient populations. Single Nucleotide Polymorphisms (SNPs) can influence oncogenic transformation and may be associated with distinct molecular landscapes in tumors and adjacent TME. Furthermore, ancestry may play a pivotal role in shaping individual susceptibility and risk for mitochondrial dysfunction and ensuing oncogenic transformation. To elucidate the biological underpinnings of racial health disparities in LUAD, 10 Black and 10 White male LUAD patients’ tumor and normal corresponding adjacent tissues underwent molecular profiling for KRAS mutation status, Whole Exome Sequencing (WES) to determine ancestry, and analysis of associated LUAD induced Mitochondrial Somatic Nucleotide Variants (mtSNVs). We also employed the 10X Visium HD spatial transcriptomic platform to evaluate spatially resolved molecular and cellular differences in KRAS mediated LUAD between Black and White men. Hypothesis: Thus, we propose that global ancestry is associated with variations in intratumoral heterogeneity, TME composition, and mitochondrial dynamics, indicating a potential role in the observed disparities in susceptibility, malignancy and mortality in LUAD across diverse patient populations. Citation Format: Eun Kyu Sung, Yuxin Jin, Yonatan Amzaleg, John Carpten, William Dean Wallace, Dan Raz, Aaron M. Neely. Investigating the effects of ancestry in KRAS mediated lung adenocarcinoma: Exploring intratumoral heterogeneity and mitochondrial dynamics [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C169.

Phylogeography of the ambrosia beetle Euwallacea interjectus (Coleoptera: Curculionidae: Scolytinae): an emerging poplar pest and its Fusarium mutualists from poplar plantations in China.

Native to Asia, Euwallacea interjectus (Blandford) (Coleoptera: Curculionidae: Scolytinae) is a destructive and invasive pest of live trees, and now it has been found in the United States and Argentina. In recent years, this pest appeared in high densities in poplar monocultures from Eastern China (Jiangsu and Shanghai) and Argentina and caused significant poplar mortality. However, the origin of the pests related to tree damage and the Fusarium mutualists from some poplar zones in China remained unclear. Here, we provided a broader phylogeographic analysis of E. interjectus based on the mitochondrial gene (cytochrome c oxidase I) to determine the global genetic structure of this species. Five mitochondrial lineages were found in the native area. Populations introduced to the United States were originated from 4 localities. The Argentine population was derived from Japan. The species was observed with strikingly high level of cytochrome c oxidase I intraspecific divergence that exceeded interspecific divergence, but the high intraspecific variation was correlated with geographical locations among the native populations. Two nuclear genes (arginine kinase and carbamoyl-phosphate synthetase 2-aspartate transcarbamylase-dihydroorotase) were more conservative, and intraspecific differences were lower than interspecific differences. The mitochondrial genetic variation was probably caused by evolution of lineages among geographically isolated populations. But it is immature to infer the existence of cryptic species based on cytochrome c oxidase I differences. All samples collected from poplar populations were indigenous and formed close relationship with a specimen from eastern and southern China. Surprisingly, pests from poplar populations in Jiangsu and Shanghai showed different haplotypes and mutualists. This suggested that the control strategies should consider the genetic and mutualistic diversity of beetles at different poplar localities.

Mitochondrial sequence variants: testing imputation accuracy and their association with dairy cattle milk traits

BackgroundMitochondrial genomes differ from the nuclear genome and in humans it is known that mitochondrial variants contribute to genetic disorders. Prior to genomics, some livestock studies assessed the role of the mitochondrial genome but these were limited and inconclusive. Modern genome sequencing provides an opportunity to re-evaluate the potential impact of mitochondrial variation on livestock traits. This study first evaluated the empirical accuracy of mitochondrial sequence imputation and then used real and imputed mitochondrial sequence genotypes to study the role of mitochondrial variants on milk production traits of dairy cattle.ResultsThe empirical accuracy of imputation from Single Nucleotide Polymorphism (SNP) panels to mitochondrial sequence genotypes was assessed in 516 test animals of Holstein, Jersey and Red breeds using Beagle software and a sequence reference of 1883 animals. The overall accuracy estimated as the Pearson’s correlation squared (R2) between all imputed and real genotypes across all animals was 0.454. The low accuracy was attributed partly to the majority of variants having low minor allele frequency (MAF < 0.005) but also due to variants in the hypervariable D-loop region showing poor imputation accuracy. Beagle software provides an internal estimate of imputation accuracy (DR2), and 10 percent of the total 1927 imputed positions showed DR2 greater than 0.9 (N = 201). There were 151 sites with empirical R2 > 0.9 (of 954 variants segregating in the test animals) and 138 of these overlapped the sites with DR2 > 0.9. This suggests that the DR2 statistic is a reasonable proxy to select sites that are imputed with higher accuracy for downstream analyses. Accordingly, in the second part of the study mitochondrial sequence variants were imputed from real mitochondrial SNP panel genotypes of 9515 Australian Holstein, Jersey and Red dairy cattle. Then, using only sites with DR2 > 0.900 and real genotypes, we undertook a genome-wide association study (GWAS) for milk, fat and protein yields. The GWAS mitochondrial SNP effects were not significant.ConclusionThe accuracy of imputation of mitochondrial genotypes from the SNP panel to sequence was generally low. The Beagle DR2 statistic enabled selection of sites imputed with higher empirical accuracy. We recommend building larger reference populations with mitochondrial sequence to improve the accuracy of imputing less common variants and ensuring that SNP panels include common variants in the D-loop region.

Mitochondrial tRNAGlu 14693A>G Mutation, an "Enhancer" to the Phenotypic Expression of Leber's Hereditary Optic Neuropathy.

Leber's hereditary optic neuropathy (LHON), a maternally inherited ocular disease, is predominantly caused by mitochondrial DNA (mtDNA) mutations. Mitochondrial tRNA variants are hypothesized to amplify the pathogenic impact of three primary mutations. However, the exact mechanisms remained unclear. In the present study, the synergistic effect of the tRNAGlu 14693A>G and ND6 14484T>C mutations in three Chinese families affected by LHON is investigated. The m.14693A>G mutation nearly abolishes the pseudouridinylation at position 55 of tRNAGlu, leading to structural abnormalities, decreased stability, aberrant mitochondrial protein synthesis, and increased autophagy. In contrast, the ND6 14484T>C mutation predominantly impairs complex I function, resulting in heightened apoptosis and virtually no induction of mitochondrial autophagy compared to control cell lines. The presence of dual mutations in the same cell lines exhibited a coexistence of both upregulated cellular stress responses to mitochondrial damage, indicating a scenario of autophagy and mutation dysregulation within these dual-mutant cell lines. The data proposes a novel hypothesis that mitochondrial tRNA gene mutations generally lead to increased mitochondrial autophagy, while mutations in genes encoding mitochondrial proteins typically induce apoptosis, shedding light on the intricate interplay between different genetic factors in the manifestation of LHON.

Haplotype variability in mitochondrial rRNA predisposes to metabolic syndrome

Metabolic syndrome is a growing concern in developed societies and due to its polygenic nature, the genetic component is only slowly being elucidated. Common mitochondrial DNA sequence variants have been associated with symptoms of metabolic syndrome and may, therefore, be relevant players in the genetics of metabolic syndrome. We investigate the effect of mitochondrial sequence variation on the metabolic phenotype in conplastic rat strains with identical nuclear but unique mitochondrial genomes, challenged by high-fat diet. We find that the variation in mitochondrial rRNA sequence represents risk factor in the insulin resistance development, which is associated with diacylglycerols accumulation, induced by tissue-specific reduction of the oxidative capacity. These metabolic perturbations stem from the 12S rRNA sequence variation affecting mitochondrial ribosome assembly and translation. Our work demonstrates that physiological variation in mitochondrial rRNA might represent a relevant underlying factor in the progression of metabolic syndrome.

Association analysis of mitochondrial DNA heteroplasmic variants: Methods and application

We rigorously assessed a comprehensive association testing framework for heteroplasmy, employing both simulated and real-world data. This framework employed a variant allele fraction (VAF) threshold and harnessed multiple gene-based tests for robust identification and association testing of heteroplasmy. Our simulation studies demonstrated that gene-based tests maintained an appropriate type I error rate at α = 0.001. Notably, when 5 % or more heteroplasmic variants within a target region were linked to an outcome, burden-extension tests (including the adaptive burden test, variable threshold burden test, and z-score weighting burden test) outperformed the sequence kernel association test (SKAT) and the original burden test. Applying this framework, we conducted association analyses on whole-blood derived heteroplasmy in 17,507 individuals of African and European ancestries (31 % of African Ancestry, mean age of 62, with 58 % women) with whole genome sequencing data. We performed both cohort- and ancestry-specific association analyses, followed by meta-analysis on both pooled samples and within each ancestry group. Our results suggest that mtDNA-encoded genes/regions are likely to exhibit varying rates in somatic aging, with the notably strong associations observed between heteroplasmy in the RNR1 and RNR2 genes (p < 0.001) and advance aging by the Original Burden test. In contrast, SKAT identified significant associations (p < 0.001) between diabetes and the aggregated effects of heteroplasmy in several protein-coding genes. Further research is warranted to validate these findings. In summary, our proposed statistical framework represents a valuable tool for facilitating association testing of heteroplasmy with disease traits in large human populations.

Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes with coexisting nemaline myopathy: a case report

BackgroundMitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes and nemaline myopathy are two rare genetic conditions. We report the first case reported in world literature with coexistence of both these rare disorders.Case presentationA 11-year-old previously healthy Sri Lankan male child, product of a nonconsanguineous marriage with normal development presented with acute onset short lasting recurring episodes of right-sided eye deviation with impaired consciousness. In between episodes he regained consciousness. Family history revealed a similar presentation in the mother at 36 years of age. Examination was significant for short stature and proximal upper and lower limb weakness. His plasma and cerebrospinal fluid lactate were elevated. Magnetic resonance imaging brain had evidence of an acute infarction in the right occipital territory. Sanger sequencing for common mitochondrial variants of mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes confirmed this diagnosis. Whole exome sequencing revealed pathogenic compound heterozygous variants in NEB gene implicating in coexisting nemaline myopathy. Acute presentation was managed with supportive care, antiepileptics, and mitochondrial supplementation. Currently he is stable on daily supplementation of arginine and limb-strengthening physiotherapy. He is being monitored closely clinically and with serum lactate level.ConclusionGenetic diseases are rare. Coexistence of two genetic conditions is even rarer. Genetic confirmation of diagnosis is imperative for prediction of complications, accurate management, and genetic counseling.

Differential Cellular Response to Mercury in Non-Farmed Fish Species Based on Mitochondrial DNA Copy Number Variation Analysis.

Mercury (Hg) pro-oxidant role on biological systems and its biogeochemical cycle represent a serious threat due to its persistence in marine environment. As the mitochondrial genome is exposed to reactive oxygen species (ROS), the aim of the present study is the validation of the variation in the number of mitochondrial DNA copies (mtDNAcn) as biomarker of oxidative stress in aquatic environment. During summer 2021, three selected fish species (Mullus barbatus, Diplodus annularis and Pagellus erythrinus) were collected in Augusta Bay, one of the most Mediterranean contaminated areas remarkable by past Hg inputs, and in a control area, both in the south-east of Sicily. The relative mtDNAcn was evaluated by qPCR on specimens of each species from both sites, characterized respectively by higher and lower Hg bioaccumulation. M. barbatus and P. erythrinus collected in Augusta showed a dramatic mtDNAcn reduction compared to their control groups while D. annularis showed an incredible mtDNAcn rising suggesting a higher resilience of this species. These results align with the mitochondrial dynamics of fission and fusion triggered by environmental toxicants. In conclusion, we suggest the implementation of the mtDNAcn variation as a valid tool for the early warning stress-related impacts in aquatic system.

Mitogenomics of a declining species, the Rio Grande silvery minnow (Hybognathus amarus), with boom–bust population dynamics

Abstract Large mitochondrial DNA fragments and nearly complete mitogenomes were obtained from nextera-tagmented reductively amplified DNA (nextRAD) data from the Rio Grande silvery minnow (Hybognathus amarus). We used these data to characterize variation across the mitogenome and to evaluate changes in mitochondrial diversity across a 20 year time series punctuated by marked species decline. We observed different evolutionary rates among protein-coding genes and inflated values of the ratio of non-synonymous change to non-synonymous sites to synonymous changes per synonymous site for several protein-coding genes, violating assumptions of selective neutrality. Analyses suggested that non-synonymous substitutions are effectively neutral, and our results were not consistent with genetic draft. Mitogenomes revealed large long-term effective population size for Rio Grande silvery minnow, and time-series data indicated recent reductions in mitochondrial diversity via genetic drift associated with population bottlenecks. The results presented in this study show that in some cases, nextRAD sequences contain informative mitochondrial DNA data.

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

High-throughput sequencing technologies have increasingly led to discovery of disease-causing genetic variants, primarily in postnatal multi-cell DNA samples. However, applying these technologies to preimplantation genetic testing (PGT) in nuclear or mitochondrial DNA from single or few-cells biopsied from in vitro fertilised (IVF) embryos is challenging. PGT aims to select IVF embryos without genetic abnormalities. Although genotyping-by-sequencing (GBS)-based haplotyping methods enabled PGT for monogenic disorders (PGT-M), structural rearrangements (PGT-SR), and aneuploidies (PGT-A), they are labour intensive, only partially cover the genome and are troublesome for difficult loci and consanguineous couples. Here, we devise a simple, scalable and universal whole genome sequencing haplarithmisis-based approach enabling all forms of PGT in a single assay. In a comparison to state-of-the-art GBS-based PGT for nuclear DNA, shallow sequencing-based PGT, and PCR-based PGT for mitochondrial DNA, our approach alleviates technical limitations by decreasing whole genome amplification artifacts by 68.4%, increasing breadth of coverage by at least 4-fold, and reducing wet-lab turn-around-time by ~2.5-fold. Importantly, this method enables trio-based PGT-A for aneuploidy origin, an approach we coin PGT-AO, detects translocation breakpoints, and nuclear and mitochondrial single nucleotide variants and indels in base-resolution.

Mitochondrial DNA copy number variation in asthma risk, severity, and exacerbations

Asthma pathophysiology is associated with mitochondrial dysfunction. Mitochondrial DNA copy number (mtDNA-CN) has been used as a proxy of mitochondrial function, with lower levels indicating mitochondrial dysfunction in population studies of cardiovascular diseases and cancers. We investigate whether lower levels of mtDNA-CN are associated with asthma diagnosis, severity, and exacerbations. MtDNA-CN is evaluated in blood from two cohorts: UK Biobank (UKB) (asthmatics n = 39,147; non-asthmatics n = 302,302) and Severe Asthma Research Program (SARP) (n = 1283 asthmatics, non-severe n = 703). Asthmatics have lower mtDNA-CN compared to non-asthmatics in UKB (beta, -0.006 [95% CI, -0.008 to -0.003], P = 6.23×10-6). Lower mtDNA-CN is associated with asthma prevalence, but not severity in UKB or SARP. mtDNA-CN declines with age but is lower in asthma than in non-asthmatics at all ages. In one-year longitudinal study in SARP, mtDNA-CN is associated with risk of exacerbation; those with highest mtDNA-CN have the lowest risk of exacerbation [OR 0.333 [95% CI, 0.173 to 0.542], P = 0.001]. Biomarkers of inflammation and oxidative stress are higher in asthma than non-asthmatics, but the lower mtDNA-CN in asthma are independent of general inflammation or oxidative stress. Mendelian Randomization (MR) studies suggest a potential causal relationship between asthma-associated genetic variants and mtDNA-CN. MtDNA-CN are lower in asthmatics than in non-asthmatics and are associated with exacerbations. Low mtDNA-CN in asthma are not mediated through inflammation but are associated with the genetic predisposition to asthma.