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Biomedicine & Pharmacotherapy =... Dec 2023Hepatocytes, the predominant cellular constituents of the liver, exhibit the highest mitochondrial density within the human body. Remarkably, experimental insights from... (Review)
Review
Hepatocytes, the predominant cellular constituents of the liver, exhibit the highest mitochondrial density within the human body. Remarkably, experimental insights from the latter part of the previous century involving extracellular injection of mitochondrial DNA (mtDNA) elucidated its potential to incite autoimmune disorders. Consequently, in instances of liver injury, the substantial release of mtDNA has the potential to trigger the activation of the innate immune response, thereby inducing sustained pathogenic consequences within the organism. This article provides a comprehensive retrospective analysis of recent literature pertaining to the impact of mtDNA release on various hepatic cell populations, elucidating its role and potential mechanisms in liver injury. The findings underscore the central role of mtDNA in modulating the immune system, primarily through the orchestration of a cytokine storm, further exacerbating the occurrence of liver injury.
Topics: Humans; DNA, Mitochondrial; Retrospective Studies; Liver; Hepatocytes; Mitochondria
PubMed: 37844357
DOI: 10.1016/j.biopha.2023.115692 -
British Journal of Cancer Apr 2011Mitochondrial DNA (mtDNA) mutations occur in head and neck squamous cell carcinoma (HNSCC) and are most frequently detected in the displacement-loop (D-loop) region. The...
BACKGROUND
Mitochondrial DNA (mtDNA) mutations occur in head and neck squamous cell carcinoma (HNSCC) and are most frequently detected in the displacement-loop (D-loop) region. The D-loop is considered to be important because it controls mitochondrial gene expression and mtDNA replication. There is currently no evidence that mtDNA mutations can be used as prognostic or predictive biomarkers in HNSCC.
METHODS
We used denaturing high performance liquid chromatography to screen the entire mitochondrial genome of six oral squamous cell carcinoma-derived cell lines and then focused on detecting D-loop abnormalities in 34 HNSCC tissue samples.
RESULTS
Mitochondrial DNA mutations are not ubiquitous in HNSCC because only half of the cell lines had detectable mtDNA abnormalities following screening of the entire mitochondrial genome and only 18% (6 of 34) of tissue samples had D-loop mutations. There was no correlation between D-loop mutations and determinates of clinical outcome; specifically, tumour stage and the expression of hypoxia-inducible genes included in a highly prognostic hypoxia metagene.
CONCLUSIONS
Taken together, these data suggest that mtDNA D-loop mutations are stochastic events that may not significantly influence the biology of HNSCC and supports the hypothesis that mtDNA mutations in cancer represent bystander genotoxic damage as a consequence of tumour development and progression.
Topics: Adult; Aged; Carcinoma; Cell Line; DNA Mutational Analysis; DNA, Mitochondrial; Female; Gene Frequency; Head and Neck Neoplasms; High-Throughput Nucleotide Sequencing; Humans; Male; Middle Aged; Mutation; Predictive Value of Tests; Prognosis
PubMed: 21427725
DOI: 10.1038/bjc.2011.96 -
PloS One 2015Recent advances in sequencing technology allow for accurate detection of mitochondrial sequence variants, even those in low abundance at heteroplasmic sites....
Recent advances in sequencing technology allow for accurate detection of mitochondrial sequence variants, even those in low abundance at heteroplasmic sites. Considerable sequencing cost savings can be achieved by enriching samples for mitochondrial (relative to nuclear) DNA. Reduction in nuclear DNA (nDNA) content can also help to avoid false positive variants resulting from nuclear mitochondrial sequences (numts). We isolate intact mitochondrial organelles from both human cell lines and blood components using two separate methods: a magnetic bead binding protocol and differential centrifugation. DNA is extracted and further enriched for mitochondrial DNA (mtDNA) by an enzyme digest. Only 1 ng of the purified DNA is necessary for library preparation and next generation sequence (NGS) analysis. Enrichment methods are assessed and compared using mtDNA (versus nDNA) content as a metric, measured by using real-time quantitative PCR and NGS read analysis. Among the various strategies examined, the optimal is differential centrifugation isolation followed by exonuclease digest. This strategy yields >35% mtDNA reads in blood and cell lines, which corresponds to hundreds-fold enrichment over baseline. The strategy also avoids false variant calls that, as we show, can be induced by the long-range PCR approaches that are the current standard in enrichment procedures. This optimization procedure allows mtDNA enrichment for efficient and accurate massively parallel sequencing, enabling NGS from samples with small amounts of starting material. This will decrease costs by increasing the number of samples that may be multiplexed, ultimately facilitating efforts to better understand mitochondria-related diseases.
Topics: Cells, Cultured; Colon; Colonic Neoplasms; DNA, Mitochondrial; Genetic Variation; Genome, Mitochondrial; High-Throughput Nucleotide Sequencing; Humans; Polymerase Chain Reaction; Sequence Analysis, DNA
PubMed: 26488301
DOI: 10.1371/journal.pone.0139253 -
Frontiers in Endocrinology 2022There is growing interest in the role of DNA methylation in regulating the transcription of mitochondrial genes, particularly in brain disorders characterized by...
BACKGROUND
There is growing interest in the role of DNA methylation in regulating the transcription of mitochondrial genes, particularly in brain disorders characterized by mitochondrial dysfunction. Here, we present a novel approach to interrogate the mitochondrial DNA methylome at single base resolution using targeted bisulfite sequencing. We applied this method to investigate mitochondrial DNA methylation patterns in post-mortem superior temporal gyrus and cerebellum brain tissue from seven human donors.
RESULTS
We show that mitochondrial DNA methylation patterns are relatively low but conserved, with peaks in DNA methylation at several sites, such as within the and the genes , , , and , predominantly in a non-CpG context. The elevated DNA methylation we observe in the we validate using pyrosequencing. We identify loci that show differential DNA methylation patterns associated with age, sex and brain region. Finally, we replicate previously reported differentially methylated regions between brain regions from a methylated DNA immunoprecipitation sequencing study.
CONCLUSIONS
We have annotated patterns of DNA methylation at single base resolution across the mitochondrial genome in human brain samples. Looking to the future this approach could be utilized to investigate the role of mitochondrial epigenetic mechanisms in disorders that display mitochondrial dysfunction.
Topics: Humans; DNA Methylation; DNA, Mitochondrial; Mitochondria; Brain; Genes, Mitochondrial
PubMed: 36726473
DOI: 10.3389/fendo.2022.1059120 -
Mutagenesis Jun 2023Mitochondrial DNA mutation and toxicity have been linked to several inherited and acquired diseases; however, these are challenging to diagnose and characterize due to... (Review)
Review
Mitochondrial DNA mutation and toxicity have been linked to several inherited and acquired diseases; however, these are challenging to diagnose and characterize due to clinical and genetic heterogeneity. This review investigates current techniques for the analysis of mitochondrial perturbations, and novel, emerging endpoints for routine application within the clinical setting. Particular focus is given to the biochemistry of the mitochondria influencing each endpoint and the relation of these to toxicity. Current approaches such as the use of metabolic markers (e.g. lactate production), and muscle biopsies to measure mitochondrial proteins were found to lack specificity. Newly emerging identified endpoints were: fibroblast growth factor-21, glucose uptake, mitochondrial membrane potential, mitochondrial morphology, mtDNA heteroplasmy, and mutation of mtDNA and nuclear DNA. Owed to the advancement in genetic analysis techniques, it is suggested by this review that genotypic endpoints of mtDNA mutation and heteroplasmy show particular promise as indicators of mitochondrial disease. It is, however, acknowledged that any single endpoint in isolation offers limited information; therefore, it is recommended that analysis of several endpoints simultaneously will offer the greatest benefit in terms of disease diagnosis and study. It is hoped that this review further highlights the need for advancement in understanding mitochondrial disease.
Topics: Humans; DNA, Mitochondrial; Mitochondrial Diseases; Mitochondria; Mutation; Genotype
PubMed: 37144479
DOI: 10.1093/mutage/gead010 -
Redox Biology Sep 2020The incidence of common, metabolic diseases (e.g. obesity, cardiovascular disease, diabetes) with complex genetic etiology has been steadily increasing nationally and... (Review)
Review
The incidence of common, metabolic diseases (e.g. obesity, cardiovascular disease, diabetes) with complex genetic etiology has been steadily increasing nationally and globally. While identification of a genetic model that explains susceptibility and risk for these diseases has been pursued over several decades, no clear paradigm has yet been found to disentangle the genetic basis of polygenic/complex disease development. Since the evolution of the eukaryotic cell involved a symbiotic interaction between the antecedents of the mitochondrion and nucleus (which itself is a genetic hybrid), we suggest that this history provides a rational basis for investigating whether genetic interaction and co-evolution of these genomes still exists. We propose that both mitochondrial and Mendelian, or "mito-Mendelian" genetics play a significant role in cell function, and thus disease risk. This paradigm contemplates the natural variation and co-evolution of both mitochondrial and nuclear DNA backgrounds on multiple mitochondrial functions that are discussed herein, including energy production, cell signaling and immune response, which collectively can influence disease development. At the nexus of these processes is the economy of mitochondrial metabolism, programmed by both mitochondrial and nuclear genomes.
Topics: Cell Nucleus; DNA, Mitochondrial; Eukaryotic Cells; Mitochondria
PubMed: 32512469
DOI: 10.1016/j.redox.2020.101568 -
Cells Aug 2022Nearly half a century has passed since the discovery of cytoplasmic inheritance of human chloramphenicol resistance. The inheritance was then revealed to take place... (Review)
Review
Nearly half a century has passed since the discovery of cytoplasmic inheritance of human chloramphenicol resistance. The inheritance was then revealed to take place maternally by mitochondrial DNA (mtDNA). Later, a number of mutations in mtDNA were identified as a cause of severe inheritable metabolic diseases with neurological manifestation, and the impairment of mitochondrial functions has been probed in the pathogenesis of a wide range of illnesses including neurodegenerative diseases. Recently, a growing number of preclinical studies have revealed that animal behaviors are influenced by the impairment of mitochondrial functions and possibly by the loss of mitochondrial stress resilience. Indeed, as high as 54% of patients with one of the most common primary mitochondrial diseases, mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome, present psychiatric symptoms including cognitive impairment, mood disorder, anxiety, and psychosis. Mitochondria are multifunctional organelles which produce cellular energy and play a major role in other cellular functions including homeostasis, cellular signaling, and gene expression, among others. Mitochondrial functions are observed to be compromised and to become less resilient under continuous stress. Meanwhile, stress and inflammation have been linked to the activation of the tryptophan (Trp)-kynurenine (KYN) metabolic system, which observably contributes to the development of pathological conditions including neurological and psychiatric disorders. This review discusses the functions of mitochondria and the Trp-KYN system, the interaction of the Trp-KYN system with mitochondria, and the current understanding of the involvement of mitochondria and the Trp-KYN system in preclinical and clinical studies of major neurological and psychiatric diseases.
Topics: Animals; DNA, Mitochondrial; Humans; Kynurenine; Mitochondria; Mitochondrial Diseases; Tryptophan
PubMed: 36010683
DOI: 10.3390/cells11162607 -
IUBMB Life Mar 2006Since their first association with human disease in 1988, more than 250 pathogenic point mutations and rearrangements of the 16.6 kb mitochondrial genome (mtDNA) have... (Review)
Review
Since their first association with human disease in 1988, more than 250 pathogenic point mutations and rearrangements of the 16.6 kb mitochondrial genome (mtDNA) have been reported in a spectrum of clinical disorders which exhibit prominent muscle and central nervous system involvement. With novel mutations and disease phenotypes still being described, mtDNA disorders are recognized collectively as common, inherited genetic diseases although relatively little is still known concerning the precise pathophysiological mechanisms that lead to cell dysfunction and pathology. This review considers the basic principles of mitochondrial genetics which govern both the behaviour and investigation of pathogenic mtDNA mutations summarizing recent advances in this area, and an assessment of the ongoing debate into the role of somatic mtDNA mutations in neurodegenerative disease, ageing and cancer.
Topics: DNA, Mitochondrial; DNA, Neoplasm; Humans; Mitochondrial Diseases; Mutation
PubMed: 16766381
DOI: 10.1080/15216540600686888 -
Molecules (Basel, Switzerland) Feb 2018The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed... (Review)
Review
The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.
Topics: Centrifugation, Density Gradient; Computational Biology; DNA, Mitochondrial; Genome, Mitochondrial; High-Throughput Nucleotide Sequencing; Humans; INDEL Mutation; Mitochondria; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; Polymorphism, Single Nucleotide
PubMed: 29401641
DOI: 10.3390/molecules23020323 -
Frontiers in Bioscience (Landmark... Jan 2017The small (16,569 base pair) human mitochondrial genome plays a significant role in cell metabolism and homeostasis. Mitochondrial DNA (mtDNA) contributes to the... (Review)
Review
The small (16,569 base pair) human mitochondrial genome plays a significant role in cell metabolism and homeostasis. Mitochondrial DNA (mtDNA) contributes to the generation of complexes which are essential to oxidative phosphorylation (OXPHOS). As such, mtDNA is directly integrated into mitochondrial biogenesis and signaling and regulates mitochondrial metabolism in concert with nuclear-encoded mitochondrial factors. Mitochondria are a highly dynamic, pleiomorphic network that undergoes fission and fusion events. Within this network, mtDNAs are packaged into structures called nucleoids which are actively distributed in discrete foci within the network. This sensitive organelle is frequently disrupted by insults such as oxidants and inflammatory cytokines, and undergoes genomic damage with double- and single-strand breaks that impair its function. Collectively, mtDNA is emerging as a highly sensitive indicator of cellular stress, which is directly integrated into the mitochondrial network as a contributor of a wide range of critical signaling pathways.
Topics: DNA Damage; DNA, Mitochondrial; Energy Metabolism; Genome, Mitochondrial; Humans; Mitochondria; Organelle Biogenesis; Oxidative Phosphorylation
PubMed: 27814641
DOI: 10.2741/4511