Mitochondrial Genome Screening Research Articles

Mitochondrial Genome Screening Identified 26 Novel Variants in Children with Nonsyndromic Congenital Hearing Impairment

Mitochondrial Genome Screening Identified 26 Novel Variants in Children with Nonsyndromic Congenital Hearing Impairment

First description of a novel mitochondrial mutation in the MT-TI gene associated with multiple mitochondrial DNA deletion and depletion in family with severe dilated mitochondrial cardiomyopathy

Mitochondria are essential for early cardiac development and impaired mitochondrial function was described associated with heart diseases such as hypertrophic or dilated mitochondrial cardiomyopathy.In this study, we report a family including two individuals with severe dilated mitochondrial cardiomyopathy. The whole mitochondrial genome screening showed the presence of several variations and a novel homoplasmic mutation m.4318-4322delC in the MT-TI gene shared by the two patients and their mother and leading to a disruption of the tRNAIle secondary structure. In addition, a mitochondrial depletion was present in blood leucocyte of the two affected brother whereas a de novo heteroplasmic multiple deletion in the major arc of mtDNA was present in blood leucocyte and mucosa of only one of them. These deletions in the major arc of the mtDNA resulted to the loss of several protein-encoding genes and also some tRNA genes. The mtDNA deletion and depletion could result to an impairment of the oxidative phosphorylation and energy metabolism in the respiratory chain in the studied patients.Our report is the first description of a family with severe lethal dilated mitochondrial cardiomyopathy and presenting several mtDNA abnormalities including punctual mutation, deletion and depletion.

Novel mitochondrial gene variants in Northwestern Chinese probands with non-syndromic hearing loss by whole mitochondrial genome screening

Mitochondrial DNA mutations play an important role in hereditary hearing loss. The present study aimed at identifying more novel genetic variants of mitochondrial DNA. Complete Mitochondrial genomes were detected in 97 Northwestern Chinese probands with non-syndromic hearing loss and 376 control subjects. The variants were evaluated for the pathogenicity using the following criteria: (1) present in <1% of the controls, (2) evolutional conservation, (3) potential structural and functional alterations. Mutational analysis in probands identified 706 variants, including 180 variants in the D loop region, 27 variants in the 12S rRNA gene, 29 variants in the 16S rRNA gene, 122 missense variants and 312 silent variants in the protein coding gene, 29 variants in the tRNA genes and 7 variants in the non-coding region. After further analysis assessed for the potential structural and functional significance, we identified 5 new candidate variants for hearing loss: 12S rRNA1473C>T, tRNAPhe 614A>C, tRNALys 8339A>G, ND1 3866T>C and non-coding 5656A>G. Our findings may provide the role of these genes in hearing loss development in China and valuable information for the further understanding of pathogenic mechanism of hearing loss.

Co segregation of the m.1555A>G mutation in the MT-RNR1 gene and mutations in MT-ATP6 gene in a family with dilated mitochondrial cardiomyopathy and hearing loss: A whole mitochondrial genome screening

Mitochondrial disease refers to a heterogeneous group of disorders resulting in defective cellular energy production due to dysfunction of the mitochondrial respiratory chain, which is responsible for the generation of most cellular energy. Because cardiac muscles are one of the high energy demanding tissues, mitochondrial cardiomyopathies is one of the most frequent mitochondria disorders. Mitochondrial cardiomyopathy has been associated with several point mutations of mtDNA in both genes encoded mitochondrial proteins and mitochondrial tRNA and rRNA.We reported here the first description of mutations in MT-ATP6 gene in two patients with clinical features of dilated mitochondrial cardiomyopathy. The mutational analysis of the whole mitochondrial DNA revealed the presence of m.1555A>G mutation in MT-RNR1 gene associated to the m.8527A>G (p.M>V) and the m.8392C>T (p.136P>S) variations in the mitochondrial MT-ATP6 gene in patient1 and his family members with variable phenotype including hearing impairment. The second patient with isolated mitochondrial cardiomyopathy presented the m.8605C>T (p.27P>S) mutation in the MT-ATP6 gene. The three mutations p.M1V, p.P27S and p.P136S detected in MT-ATP6 affected well conserved residues of the mitochondrial protein ATPase 6. In addition, the substitution of proline residue at position 27 and 136 effect hydrophobicity and structure flexibility conformation of the protein.

Whole mitochondrial genome screening of a family with maternally inherited diabetes and deafness (MIDD) associated with retinopathy

Mitochondrial diseases are a clinically heterogeneous group of disorders that arise as a result of dysfunction of the mitochondrial respiratory chain. They can be caused by mutations in both nuclear and mitochondrial DNA. In fact, mitochondrial DNA (mtDNA) defects are known to be associated with a large spectrum of human diseases and patients might present wide range of clinical features with various combinations. Our study reported a Tunisian family with clinical features of maternally inherited diabetes and deafness (MIDD). Accordingly, we performed a whole mitochondrial genome mutational screening using Sanger sequencing. Our results revealed several known variations and mutations in MT-ND5 gene in all patients. Exclusively, a novel substitution in the subunit II of cytochrome oxydase (MT-CO2) was detected, in one patient having MIDD associated to retinopathy. Bioinformatics tools supported the deleterious role of the novel mutation, it was found to be involved an extended imbalance in COX2 protein hydrophobicity, structure and affect its function. Beside several variations in polymorphic sites that allowed us to classify the studied patient under the sub-haplogroup H2a2a2. Otherwise, the association of the novel mutation and mutations in ND5 gene may explain the severe phenotype observed in our patient.

Whole mitochondrial genome screening of a family with maternally inherited diabetes and deafness (MIDD) associated with retinopathy: A putative haplotype associated to MIDD and a novel MT-CO2 m.8241 T > G mutation

Mitochondrial diseases are a clinically heterogeneous group of disorders that arise as a result of dysfunction of the mitochondrial respiratory chain. They can be caused by mutations in both nuclear and mitochondrial DNA. In fact, mitochondrial DNA (mtDNA) defects are known to be associated with a large spectrum of human diseases and patients might present wide range of clinical features with various combinations.Our study reported a Tunisian family with clinical features of maternally inherited diabetes and deafness (MIDD). Accordingly, we performed a whole mitochondrial genome mutational analysis, results revealed a haplotype composed by “A750G, A1438G, G8860A, T12705, T14766C and T16519C”, in homoplasmic state, in the mother and transmitted to her daughter and her son. The patient with MIDD2 and retinopathy presented, in addition to this haplotype associated to the MIDD, two de novo variations including a novel one m.8241T>G (p. F219C) in MT-CO2 gene and a known one m.13276G>A (p. M314V) in MT-ND5 gene. The coexistence of these two mutations could explain the retinopathy observed in this patient.

Two sisters with macular dystrophy caused by the 3243A>G mitochondrial DNA mutation

Case reportTwo sisters, 54 and 60 years old, with a history of diabetes and deafness, consulted for decreased visual acuity (VA). Funduscopic examination revealed patchy areas of chorioretinal atrophy with annular arrangement around the fovea. Genetic study identified the heteroplasmic mutation 3243A>G in mitochondrial DNA, which supports the syndrome maternally inherited diabetes and deafness (MIDD) or Ballinger-Wallace disease. DiscussionThe finding of such macular disorders, especially in the presence of diabetes mellitus and deafness, should suggest the performing of a mitochondrial genome screening to identify this unusual syndrome.

Dos hermanas con distrofia macular causada por la mutación 3243A>G del ADN mitocondrial

Case reportTwo sisters of 54 and 60years old, with a history of diabetes and deafness, consulted for decreased visual acuity (VA). Funduscopic examination revealed patchy areas of chorioretinal atrophy with annular arrangement around the fovea. Genetic study identified the heteroplasmic mutation 3243A>G in mitochondrial DNA, which supports syndrome maternally inherited diabetes and deafness (MIDD) or Ballinger-Wallace disease. DiscussionThe finding of such macular disorders, especially in the presence of diabetes mellitus and deafness, should suggest the performing of a mitochondrial genome screening to identify this unusual syndrome.

Frequency of mitochondrial mutations in non-syndromic hearing loss as well as possibly responsible variants found by whole mitochondrial genome screening

Mutations in mitochondrial DNA (mtDNA) are reported to be responsible for the pathogenesis of maternally inherited hearing loss. Complete mtDNA sequencing may detect pathogenic mutations, but whether they are indeed pathogenic can be difficult to interpret because of normal ethnic-associated haplogroup variation and other rare variations existing among control populations. In this study, we performed systemic mutational analysis of mtDNA in 394 Japanese patients with hearing loss. Two different cohorts were analyzed in this study: Cohort 1, 254 maternally inherited patients; and Cohort 2, 140 patients with various inheritance modes. After screening of the entire mtDNA genome with direct sequencing, we evaluated the frequency of previously reported mutations and the frequency and pathogenicity of the novel variants. As a result, the ‘Confirmed' mitochondrial mutations were found predominantly in Cohort 1 rather than in Cohort 2 (14.6 vs 0.7%). 1555A>G (n=23) is the most common mutation, followed by the 3243A>G (n=11) mutations. On the basis of prediction analysis, we detected 10 novel homoplasmic mitochondrial variants. After further classification, the 3595A>G and 6204A>G variants were found to be new candidate mutations possibly associated with hearing loss.

A novel MT-CO1 m.6498C>A variation associated with the m.7444G>A mutation in the mitochondrial COI/tRNASer(UCN) genes in a patient with hearing impairment, diabetes and congenital visual loss

Mitochondrial diseases are a clinically heterogeneous group of disorders that arise as a result of dysfunction of the mitochondrial respiratory chain. Sensorineural hearing loss (SNHL) has been described in association to different mitochondrial multisystem syndromes, often involving the central nervous system, neuromuscular, or endocrine organs. In this study, we described a Tunisian young girl with hearing impairment, congenital visual loss and maternally inherited diabetes. No mutation was found in the mitochondrial tRNALeu(UUR) and the 12S rRNA genes. However, we detected the m.7444G>A mutation in the mitochondrial COI/tRNASer(UCN) genes. This mutation eliminates the termination codon of the MT-CO1 gene and extends the COI polypeptide by three amino acids (Lys–Gln–Lys) to the C-terminal. The whole mitochondrial genome screening revealed the presence of a novel mutation m.6498C>A (L199I) in the mitochondrial DNA-encoded subunit I of the cytochrome c oxidase (COX). This “probably damaging” transversion affects a highly conserved domain and it was absent in 200 Tunisian controls. The studied patient was classified under the haplogroup H2a.

A whole mitochondrial genome screening in a MELAS patient: A novel mitochondrial tRNAVal mutation

Mitochondrial encephalopathy, lactic acidosis and strokelike episodes (MELAS) syndrome is a mitochondrial disorder characterized by a wide variety of clinical presentations and a multisystemic organ involvement. In this study, we report a Tunisian girl with clinical features of MELAS syndrome who was negative for the common m.3243A>G mutation, but also for the reported mitochondrial DNA (mtDNA) mutations and deletions. Screening of the entire mtDNA genome showed several known mitochondrial variants besides to a novel transition m.1640A>G affecting a wobble adenine in the anticodon stem region of the tRNAVal. This nucleotide was conserved and it was absent in 150 controls suggesting its pathogenicity. In addition, no mutations were found in the nuclear polymerase gamma-1 gene (POLG1). These results suggest further investigation nuclear genes encoding proteins responsible for stability and structural components of the mtDNA or to the oxidative phosphorylation machinery to explain the phenotypic variability in the studied family.

Whole mitochondrial genome screening in two families with hearing loss: detection of a novel mutation in the 12S rRNA gene

Sensorineural hearing loss has been described in association with different mitochondrial multisystemic syndromes, often characterized by an important neuromuscular involvement. Until now, mutations in mitochondrial DNA, especially in the 12S rRNA, the tRNASer(UCN) and the tRNALeu(UUR) genes, were implicated in syndromic or non-syndromic hearing loss either as a primary cause or as predisposing factors. In the present study, we performed a whole mitochondrial genome screening in two unrelated Tunisian families with inherited hearing loss. Results showed the presence of a novel mutation in the mitochondrial 12S rRNA gene in the two probands of these two families who belong to two different haplogroups: L3 and H6a1. The m.735A>G mutation affects a conserved nucleotide of the mitochondrial 12S rRNA gene in primates and other species and had a conservation index of 78.5% (11/14). We also detected known polymorphisms and sic novel mitochondrial variants. The present study confirmed that the mitochondrial 12S rRNA gene is a hot spot for mutations associated with hearing impairment.

A De Novo Mutation in the Adenosine Triphosphatase (ATPase) 8 Gene in a Patient With Mitochondrial Disorder

Mitochondrial DNA defects were known to be associated with a wide spectrum of human diseases and patients might present a wide range of clinical features in various combinations. In the current study, we described a patient with psychomotor and neurodevelopmental delay, mild hyperintensity of posterior periventicular white matter, generalized clonic seizures, leukodystrophy, and congenital deafness. He also had tetraplegia, with central blindness and swallowing difficulty. Brain magnetic resonance imaging (MRI) showed involvement of the interpeduncular nucleus and central tegmental tract, white matter abnormalities, and cerebellar atrophy. A whole mitochondrial genome screening revealed the presence of 19 reported polymorphisms and an undescribed A to G mutation at nucleotide 8411 (p.M16V) affecting a conserved region of the mitochondrial adenosine triphosphatase (ATPase) 8 protein. This de novo mutation was detected in heteroplasmic form (97%) and was absent in 120 controls. Thus, the m.8411A>G mutation could strongly be associated with the disease in the tested patient.

Whole mitochondrial genome screening in maternally inherited non-syndromic hearing impairment using a microarray resequencing mitochondrial DNA chip

Mitochondrial DNA (mtDNA) mutations have been implicated in non-syndromic hearing loss either as primary or as predisposing factors. As only a part of the mitochondrial genome is usually explored in deafness, its prevalence is probably under-estimated. Among 1350 families with non-syndromic sensorineural hearing loss collected through a French collaborative network, we selected 29 large families with a clear maternal lineage and screened them for known mtDNA mutations in 12S rRNA, tRNASer(UCN) and tRNALeu(UUR) genes. When no mutation could be identified, a whole mitochondrial genome screening was performed, using a microarray resequencing chip: the MitoChip version 2.0 developed by Affymetrix Inc. Known mtDNA mutations was found in nine of the 29 families, which are described in the article: five with A1555G, two with the T7511C, one with 7472insC and one with A3243G mutation. In the remaining 20 families, the resequencing Mitochip detected 258 mitochondrial homoplasmic variants and 107 potentially heteroplasmic variants. Controls were made by direct sequencing on selected fragments and showed a high sensibility of the MitoChip but a low specificity, especially for heteroplasmic variations. An original analysis on the basis of species conservation, frequency and phylogenetic investigation was performed to select the more probably pathogenic variants. The entire genome analysis allowed us to identify five additional families with a putatively pathogenic mitochondrial variant: T669C, C1537T, G8078A, G12236A and G15077A. These results indicate that the new MitoChip platform is a rapid and valuable tool for identification of new mtDNA mutations in deafness.