Duplications of mitochondrial DNA: implications for pathogenesis

High number of mitochondrial DNA alterations in postmortem brain tissue of patients with schizophrenia compared to healthy controls

Previous studies have shown mitochondrial dysfunction in schizophrenia (SZ) patients, which may be caused by mitochondrial DNA (mtDNA) alterations. However, there are few studies in SZ that have analyzed mtDNA in brain samples by next-generation sequencing (NGS). To address this gap, we used mtDNA-targeted NGS and qPCR to characterize mtDNA alterations in brain samples from patients with SZ (n = 40) and healthy controls (HC) (n = 40). 35 % of SZ patients showed mtDNA alterations, a significantly higher prevalence compared to 10 % of HC. Specifically, SZ patients had a significantly higher frequency of deletions (35 vs. 5 in HC), with a mean number of deletions of 3.8 in SZ vs. 1.0 in HC. Likely pathogenic missense variants were also significantly more frequent in patients with SZ than in HC (10 vs. three HC), encompassing 14 variants in patients and three in HC. The pathogenic tRNA variant m.3243A>G was identified in one SZ patient with a high heteroplasmy level of 32.2 %. While no significant differences in mtDNA copy number (mtDNA-CN) were observed between SZ and HC, antipsychotic users had significantly higher mtDNA-CN than non-users. These findings suggest a potential role for mtDNA alterations in the pathophysiology of SZ that require further validation and functional studies.

Reduced nuclear DNA methylation and mitochondrial transcript changes in adenomas do not associate with mtDNA methylation

Background

Altered mitochondrial function and large-scale changes to DNA methylation patterns in the nuclear genome are both hallmarks of colorectal cancer (CRC). Mitochondria have multiple copies of a 16 kb circular genome that contains genes that are vital for their function. While DNA methylation is known to alter the nuclear genome in CRC, it is not clear whether it could have a similar influence in mtDNA; indeed, currently, the issue of whether mitochondrial genome (mtDNA) methylation occurs is controversial. Thus our goal here was to determine whether the methylation state of mtDNA is linked to mitochondrial gene transcription in colorectal adenomas, and to assess its suitability as a biomarker in CRC.

Methods

To investigate the relationship between DNA methylation and mitochondrial transcripts in adenomas, we performed RNA-sequencing and Whole Genome Bisulphite Sequencing (WGBS) of mtDNA-enriched DNA from normal mucosa and paired adenoma patient samples.

Results

Transcriptional profiling indicated that adenomas had reduced mitochondrial proton transport versus normal mucosa, consistent with altered mitochondrial function. The expression of 3 tRNAs that are transcribed from mtDNA were also decreased in adenoma. Overall methylation of CG dinucleotides in the nuclear genome was reduced in adenomas (68%) compared to normal mucosa (75%, P < 0.01). Methylation in mtDNA was low (1%) in both normal and adenoma tissue but we observed clusters of higher methylation at the ribosomal RNA genes. Levels of methylation within these regions did not differ between normal and adenoma tissue.

Conclusions

We provide evidence that low-level methylation of specific sites does exist in the mitochondrial genome but that it is not associated with mitochondrial gene transcription changes in adenomas. Furthermore, as no large scale changes to mtDNA methylation were observed it is unlikely to be a suitable biomarker for early-stage CRC.

Electronic supplementary material

The online version of this article (10.1186/s40364-018-0151-x) contains supplementary material, which is available to authorized users.

Mitochondrial DNA Depletion and Deletions in Paediatric Patients with Neuromuscular Diseases: Novel Phenotypes

OBJECTIVE

To study the clinical manifestations and occurrence of mtDNA depletion and deletions in paediatric patients with neuromuscular diseases and to identify novel clinical phenotypes associated with mtDNA depletion or deletions.

METHODS

Muscle DNA samples from patients presenting with undefined encephalomyopathies or myopathies were analysed for mtDNA content by quantitative real-time PCR and for deletions by long-range PCR. Direct sequencing of mtDNA maintenance genes and whole-exome sequencing were used to study the genetic aetiologies of the diseases. Clinical and laboratory findings were collected.

RESULTS

Muscle samples were obtained from 104 paediatric patients with neuromuscular diseases. mtDNA depletion was found in three patients with severe early-onset encephalomyopathy or myopathy. Two of these patients presented with novel types of mitochondrial DNA depletion syndromes associated with increased serum creatine kinase (CK) and multiorgan disease without mutations in any of the known mtDNA maintenance genes; one patient had pathologic endoplasmic reticulum (ER) membranes in muscle. The third patient with mtDNA depletion was diagnosed with merosine-deficient muscular dystrophy caused by a homozygous mutation in the LAMA2 gene. Two patients with an early-onset Kearns-Sayre/Pearson-like phenotype harboured a large-scale mtDNA deletion, minor multiple deletions and high mtDNA content.

CONCLUSIONS

Novel encephalomyopathic mtDNA depletion syndrome with structural alterations in muscle ER was identified. mtDNA depletion may also refer to secondary mitochondrial changes related to muscular dystrophy. We suggest that a large-scale mtDNA deletion, minor multiple deletions and high mtDNA content associated with Kearns-Sayre/Pearson syndromes may be secondary changes caused by mutations in an unknown nuclear gene.

Mitochondrial DNA rearrangements in health and disease--a comprehensive study

Mitochondrial DNA (mtDNA) rearrangements cause a wide variety of highly debilitating and often fatal disorders and have been implicated in aging and age-associated disease. Here, we present a meta-analytical study of mtDNA deletions (n = 730) and partial duplications (n = 37) using information from more than 300 studies published over the last 30 years. We show that both classes of mtDNA rearrangements are unequally distributed among disorders and their breakpoints have different genomic locations. We also demonstrate that 100% of cases with sporadic mtDNA deletions and 97.3% with duplications have no breakpoints in the 16,071 breakage hotspot site, in contrast with deletions from healthy and aged tissues. Notably, most deletions removing a section of the D-loop are found in tumors. Deleted mtDNA molecules lacking the origin of L-strand replication (O(L)) represent only 9.5% of all reported cases, whereas extra origins of replication occur in all duplications. As previously shown for deletions, imperfect stretches of homology are common in duplication breakpoints. Finally, we provide a dedicated Website with detailed information on deleted/duplicated mtDNA regions to facilitate the design of efficient methods for identification and screening of rearranged mitochondrial genomes (available at http://www.portugene.com/mtDNArearrangements.html).

Functional, structural, and genetic mitochondrial abnormalities in myocardial diseases

Myocardial tissue is highly dependent on energy supplied by normal mitochondrial function. Therefore defects of energy production or utilization affect the heart in both syndromic and isolated disorders. Knowledge of the peculiar structural, functional, and genetic characteristics of mitochondria provides the basis for identification and classification of mitochondrial defects as well as for establishment of a diagnostic workup useful for related cardiac disorders. This review is therefore dedicated to the characteristics of normal mitochondria and the pathologic alterations of these organelles in various cardiovascular diseases.

Mitochondrial disorders: clinical and genetic features

Virtually all cells in humans depend on mitochondrial oxidative phosphorylation to generate energy, accounting for the remarkable diversity of clinical disorders associated with mitochondrial DNA mutations. However, certain tissues are particularly susceptible to mitochondrial dysfunction, resulting in recognizable clinical syndromes. Mitochondrial DNA mutations have been linked to seizures, strokes, optic atrophy, neuropathy, myopathy, cardiomyopathy, sensorineural hearing loss, diabetes mellitus, and other clinical features. Mitochondrial DNA mutations also may play an important role in aging, as well as in common age-related neurodegenerative disorders such as Parkinson's disease. Therefore, it is becoming increasingly important for clinicians to recognize the clinical syndromes suggestive of a mitochondrial disorder, and to understand the unique features of mitochondrial genetics that complicate diagnosis and genetic counseling.

Efficient and specific amplification of identified partial duplications of human mitochondrial DNA by long PCR

The use of PCR to identify mtDNAs containing a partial duplication (dup-mtDNA) in the presence of a heteroplasmic population of mtDNAs harboring the corresponding deletion (delta-mtDNA) leads to ambiguous results: when the primers anneal in the duplicated portion of the dup-mtDNA (which is also the non-deleted region of the delta-mtDNA) and point towards the abnormal breakpoint junction, both templates are amplified indiscriminately. We have developed two different 'long PCR' approaches to amplify dup-mtDNA even in the presence of delta-mtDNA and wild-type mtDNA (wt-mtDNA). Long PCR with two primers annealing in the non-duplicated region in dup-mtDNA (equivalent to the region missing in delta-mtDNA) and whose 3' ends pointed towards the duplicated area amplified both dup-mtDNA and coexisting wt-mtDNA. We observed, however, a preferential amplification of the wt-mtDNA over that of the longer dup-mtDNAs. This problem was partly overcome by modifying the PCR conditions (extension time, amplicon length, amount of template). In order to overcome the problem of co-amplification, we developed a novel PCR method to amplify specifically dup-mtDNAs. A forward primer annealing across the breakpoint junction was used in conjunction with a backward primer annealing in the non-duplicated region. For those duplication breakpoints flanked by direct repeats, we designed a 'breakpoint loop-out' primer whose sequence omitted the repeated region, in order to avoid the annealing of this primer to wt-mtDNA. This second approach was able to amplify specifically and efficiently the dup-mtDNA in all samples analyzed, irrespective of the size of the duplication or its proportion in the samples.

The ophthalmologic manifestations of mitochondrial disease

The cardinal eye manifestations of mtDNA diseases are ophthalmoplegia, optic neuropathy, and pigmentary retinopathy. A number of other eye structures may also be affected in these disorders and the ophthalmologist is in a unique position to detect and interpret these findings. The presence of these ophthalmologic manifestations may be the first clue that the patient has an underlying mitochondrial disease with the eye as the initial or most prominently affected organ. The phenotypic manifestations of mitochondrial disease are protean and variable, and there are no clear-cut, minimal features that define these disorders. The possibility of a mitochondrial disorder should be raised when any of the mitochondrial eye manifestations (Table 1) are present, either alone or in concert with the neurological and systemic (Table 2) manifestations of mitochondrial disease. A maternal family history of an ophthalmologic, neurological, or systemic illness is also compatible with a mitochondrial disorder. The ophthalmologist should not loose sight of the fact that mitochondrial disorders have systemic manifestations and implications, even when the primary manifestations are ocular. Detection of and proactive intervention into comorbid features (eg, diabetes mellitus, hearing loss, heart block) is an important component.

Mitochondrial cytopathies

Defects of the mitochondrial respiratory chain and mutations of mitochondrial DNA have now been associated with a wide range of human diseases. The precise pathogenetic mechanisms by which these biochemical abnormalities induce tissue dysfunction are not understood. The identification of a mutation in the proline anticodon and in the 12S RNA genes of mitochondrial DNA are interesting new additions to the catalogue of pathogenetic mutations of this genome. The recent demonstration of nuclear complementation of mitochondrial DNA depletion provides the opportunity to identify nuclear genes involved in mitochondrial DNA replication. The possible role for mitochondrial deficiencies in certain neurodegenerative diseases and in the ageing process have given additional momentum to research in this area. Treatment for the mitochondrial 'cytopathies' remains disappointing and improvement in this area awaits a better understanding of their aetiology.

Mitochondrial disorders

Several different types of mitochondrial DNA mutations have now been identified in a wide spectrum of human disorders. There is some correlation between certain of these mutations and the patient's clinical phenotype, although this relationship is not absolute. The mechanisms by which these mutations produce respiratory chain deficiency and the dysfunction of different tissues are unknown. It is becoming increasingly likely that the nuclear genome plays an important role in the expression of the mitochondrial DNA mutation and the pathogenesis of these diseases.