A reappraisal of complete mtDNA variation in East Asian families with hearing impairment

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.

High prevalence of m.1555A > G in patients with hearing loss in the Baikal Lake region of Russia as a result of founder effect

Mitochondrial forms account approximately 1-2% of all nonsyndromic cases of hearing loss (HL). One of the most common causative variants of mtDNA is the m.1555A > G variant of the MT-RNR1 gene (OMIM 561000). Currently the detection of the m.1555A > G variant of the MT-RNR1 gene is not included in all research protocols. In this study this variant was screened among 165 patients with HL from the Republic of Buryatia, located in the Baikal Lake region of Russia. In our study, the total contribution of the m.1555A > G variant to the etiology of HL was 12.7% (21/165), while the update global prevalence of this variant is 1.8% (863/47,328). The m.1555A > G variant was notably more prevalent in Buryat (20.2%) than in Russian patients (1.3%). Mitogenome analysis in 14 unrelated Buryat families carrying the m.1555A > G variant revealed a predominant lineage: in 13 families, a cluster affiliated with sub-haplogroup A5b (92.9%) was identified, while one family had the D5a2a1 lineage (7.1%). In a Russian family with the m.1555A > G variant the lineage affiliated with sub-haplogroup F1a1d was found. Considering that more than 90% of Buryat families with the m.1555A > G variant belong to the single maternal lineage cluster we conclude that high prevalence of this variant in patients with HL in the Baikal Lake region can be attributed to a founder effect.

Increased risk of hearing loss associated with MT-RNR1 gene mutations: a real-world investigation among Han Taiwanese Population

BACKGROUND

Previous studies have implicated inherited mutations in mitochondrial DNA (mtDNA) in sensorineural hearing loss (SNHL). However, the definitive association between mitochondrial 12S rRNA (MT-RNR1) variants and hearing loss in the population has not been well established, particularly in Asia. The objective of this retrospective cohort study was to assess the association between MT-RNR1 variants and the risk of SNHL in patients in Taiwan.

METHODS

The cohort included 306,068 participants from Taiwan between January 2003 and December 2020. Participants were classified based on genetic variants, particularly mitochondrial mutations (rs267606618, rs267606619, rs267606617). MT-RNR1 variant cases were matched 1:10 with non-mutant patients by age, gender, and visit year, excluding those with pre-existing hearing loss. The primary endpoint was SNHL, identified using specific ICD-TM codes with a 90% positive predictive value. Medication exposure history was determined via self-report or electronic medical records in the hospital. Cox proportional hazard regression models were used to assess the association between MT-RNR1 variants and hearing loss, adjusting for various covariates. Kaplan-Meier survival curves and log-rank tests compared hearing loss incidence between groups.

RESULTS

The mean age of the mtDNA variants group is 32.4 years, with a standard deviation of 19.2 years. The incidence density of hearing loss for the mutation group was 36.42 per 10,000 person-years (95% Confidence Interval [CI], 27.21-47.73), which was higher than the 23.77per 10,000 person-years (95% CI, 21.32-26.42) in the wild-type group (p = 0.0036). Additionally, diabetes mellitus was associated with an increased risk of developing SNHL in individuals with MT-RNR1 variants (adjusted hazard ratio = 1.76 [95% CI, 1.00-3.09], p < 0.05).

CONCLUSION

This study highlights the increased risk of hearing loss in patients carrying MT-RNR1 variants, particularly those with diabetes mellitus. Future research that integrates genetic and clinical data is crucial for developing more precise interventions to monitor and treat hearing loss in this vulnerable population.

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.

Co-occurrence of m.15992A>G and m.15077G>A Is Associated With a High Penetrance of Maternally Inherited Hypertension in a Chinese Pedigree

BACKGROUND

Mitochondrial DNA (mtDNA) pathogenic variants have been identified to be associated with maternally inherited essential hypertension (MIEH). However, the distinctive clinical features and molecular pathogenesis of MIEH are not fully understood.

METHODS

In this study, we collected a Chinese MIEH family with extraordinary higher penetrance of essential hypertension (88.89%) and early ages of onset (31-40 years old), and performed clinical and genetic characterization for this family. The complete mitochondrial genome of the proband was sequenced and analyzed.

RESULTS

The maternally related members in this family were presented with severe increased blood pressure, left ventricular remodeling, and metabolic abnormalities. Through sequencing the entire mtDNA of the proband and performing systematic analysis of the mtDNA variants with a phylogenic approach, we identified a potentially pathogenic tRNA variant (m.15992A>G in the MT-TP gene) that may account for the MIEH in this family. One nonsynonymous variant (m.15077G>A in the MT-CYB gene) was identified to play a synergistic role with m.15992A>G to cause a high penetrance of MIEH.

CONCLUSIONS

Our results, together with previous findings, have indicated that tRNA pathogenic variants in the mtDNA could act important roles in the pathogenesis of MIEH through reducing mitochondrial translation and disturbing mitochondrial function.

[Progress in genetic susceptibility to aminoglycoside-induced deafness]

Aminoglycoside antibiotics can cause irreversible hearing loss, but they are still widely used because of their low production cost and broad-spectrum effect on most infections. Although it has been studied for decades, the mechanism of aminoglycoside-induced deafness has not been fully elucidated. Since patients'individual susceptibility to aminoglycoside-ototoxicity varies considerably, it is necessary to identify high-risk patients. This review summarizes the genetic mutations linked to aminoglycoside-induced deafness, in order to provide reference for further prevention and treatment of aminoglycoside-induced deafness.

'Infertile' studies on mitochondrial DNA variation in asthenozoospermic Tunisian men

We reviewed five studies undertaken by the same research group on the possible links between mitochondrial DNA (mtDNA) variation and asthenozoospermia, all carried out on Tunisian men. A thorough assessment of these articles reveals that all five studies were carried out on virtually the same cohort of patients, although this information was concealed by the authors. Thus, the results were ‘sliced’ in order to unjustifiably maximize the number of publications. In addition, a phylogenetic analysis of their data indicates that the reported results are notably incomplete and deficient. Overall, contrary to the original claims, the association of mtDNA variants with asthenozoospermia finds no support on this saga on Tunisian infertile men.

•

We re-analyze the seeming association of mtDNA with infertility in Tunisians.

•

The existing data are incomplete and deficient.

•

The data do not support association of mtDNA and infertility.

MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders

Tibetan highlanders, including Tibetans, Monpas, Lhobas, Dengs and Sherpas, are considered highly adaptive to severe hypoxic environments. Mitochondrial DNA (mtDNA) might be important in hypoxia adaptation given its role in coding core subunits of oxidative phosphorylation. In this study, we employed 549 complete highlander mtDNA sequences (including 432 random samples) to obtain a comprehensive view of highlander mtDNA profile. In the phylogeny of a total of 36,914 sequences, we identified 21 major haplogroups representing founding events of highlanders, most of which were coalesced in 10 kya. Through founder analysis, we proposed a three-phase model of colonizing the plateau, i.e., pre-LGM Time (30 kya, 4.68%), post-LGM Paleolithic Time (16.8 kya, 29.31%) and Neolithic Time (after 8 kya, 66.01% in total). We observed that pathogenic mutations occurred far more frequently in 22 highlander-specific lineages (five lineages carrying two pathogenic mutations and six carrying one) than in the 6,857 haplogroups of all the 36,914 sequences (P = 4.87 × 10⁻⁸). Furthermore, the number of possible pathogenic mutations carried by highlanders (in average 3.18 ± 1.27) were significantly higher than that in controls (2.82 ± 1.40) (P = 1.89 × 10⁻⁴). Considering that function-altering and pathogenic mutations are enriched in highlanders, we therefore hypothesize that they may have played a role in hypoxia adaptation.

Genetic and clinical analysis of nonsyndromic hearing impairment in pediatric and adult cases

Previous studies have linked GJB2 gene and mitochondrial DNA (mtDNA) mutations to nonsyndromic hearing impairment (NSHI), but no study in China has yet investigated these mutations across all age groups. To fill the gap, this study ascertained 263 patients with NSHI between ages 2 months and 60 years and analyzed the presence of GJB2 gene and mtDNA A1555G/C1494T mutations by polymerase chain reaction (PCR) and DNA sequencing. A total of 20 types of mutations were detected for the GJB2 gene. The GJB2 gene and mtDNA A1555G/C1494T mutations were detected in 18.63 and 11.41% cases, respectively. At the first hospital visit, GJB2 gene mutations were detected in 5.97% of adult patients (>18 years) and 22.96% pediatric patients (<18 years) (χ² =9.506, p = 0.002), and mtDNA A1555G/C1494T mutations were detected in 31.34% of adult patients and 4.59% of pediatric patients (χ² = 35.359, p <0.001). When patients were classified by age at onset of deafness, significantly more (20.68%) pediatric patients had GJB2 gene mutations than did adult patients (0.0%) (χ² = 4.685; p = 0.006). Mitochondrial DNA A1555G/C1494T mutations were detected in 15.38% of adult-onset and 8.86% pediatric-onset patients, respectively. Interestingly, most GJB2 gene mutation carriers experienced NSHI onset within the first year of life (65.31%), while mtDNA A1555G/C1494T mutation carriers experienced onset at any age. Therefore, GJB2 gene mutations appear to contribute to congenital deafness, while mtDNAA1555G/C1494T mutations contribute mainly to acquired deafness in Chinese individuals. Both newborn hearing screening and genetic testing are important to diagnose and treat deafness.

Assessment of mitochondrial DNA mutations in Chinese family with essential hypertension

Mitochondrial DNA (MtDNA) mutations played an important role in the development of essential hypertension. Mitochondrial tRNA point mutations, caused the failure in tRNA metabolism, responsible for the pathogenesis of this complex disease. In this study, we evaluated the possible role of the 4329C >G mutation in the clinical expression of hypertension in a Chinese family. Analysis of the complete mtDNA sequence variants showed that other mutations may play synergic roles in the phenotypic manifestation of hypertension. In addition, other potential pitfalls were also discussed in this context.

The tRNA(Gly) T10003C mutation in mitochondrial haplogroup M11b in a Chinese family with diabetes decreases the steady-state level of tRNA(Gly), increases aberrant reactive oxygen species production, and reduces mitochondrial membrane potential

Mitochondrial diabetes originates mainly from mutations located in maternally transmitted, mitochondrial tRNA-coding genes. In a genetic screening program of type 2 diabetes conducted with a Chinese Han population, we found one family with suggestive maternally transmitted diabetes. The proband's mitochondrial genome was analyzed using DNA sequencing. Total 42 known nucleoside changes and 1 novel variant were identified, and the entire mitochondrial DNA sequence was assigned to haplogroup M11b. Phylogenetic analysis showed that a homoplasmic mutation, 10003T>C transition, occurred at the highly conserved site in the gene encoding tRNA(Gly). Using a transmitochondrial cybrid cell line harboring this mutation, we observed that the steady-state level of tRNA(Gly) significantly affected and the amount of tRNA(Gly) decreased by 97%, production of reactive oxygen species was enhanced, and mitochondrial membrane potential, mtDNA copy number and cellular oxygen consumption rate were remarkably decreased compared with wild-type cybrid cells. The homoplasmic 10003T>C mutation in the mitochondrial tRNA(Gly) gene suggested to be as a pathogenesis-related mutation which might contribute to the maternal inherited diabetes in the Han Chinese family.

The role of the mitochondrial ribosome in human disease: searching for mutations in 12S mitochondrial rRNA with high disruptive potential

Mutations of mitochondrial DNA are linked to many human diseases. Despite the identification of a large number of variants in the mitochondrially encoded rRNA (mt-rRNA) genes, the evidence supporting their pathogenicity is, at best, circumstantial. Establishing the pathogenicity of these variations is of major diagnostic importance. Here, we aim to estimate the disruptive effect of mt-rRNA variations on the function of the mitochondrial ribosome. In the absence of direct biochemical methods to study the effect of mt-rRNA variations, we relied on the universal conservation of the rRNA fold to infer their disruptive potential. Our method, named heterologous inferential analysis or HIA, combines conservational information with functional and structural data obtained from heterologous ribosomal sources. Thus, HIA's predictive power is superior to the traditional reliance on simple conservation indexes. By using HIA, we have been able to evaluate the disruptive potential for a subset of uncharacterized 12S mt-rRNA variations. Our analysis revealed the existence of variations in the rRNA component of the human mitoribosome with different degrees of disruptive power. In cases where sufficient information regarding the genetic and pathological manifestation of the mitochondrial phenotype is available, HIA data can be used to predict the pathogenicity of mt-rRNA mutations. In other cases, HIA analysis will allow the prioritization of variants for additional investigation. Eventually, HIA-inspired analysis of potentially pathogenic mt-rRNA variations, in the context of a scoring system specifically designed for these variants, could lead to a powerful diagnostic tool.

No association between mitochondrial tRNA(Val) T1658C mutation and chronic progressive external ophthalmoplegia (CPEO)

Mutations in mitochondrial tRNA genes are one of the most important causes of mitochondrial diseases. Recently, a novel mt-tRNA(Val) T1658C mutation has been reported to be associated with chronic progressive external ophthalmoplegia (CPEO). To test this association, we performed a phylogenetic analysis of T1658C mutation, moreover, we used the bioinformatic tool to predict the thermodynamic change of tRNA(Val) with and without this mutation. Surprisingly, T1658C mutation was not evolutionary conserved and had little effect on tRNA(Val) folding. These data indicated that T1658C mutation should still be categorized as a polymorphism.

The carrier rate and mutation spectrum of genes associated with hearing loss in South China hearing female population of childbearing age

Background

Given that hearing loss occurs in 1 to 3 of 1,000 live births and approximately 90 to 95 percent of them are born into hearing families, it is of importance and necessity to get better understanding about the carrier rate and mutation spectrum of genes associated with hearing impairment in the general population.

Methods

7,263 unrelated women of childbearing age with normal hearing and without family history of hearing loss were tested with allele-specific PCR-based universal array. Further genetic testing were provided to the spouses of the screened carriers. For those couples at risk, multiple choices were provided, including prenatal diagnosis.

Results

Among the 7,263 normal hearing participants, 303 subjects carried pathogenic mutations included in the screening chip, which made the carrier rate 4.17%. Of the 303 screened carriers, 282 harbored heterozygous mutated genes associated with autosomal recessive hearing loss, and 95 spouses took further genetic tests. 8 out of the 9 couples harbored deafness-causing mutations in the same gene received prenatal diagnosis.

Conclusions

Given that nearly 90 to 95 percent of deaf and hard-of-hearing babies are born into hearing families, better understanding about the carrier rate and mutation spectrum of genes associated with hearing impairment in the female population of childbearing age may be of importance in carrier screening and genetic counseling.

An update to MitoTool: using a new scoring system for faster mtDNA haplogroup determination

The determination of human mitochondrial DNA (mtDNA) haplogroups is not only crucial in anthropological and forensic studies, but is also helpful in the medical field to prevent establishment of wrong disease associations. In recent years, high-throughput technologies and the huge amounts of data they create, as well as the regular updates to the mtDNA phylogenetic tree, mean that there is a need for an automated approach which can make a speedier determination of haplogroups than can be made by using the traditional manual method. Here, we update the MitoTool (www.mitotool.org) by incorporating a novel scoring system for the determination of mtDNA into haplogroups, which has advantages on speed, accuracy and ease of implementation. In order to make the access to MitoTool easier, we also provide a stand-alone version of the program that will run on a local computer and this version is freely available at the MitoTool website.

The role of mitochondrial DNA mutations in hearing loss

Mutations in mitochondrial DNA (mtDNA) are one of the most important causes of hearing loss. Of these, the homoplasmic A1555G and C1494T mutations at the highly conserved decoding site of the 12S rRNA gene are well documented as being associated with either aminoglycoside-induced or nonsyndromic hearing loss in many families worldwide. Moreover, five mutations associated with nonsyndromic hearing loss have been identified in the tRNA(Ser(UCN)) gene: A7445G, 7472insC, T7505C, T7510C, and T7511C. Other mtDNA mutations associated with deafness are mainly located in tRNA and protein-coding genes. Failures in mitochondrial tRNA metabolism or protein synthesis were observed from cybrid cells harboring these primary mutations, thereby causing the mitochondrial dysfunctions responsible for deafness. This review article provides a detailed summary of mtDNA mutations that have been reported in deafness and further discusses the molecular mechanisms of these mtDNA mutations in deafness expression.

The mitochondrion: a perpetrator of acquired hearing loss

Age, drugs, and noise are major causes of acquired hearing loss. The involvement of reactive oxygen species (ROS) in hair cell death has long been discussed, but there is considerably less information available as to the mechanisms underlying ROS formation. Most cellular ROS arise in mitochondria and this review will evaluate evidence for mitochondrial pathology in general and dysfunction of the mitochondrial respiratory chain in particular in acquired hearing loss. We will discuss evidence that different pathways can lead to the generation of ROS and that oxidative stress might not necessarily be causal to all three pathologies. Finally, we will detail recent advances in exploiting knowledge of aminoglycoside-mitochondria interactions for the development of non-ototoxic antibacterials. This article is part of a Special Issue entitled "Annual Reviews 2013".

Novel nucleotide changes in mutational analysis of mitochondrial 12SrRNA gene in patients with nonsyndromic and aminoglycoside-induced hearing loss

Mitochondria have essential role in cellular energy metabolism and defects in their function lead to many metabolic diseases. Mitochondrial DNA (mtDNA) mutations have been associated with number diseases such as nonsyndromic and aminoglycoside-induced hearing loss. Mutational screening of entire 12SrRNA and tRNA (ser (UCN)) genes in 107 unrelated Iranian patients with amino glycoside-induced and nonsyndromic bilateral hearing loss by direct sequencing analysis method were performed. Twenty different homoplasmic sequence variants were identified; including fifteen common polymorphisms, two putatively pathogenic variants: m.921T>C and m.1005T>C, one 12SrRNA sequence variant m.739C>T and two nucleotides substitution; m.1245T>C and m.1545T>C. Deafness-associated mutation, m.1555A>G, was not found. In our patients we found the mutation 1005 was associated with R haplogroup. These finding show that m.1555A>G mutation is not important in our population. Nucleotide change, m.739C>T, previously reported with very low frequency. We suggested the variation of two nucleotides 1245 and 1545 that localized at conserved site of 12SrRNA may be new candidate for amino glycoside-induced and nonsyndromic hearing impairment associated mutations. However, aminoglycoside exposure is a risk factor for clinical phenotype appearance of these mutations.

The mitochondrial T1095C mutation increases gentamicin-mediated apoptosis

We have previously reported a heteroplasmic mtDNA mutation (T1095C) in the 12SrRNA gene of an Italian family with features of maternally-inherited parkinsonism, antibiotic-mediated deafness and peripheral neuropathy. In the present study, we demonstrate that a transmitochondrial cybrid line derived from the proband of this family shows selective depletion of mitochondrial glutathione and decreases in the activity of complex II/III. Moreover, when exposed to an aminoglycoside antibiotic these cells responded with a ten-fold increase in the number of apoptotic cells compared to controls. These results support a pathogenic role for the T1095C mutation and indicate that the mutation increases the risk for aminoglycoside-induced toxicity.

Rapid screening for the mitochondrial DNA C1494T mutation in a deaf population in China using real-time quantitative PCR

CONCLUSION

Real-time quantitative polymerase chain reaction (qPCR) with a TaqMan minor groove binding (MGB) probe is useful for large-scale screening for the C1494T mutation. The mitochondrial DNA(mtDNA) C1494T mutation has a low carrier frequency in Chinese patients with nonsyndromic hearing loss.

OBJECTIVE

To develop a simple, rapid, and reliable real-time qPCR assay based on TaqMan technology using a new MGB probe for detecting the mtDNA C1494T mutation directly, and to investigate the carrier frequency in nonsyndromic deaf Chinese subjects.

METHODS

A TaqMan-MGB probe was constructed. Peripheral blood samples were collected from 3133 nonsyndromic deaf patients and genomic DNA was extracted. A real-time qPCR using MGB probes (wild-type) in a single tube was used to detect the mtDNA C1494T mutation. The results were then compared to the DNA sequence of the PCR products.

RESULTS

A total of 13 of 3133 (0.4%) Chinese nonsyndromic hearing loss patients were C1494T-positive. The results of the TaqMan-MGB probe method were consistent with those of sequencing.

A "Copernican" reassessment of the human mitochondrial DNA tree from its root

Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations, and errors in medical, forensic, and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence, which was identified by considering all available mitogenomes from Homo neanderthalensis. This "Copernican" reassessment of the human mtDNA tree from its deepest root should resolve previous problems and will have a substantial practical and educational influence on the scientific and public perception of human evolution by clarifying the core principles of common ancestry for extant descendants.

Is mitochondrial tRNA(phe) variant m.593T>C a synergistically pathogenic mutation in Chinese LHON families with m.11778G>A?

Mitochondrial transfer RNA (mt-tRNA) mutations have been reported to be associated with a variety of diseases. In a previous paper that studied the mtDNA background effect on clinical expression of Leber's hereditary optic neuropathy (LHON) in 182 Chinese families with m.11778G>A, we found a strikingly high frequency (7/182) of m.593T>C in the mitochondrially encoded tRNA phenylalanine (MT-TF) gene in unrelated LHON patients. To determine the potential role of m.593T>C in LHON, we compared the frequency of this variant in 479 LHON patients with m.11778G>A, 843 patients with clinical features of LHON but without the three known primary mutations, and 2374 Han Chinese from the general populations. The frequency of m.593T>C was higher in LHON patients (14/479) than in suspected LHON subjects (12/843) or in general controls (49/2374), but the difference was not statistically significant. The overall penetrance of LHON in families with both m.11778G>A and m.593T>C (44.6%) was also substantially higher than that of families with only m.11778G>A (32.9%) (P = 0.083). Secondary structure prediction of the MT-TF gene with the wild type or m.593T>C showed that this nucleotide change decreases the free energy. Electrophoretic mobility of the MT-TF genes with the wild type or m.593T>C transcribed in vitro further confirmed the change of secondary structure in the presence of this variant. Although our results could suggest a modest synergistic effect of variant m.593T>C on the LHON causing mutation m.11778G>A, the lack of statistical significance probably due to the relatively small sample size analyzed, makes necessary more studies to confirm this effect.

Systematic analysis of mitochondrial genes associated with hearing loss in the Japanese population: dHPLC reveals a new candidate mutation

Background

Variants of mitochondrial DNA (mtDNA) have been evaluated for their association with hearing loss. Although ethnic background affects the spectrum of mtDNA variants, systematic mutational analysis of mtDNA in Japanese patients with hearing loss has not been reported.

Methods

Using denaturing high-performance liquid chromatography combined with direct sequencing and cloning-sequencing, Japanese patients with prelingual (N = 54) or postlingual (N = 80) sensorineural hearing loss not having pathogenic mutations of m.1555A > G and m.3243A > G nor GJB2 were subjected to mutational analysis of mtDNA genes (12S rRNA, tRNA^Leu(UUR), tRNA^Ser(UCN), tRNA^Lys, tRNA^His, tRNA^Ser(AGY), and tRNA^Glu).

Results

We discovered 15 variants in 12S rRNA and one homoplasmic m.7501A > G variant in tRNA^Ser(UCN); no variants were detected in the other genes. Two criteria, namely the low frequency in the controls and the high conservation among animals, selected the m.904C > T and the m.1105T > C variants in 12S rRNA as candidate pathogenic mutations. Alterations in the secondary structures of the two variant transcripts as well as that of m.7501A > G in tRNA^Ser(UCN) were predicted.

Conclusions

The m.904C > T variant was found to be a new candidate mutation associated with hearing loss. The m.1105T > C variant is unlikely to be pathogenic. The pathogenicity of the homoplasmic m.7501T > A variant awaits further study.

Unique penetrance of hearing loss in a five-generation Chinese family with the mitochondrial 12S rRNA 1555A > G mutation

CONCLUSIONS

Analysis of the complete mtDNA genome and X-linkage of this five-generation Chinese family revealed that the 1555A > G mutation may lead to deafness.

OBJECTIVES

Mutations in mitochondrial DNA (mtDNA) have been found to be associated with sensorineural hearing loss. However, the variable clinical phenotype and incomplete penetrance of mtDNA 1555A > G-induced hearing loss complicate our understanding of this mutation. We aimed to identify whether nuclear genes, mitochondrial haplotypes/variants, and a possible threshold effect are involved in its manifestation in the pedigree.

METHODS

We performed clinical, genetic, and X-linkage analysis of a five-generation Chinese family in which all the affected individuals were male.

RESULTS

Clinical evaluation revealed that affected individuals with or without aminoglycoside exposure developed hearing loss extending gradually from 8000 Hz to 4000 Hz and then to 1000 Hz. Using X-linkage analysis and sequencing, we detected an identical homoplasmic 1555A > G mutation in nine individuals, and a previously unreported variant 14163C > T in mtDNA. The new variant 14163C > T coexisted with the 1555A > G mutation in six affected subjects of our pedigree. The previously unreported variant 14163C > T and aminoglycoside exposure may synergize the development of this deafness.

Rapid identification of mtDNA somatic mutations in gastric cancer tissues based on the mtDNA phylogeny

Mitochondrial DNA (mtDNA) somatic mutations have been identified in nearly all kinds of cancer during the past decade. Normally one need to determine the complete mtDNA sequences from both cancerous and normal tissues of the same patient to score the somatic mutation in cancer. In this study, we intended to explore a strategy to quickly identify somatic mutations in the entire mtDNA genome based on its phylogeny. The principal assumption for this strategy is that somatic mutations, as recently accumulated in cancerous tissue, have younger age and will be located in the terminal branches of mtDNA phylogenetic tree. In contrast, the haplogroup-specific variants, which appear as germline variants and have ancient age, will be located in the basal or intermediate-node branches of the tree, depending on their relative age. When the complete mtDNA sequence of the cancerous tissue is determined and is classified relative to the available mtDNA phylogeny, we only need to screen the variants that are located in the terminal branch in the paracancerous tissue or other normal tissue from the same patient to identify somatic mutations in cancer. We validated this strategy by using paired gastric cancer tissue and paracancerous tissue or blood from 10 Chinese patients (including one with gastric stromal tumor). A total of seven somatic mutations were identified in the cancerous tissues from four patients. Our result suggests that employing mtDNA phylogenetic knowledge facilitates rapid identification of mitochondrial genome somatic mutations in cancer.

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 six-generation Chinese family in haplogroup B4C1C exhibits high penetrance of 1555A > G-induced hearing Loss

Background

The 1555A > G mutation is the most common cause of aminoglycoside-induced and non-syndromic deafness. However, the variable clinical phenotype and incomplete penetrance of A1555G-induced hearing loss complicate our understanding of this mutation. Environmental factors, nuclear genes, mitochondrial haplotypes/variants and a possible threshold effect have been reported to may be involved in its manifestation.

Methods

Here, we performed a clinical, molecular, genetic and phylogenic analysis in a six-generation Chinese family.

Results

A clinical evaluation revealed that affected individuals without aminoglycoside exposure developed hearing loss extending gradually from 12000 Hz to 8000 Hz and then to 4000 Hz. Using pyrosequencing, we detected an identical homoplasmic 1555A > G mutation in all individuals except one. We did not find any correlation between the mutation load and the severity of hearing loss. T123N coexisted with the 1555A > G mutation in six affected subjects in our pedigree. Analysis of the complete mtDNA genome of this family revealed that this family belonged to haplotype B4C1C and exhibited high penetrance. Upon the inclusion of subjects that had been exposed to aminoglycosides, the penetrance of the hearing loss was 63.6%.; without exposure to aminoglycosides, it was 51.5%. This pedigree and another reported Chinese pedigree share the same haplotype (B4C1C) and lack functionally significant mitochondrial tRNA variants, but nevertheless they exhibit a different penetrance of hearing loss.

Conclusions

Our results imply that the factors responsible for the higher penetrance and variable expression of the deafness associated with the 1555A > G mutation in this pedigree may not be mtDNA haplotype/variants, but rather nuclear genes and/or aminoglycosides.

The search of a genetic basis for noise-induced hearing loss (NIHL)

BACKGROUND AND AIM

Knowledge about the genetic factors responsible for noise-induced hearing loss (NIHL) is still limited. This study investigated whether genetic factors are associated or not to susceptibility to NIHL.

SUBJECTS AND METHODS

The family history and genotypes were studied for candidate genes in 107 individuals with NIHL, 44 with other causes of hearing impairment and 104 controls. Mutations frequently found among deaf individuals were investigated (35delG, 167delT in GJB2, Δ(GJB6- D13S1830), Δ(GJB6- D13S1854) in GJB6 and A1555G in MT-RNR1 genes); allelic and genotypic frequencies were also determined at the SNP rs877098 in DFNB1, of deletions of GSTM1 and GSTT1 and sequence variants in both MTRNR1 and MTTS1 genes, as well as mitochondrial haplogroups.

RESULTS

When those with NIHL were compared with the control group, a significant increase was detected in the number of relatives affected by hearing impairment, of the genotype corresponding to the presence of both GSTM1 and GSTT1 enzymes and of cases with mitochondrial haplogroup L1.

CONCLUSION

The findings suggest effects of familial history of hearing loss, of GSTT1 and GSTM1 enzymes and of mitochondrial haplogroup L1 on the risk of NIHL. This study also described novel sequence variants of MTRNR1 and MTTS1 genes.

Effect of mtDNA mutation on tumor malignant degree in patients with prostate cancer

OBJECTIVES

To understand mtDNA mutation frequency in patients with prostate cancer (Pca) and its effect on malignant degree of PCa.

METHODS

A total of 130 patients (mean age, 70.1 +/- 2.4; range, 58-97 years) undergoing either prostate biopsy or radical prostatectomy between October 2006 and March 2008 were included. Additionally, 61 patients with benign prostatic hyperplasia (mean age, 69.9 +/- 1.1; range, 60-92 years) were included as a control group. The normal cells were isolated from each prostate cancer specimen by microdissection. Mitochondrial DNA (mtDNA4977) deletion mutations were identified by polymerase chain reaction. Gleason scores were determined by histopathology.

RESULTS

Among the 130 Pca samples vs. 61 BPH samples, mtDNA4977 deletion mutation was detected in 98 cases (98/130, 75.4%) vs. in 9 cases (9/61, 14.7%) (P < 0.01, P = 0.001). There was a significantly higher prevalence of the mtDNA4977 deletion mutation in patients with prostate cancer compared to patients with BPH (P < 0.01). The incidence of the mtDNA4977 deletion in normal cells isolated from cancer specimen was 10.76% (14/130), which was significantly lower than that in prostate cancer group(P < 0.01). However, there was no significant difference versus BPH group (P > 0.5). Gleason scores were significantly higher in the group of patients with cancer with the mutation (7.6 +/- 2.4), compared to those without the mutation (6.2 +/- 1.1, P < 0.01). Logistic regression analysis demonstrated that Gleason scores (OR = 1.642, 95% CI: 1.232-2.183) and age (OR = 1.061, 95% CI: 1.041-1.082) are both independent predictors of the mtDNA4977 deletion mutations.

CONCLUSIONS

mtDNA4977 deletion mutation frequency may be useful as a biomarker in malignant degree appraisal in patients with Pca.

Large-scale mtDNA screening reveals a surprising matrilineal complexity in east Asia and its implications to the peopling of the region

In order to achieve a thorough coverage of the basal lineages in the Chinese matrilineal pool, we have sequenced the mitochondrial DNA (mtDNA) control region and partial coding region segments of 6,093 mtDNAs sampled from 84 populations across China. By comparing with the available complete mtDNA sequences, 194 of those mtDNAs could not be firmly assigned into the available haplogroups. Completely sequencing 51 representatives selected from these unclassified mtDNAs identified a number of novel lineages, including five novel basal haplogroups that directly emanate from the Eurasian founder nodes (M and N). No matrilineal contribution from the archaic hominid was observed. Subsequent analyses suggested that these newly identified basal lineages likely represent the genetic relics of modern humans initially peopling East Asia instead of being the results of gene flow from the neighboring regions. The observation that most of the newly recognized mtDNA lineages have already differentiated and show the highest genetic diversity in southern China provided additional evidence in support of the Southern Route peopling hypothesis of East Asians. Specifically, the enrichment of most of the basal lineages in southern China and their rather ancient ages in Late Pleistocene further suggested that this region was likely the genetic reservoir of modern humans after they entered East Asia.

Mutation analysis of mitochondrial 12S rRNA gene in Polish patients with non-syndromic and aminoglycoside-induced hearing loss

Mutations in mitochondrial DNA have been reported as associated with non-syndromic and aminoglycoside-induced hearing loss. In the present study, we have performed mutational screening of entire 12S rRNA gene in 250 unrelated patients with non-syndromic and aminoglycoside-induced hearing loss. Twenty-one different homoplasmic sequence variants were identified, including eight common polymorphisms, one deafness-associated mutation m.1555 A>G and three putatively pathogenic variants: m.669 T>C, m.827 A>G, m.961 delT+C(n)ins. The incidence of m.1555 A>G was estimated for 3.6% (9/250); however, where aminoglycoside exposure was taken as a risk factor, the frequency was 5.5% (7/128). Substitution m.669 T>C was identified only in patients with hearing impairment and episode of aminoglycoside exposure, which may suggest that such additional risk factors must appear to induce clinical phenotype. Moreover, two 12S rRNA sequence variants: m.988 G>A and m.1453 A>G, localized at conserved sites and affected RNA secondary structure, may be new candidates for non-syndromic and aminoglycoside-induced hearing loss associated mutations.

High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia

BACKGROUND

Chronic Lymphocytic Leukemia (CLL) leads to progressive accumulation of lymphocytes in the blood, bone marrow, and lymphatic tissues. Previous findings have suggested that the mtDNA could play an important role in CLL.

METHODOLOGY/PRINCIPAL FINDINGS

The mitochondrial DNA (mtDNA) control-region was analyzed in lymphocyte cell DNA extracts and compared with their granulocyte counterpart extract of 146 patients suffering from B-Cell CLL; B-CLL (all recruited from the Basque country). Major efforts were undertaken to rule out methodological artefacts that would render a high false positive rate for mtDNA instabilities and thus lead to erroneous interpretation of sequence instabilities. Only twenty instabilities were finally confirmed, most of them affecting the homopolymeric stretch located in the second hypervariable segment (HVS-II) around position 310, which is well known to constitute an extreme mutational hotspot of length polymorphism, as these mutations are frequently observed in the general human population. A critical revision of the findings in previous studies indicates a lack of proper methodological standards, which eventually led to an overinterpretation of the role of the mtDNA in CLL tumorigenesis.

CONCLUSIONS/SIGNIFICANCE

Our results suggest that mtDNA instability is not the primary causal factor in B-CLL. A secondary role of mtDNA mutations cannot be fully ruled out under the hypothesis that the progressive accumulation of mtDNA instabilities could finally contribute to the tumoral process. Recommendations are given that would help to minimize erroneous interpretation of sequencing results in mtDNA studies in tumorigenesis.

Comprehensive molecular etiology analysis of nonsyndromic hearing impairment from typical areas in China

Background

Every year, 30,000 babies are born with congenital hearing impairment in China. The molecular etiology of hearing impairment in the Chinese population has not been investigated thoroughly. To provide appropriate genetic testing and counseling to families, we performed a comprehensive investigation of the molecular etiology of nonsyndromic deafness in two typical areas from northern and southern China.

Methods

A total of 284 unrelated school children with hearing loss who attended special education schools in China were enrolled in this study, 134 from Chifeng City in Inner Mongolia and the remaining 150 from Nangtong City in JiangSu Province. Screening was performed for GJB2, GJB3, GJB6, SLC26A4, 12S rRNA, and tRNA^ser(UCN) genes in this population. All patients with SLC26A4 mutations or variants were subjected to high-resolution temporal bone CT scan to verify the enlarged vestibular aqueduct.

Results

Mutations in the GJB2 gene accounted for 18.31% of the patients with nonsyndromic hearing loss, 1555A>G mutation in mitochondrial DNA accounted for 1.76%, and SLC26A4 mutations accounted for 13.73%. Almost 50% of the patients with nonsyndromic hearing loss in these typical Chinese areas carried GJB2 or SLC26A4 mutations. No significant differences in mutation spectrum or prevalence of GJB2 and SLC26A4 were found between the two areas.

Conclusion

In this Chinese population, 54.93% of cases with hearing loss were related to genetic factors. The GJB2 gene accounted for the etiology in about 18.31% of the patients with hearing loss, SLC26A4 accounted for about 13.73%, and mtDNA 1555A>G mutation accounted for 1.76%. Mutations in GJB3, GJB6, and mtDNA tRNA^ser(UCN) were not common in this Chinese cohort. Conventionally, screening is performed for GJB2, SLC26A4, and mitochondrial 12S rRNA in the Chinese deaf population.

Mitochondrial echoes of first settlement and genetic continuity in El Salvador

Background

From Paleo-Indian times to recent historical episodes, the Mesoamerican isthmus played an important role in the distribution and patterns of variability all around the double American continent. However, the amount of genetic information currently available on Central American continental populations is very scarce. In order to shed light on the role of Mesoamerica in the peopling of the New World, the present study focuses on the analysis of the mtDNA variation in a population sample from El Salvador.

Methodology/Principal Findings

We have carried out DNA sequencing of the entire control region of the mitochondrial DNA (mtDNA) genome in 90 individuals from El Salvador. We have also compiled more than 3,985 control region profiles from the public domain and the literature in order to carry out inter-population comparisons. The results reveal a predominant Native American component in this region: by far, the most prevalent mtDNA haplogroup in this country (at ∼90%) is A2, in contrast with other North, Meso- and South American populations. Haplogroup A2 shows a star-like phylogeny and is very diverse with a substantial proportion of mtDNAs (45%; sequence range 16090–16365) still unobserved in other American populations. Two different Bayesian approaches used to estimate admixture proportions in El Salvador shows that the majority of the mtDNAs observed come from North America. A preliminary founder analysis indicates that the settlement of El Salvador occurred about 13,400±5,200 Y.B.P.. The founder age of A2 in El Salvador is close to the overall age of A2 in America, which suggests that the colonization of this region occurred within a few thousand years of the initial expansion into the Americas.

Conclusions/Significance

As a whole, the results are compatible with the hypothesis that today's A2 variability in El Salvador represents to a large extent the indigenous component of the region. Concordant with this hypothesis is also the observation of a very limited contribution from European and African women (∼5%). This implies that the Atlantic slave trade had a very small demographic impact in El Salvador in contrast to its transformation of the gene pool in neighbouring populations from the Caribbean facade.

Mitochondrial DNA mutation m.3635G>A may be associated with Leber hereditary optic neuropathy in Chinese

Leber hereditary optic neuropathy (LHON) was the first disease to be linked to the presence of a mitochondrial DNA (mtDNA) mutation. Nowadays over 95% of LHON cases are known to be caused by one of three primary mutations (m.11778G>A, m.14484T>C, and m.3460G>A). Reports for other (rare) primary mutations in LHON patients are not infrequent. Among those is the mutation m.3635G>A in the MT-ND1 gene which was reported to be pathogenic in a Russian LHON family. In this study, we report on a Chinese family with clinical features of LHON but without any of the three well-known primary mutations. Analysis of the complete mitochondrial genome in the proband revealed the presence of m.3635G>A and m.6228C>T, along with a full array of other variants that suggest the haplogroup M7b1. Evolutionary analysis indicates that site 3635, but not 6228, is highly conserved in vertebrates. Protein secondary-structure modeling for the MT-ND1 protein harboring amino acid change S110N indicates that mutant m.3635G>A decreases the protein hydrophobicity. Our current observations provide further support for a pathogenic role of m.3635G>A in patients with LHON.

Exaggerated status of "novel" and "pathogenic" mtDNA sequence variants due to inadequate database searches

Given its relative ease, screening the entire mitochondrial DNA (mtDNA) for heteroplasmic or novel homoplasmic mutations has become part of the routine diagnostic workup for the molecular geneticist confronted with a disease case exhibiting clinical and biochemical features of mitochondrial dysfunction. "Novelty" of a given mtDNA variant is most often equated with nonregistration in the extensive MITOMAP database (www.mitomap.org). This practice has led to a number of spurious findings and wrong conclusions concerning the pathogenic status of specific mtDNA mutations, especially in the absence of proper evaluation and pathogenicity scoring. We demonstrate by way of real cases targeting the mt-tRNA(Cys) (MT-TC) gene and a stretch within the MT-ND3 gene, that a straightforward Google search can identify twice as many previously observed mutations than any MITOMAP query could achieve. Further, we reassess the recent rediscovery of m.15287T>C by listing all known occurrences and, where possible, providing the haplogroup context, shedding new light on the potential pathogenicity status of m.15287T>C.