Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma

Abstract Many studies have suggested that mitochondria and mitochondrial DNA (mtDNA) might be functionally associated with tumor genesis and development. Although the heterogeneity of tumors is well known, most studies were based on the analysis of a single tumor sample. The extent of mtDNA diversity in the same tumor is unclear, as is whether the diversity is influenced by selection pressure. Here, we analyzed the whole exon data from 1 nontumor sample and 23 tumor samples from different locations of one single tumor tissue from a hepatocellular carcinoma (HCC) patient. Among 18 heteroplasmic sites identified in the tumor, only 2 heteroplasmies were shared among all tumor samples. By investigating the correlations between the occurrence and frequency of heteroplasmy (Het) and sampling locations (Coordinate), relative mitochondrial copy numbers, and single-nucleotide variants in the nuclear genome, we found that the Coordinate was significantly correlated with Het, suggesting no strong purifying selection or positive selection acted on the mtDNA in HCC. By further investigating the allele frequency and proportion of nonsynonymous mutations in the tumor mtDNA, we found that mtDNA in HCC did not undergo extra selection compared with mtDNA in the adjacent nontumor tissue, and they both likely evolved under neutral selection.

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Entropy of mitochondrial DNA circulating in blood is associated with hepatocellular carcinoma

BMC Medical Genomics ◽

10.1186/s12920-019-0506-7 ◽

2019 ◽

Vol 12 (S4) ◽

Cited By ~ 2

Author(s):

David S. Campo ◽

Vishal Nayak ◽

Ganesh Srinivasamoorthy ◽

Yury Khudyakov

Keyword(s):

Hepatocellular Carcinoma ◽

Mitochondrial Dna ◽

Malignant Tumors ◽

Machine Learning Algorithms ◽

Validation Dataset ◽

Average Accuracy ◽

Cancer Types ◽

Mtdna Diversity ◽

Mtdna Variants ◽

Diagnostic Detection

Abstract Background Ultra-Deep Sequencing (UDS) enabled identification of specific changes in human genome occurring in malignant tumors, with current approaches calling for the detection of specific mutations associated with certain cancers. However, such associations are frequently idiosyncratic and cannot be generalized for diagnostics. Mitochondrial DNA (mtDNA) has been shown to be functionally associated with several cancer types. Here, we study the association of intra-host mtDNA diversity with Hepatocellular Carcinoma (HCC). Results UDS mtDNA exome data from blood of patients with HCC (n = 293) and non-cancer controls (NC, n = 391) were used to: (i) measure the genetic heterogeneity of nucleotide sites from the entire population of intra-host mtDNA variants rather than to detect specific mutations, and (ii) apply machine learning algorithms to develop a classifier for HCC detection. Average total entropy of HCC mtDNA is 1.24-times lower than of NC mtDNA (p = 2.84E-47). Among all polymorphic sites, 2.09% had a significantly different mean entropy between HCC and NC, with 0.32% of the HCC mtDNA sites having greater (p < 0.05) and 1.77% of the sites having lower mean entropy (p < 0.05) as compared to NC. The entropy profile of each sample was used to further explore the association between mtDNA heterogeneity and HCC by means of a Random Forest (RF) classifier The RF-classifier separated 232 HCC and 232 NC patients with accuracy of up to 99.78% and average accuracy of 92.23% in the 10-fold cross-validation. The classifier accurately separated 93.08% of HCC (n = 61) and NC (n = 159) patients in a validation dataset that was not used for the RF parameter optimization. Conclusions Polymorphic sites contributing most to the mtDNA association with HCC are scattered along the mitochondrial genome, affecting all mitochondrial genes. The findings suggest that application of heterogeneity profiles of intra-host mtDNA variants from blood may help overcome barriers associated with the complex association of specific mutations with cancer, enabling the development of accurate, rapid, inexpensive and minimally invasive diagnostic detection of cancer.

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Molecular Genetic Analyses of Mating Pheromones Reveal Intervariety Mating or Hybridization in Cryptococcus neoformans

Infection and Immunity ◽

10.1128/iai.70.9.5225-5235.2002 ◽

2002 ◽

Vol 70 (9) ◽

pp. 5225-5235 ◽

Cited By ~ 42

Author(s):

Vishnu Chaturvedi ◽

Jinjiang Fan ◽

Birgit Stein ◽

Melissa J. Behr ◽

William A. Samsonoff ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Phylogenetic Analyses ◽

Molecular Genetic ◽

Purifying Selection ◽

Neutral Evolution ◽

Nucleotide Polymorphisms ◽

Pathogenic Yeast ◽

Fungal Virulence ◽

Mating Pheromones ◽

Copy Numbers

ABSTRACT The sexual mating of the pathogenic yeast Cryptococcus neoformans is important for pathogenesis studies because the fungal virulence is linked to the α mating type (MATα). We characterized C. neoformans mating pheromones (MFα 1 and MFa1) from 122 strains to understand intervariety hybridization or mating and intervariety virulence. MFα 1 in three C. neoformans varieties showed (a) specific nucleotide polymorphisms, (b) different copy numbers and chromosomal localizations, and (c) unique deduced amino acids in two geographic populations of C. neoformans var. gattii. MFα 1 of different varieties cross-hybridized in Southern hybridizations. Their phylogenetic analyses showed purifying selection (neutral evolution). These observations suggested that MATα strains from any of the three C. neoformans varieties could mate or hybridize in nature with MAT a strains of C. neoformans var. neoformans. A few serotype A/D diploid strains provided evidence for mating or hybridization, while a majority of A/D strains tested positive for haploid MFα 1 identical to that of C. neoformans var. grubii. MFα 1 sequence and copy numbers in diploids were identical to those of C. neoformans var. grubii, while their MFa1 sequences were identical to those of C. neoformans var. neoformans; thus, these strains were hybrids. The mice survival curves and histological lesions revealed A/D diploids to be highly pathogenic, with pathogenicity levels similar to that of the C. neoformans var. grubii type strain and unlike the low pathogenicity levels of C. neoformans var. neoformans strains. In contrast to MFα 1 in three varieties, MFa1 amplicons and hybridization signals could be obtained only from two C. neoformans var. neoformans reference strains and eight A/D diploids. This suggested that a yet undiscovered MFa pheromone(s) in C. neoformans var. gattii and C. neoformans var. grubii is unrelated to, highly divergent from, or rarer than that in C. neoformans var. neoformans. These observations could form the basis for future studies on the role of intervariety mating in C. neoformans biology and virulence.

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Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽

10.1093/genetics/164.4.1511 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1511-1518 ◽

Cited By ~ 1

Author(s):

Ning Yu ◽

Michael I Jensen-Seaman ◽

Leona Chemnick ◽

Judith R Kidd ◽

Amos S Deinard ◽

...

Keyword(s):

Nucleotide Diversity ◽

Nuclear Dna ◽

Demographic History ◽

Nuclear Genome ◽

Limited Data ◽

Effective Population ◽

East Central ◽

Dna Diversity ◽

History Of ◽

Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

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Development of a mito-CRISPR system for generating mitochondrial DNA-deleted strain in Saccharomyces cerevisiae

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbaa119 ◽

2020 ◽

Vol 85 (4) ◽

pp. 895-901

Author(s):

Takamitsu Amai ◽

Tomoka Tsuji ◽

Mitsuyoshi Ueda ◽

Kouichi Kuroda

Keyword(s):

Saccharomyces Cerevisiae ◽

Mitochondrial Dna ◽

Ethidium Bromide ◽

Nuclear Genome ◽

Target Sequence ◽

Guide Rna ◽

Crispr System ◽

Mitochondrial Target ◽

Gene Treatment ◽

Mtdna Deletion

ABSTRACT Mitochondrial dysfunction can occur in a variety of ways, most often due to the deletion or mutation of mitochondrial DNA (mtDNA). The easy generation of yeasts with mtDNA deletion is attractive for analyzing the functions of the mtDNA gene. Treatment of yeasts with ethidium bromide is a well-known method for generating ρ° cells with complete deletion of mtDNA from Saccharomyces cerevisiae. However, the mutagenic effects of ethidium bromide on the nuclear genome cannot be excluded. In this study, we developed a “mito-CRISPR system” that specifically generates ρ° cells of yeasts. This system enabled the specific cleavage of mtDNA by introducing Cas9 fused with the mitochondrial target sequence at the N-terminus and guide RNA into mitochondria, resulting in the specific generation of ρ° cells in yeasts. The mito-CRISPR system provides a concise technology for deleting mtDNA in yeasts.

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Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Diversity ◽

10.3390/d13030126 ◽

2021 ◽

Vol 13 (3) ◽

pp. 126

Author(s):

Emily K. Latch ◽

Kenneth L. Gee ◽

Stephen L. Webb ◽

Rodney L. Honeycutt ◽

Randy W. DeYoung ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Wildlife Management ◽

Field Observations ◽

Adaptive Potential ◽

Population Isolation ◽

Potential Benefits ◽

Wildlife Populations ◽

Mtdna Diversity

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.

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Mitochondrial DNA Heteroplasmy as an Informational Reservoir Dynamically Linked to Metabolic and Immunological Processes Associated with COVID-19 Neurological Disorders

Cellular and Molecular Neurobiology ◽

10.1007/s10571-021-01117-z ◽

2021 ◽

Author(s):

George B. Stefano ◽

Richard M. Kream

Keyword(s):

Mitochondrial Dna ◽

Mitochondrial Function ◽

Neurological Disorders ◽

Nuclear Dna ◽

Mitochondrial Dynamics ◽

Cell Types ◽

Tissue Specific ◽

Copy Numbers ◽

The Central Nervous System ◽

Mitochondrial Dna Heteroplasmy

AbstractMitochondrial DNA (mtDNA) heteroplasmy is the dynamically determined co-expression of wild type (WT) inherited polymorphisms and collective time-dependent somatic mutations within individual mtDNA genomes. The temporal expression and distribution of cell-specific and tissue-specific mtDNA heteroplasmy in healthy individuals may be functionally associated with intracellular mitochondrial signaling pathways and nuclear DNA gene expression. The maintenance of endogenously regulated tissue-specific copy numbers of heteroplasmic mtDNA may represent a sensitive biomarker of homeostasis of mitochondrial dynamics, metabolic integrity, and immune competence. Myeloid cells, monocytes, macrophages, and antigen-presenting dendritic cells undergo programmed changes in mitochondrial metabolism according to innate and adaptive immunological processes. In the central nervous system (CNS), the polarization of activated microglial cells is dependent on strategically programmed changes in mitochondrial function. Therefore, variations in heteroplasmic mtDNA copy numbers may have functional consequences in metabolically competent mitochondria in innate and adaptive immune processes involving the CNS. Recently, altered mitochondrial function has been demonstrated in the progression of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Accordingly, our review is organized to present convergent lines of empirical evidence that potentially link expression of mtDNA heteroplasmy by functionally interactive CNS cell types to the extent and severity of acute and chronic post-COVID-19 neurological disorders.

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Mitochondrial DNA Methylation and Human Diseases

International Journal of Molecular Sciences ◽

10.3390/ijms22094594 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4594

Author(s):

Andrea Stoccoro ◽

Fabio Coppedè

Keyword(s):

Dna Methylation ◽

Mitochondrial Dna ◽

Mitochondrial Genome ◽

Nuclear Dna ◽

Epigenetic Modification ◽

Nuclear Genome ◽

Epigenetic Modifications ◽

Human Diseases ◽

Loop Region ◽

D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

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Oxidative Stress and Nonalcoholic Fatty Liver Disease in Hemodialysis Patients

BioMed Research International ◽

10.1155/2018/3961748 ◽

2018 ◽

Vol 2018 ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Po-Jung Wu ◽

Jin-Bor Chen ◽

Wen-Chin Lee ◽

Hwee-Yeong Ng ◽

Shu-Ching Lien ◽

...

Keyword(s):

Oxidative Stress ◽

Mitochondrial Dna ◽

Liver Disease ◽

Fatty Liver ◽

Nonalcoholic Fatty Liver Disease ◽

Fatty Liver Disease ◽

Cellulose Membrane ◽

Nonalcoholic Fatty Liver ◽

Factors Associated ◽

Copy Numbers

Introduction. Nonalcoholic fatty liver disease (NAFLD) is becoming more common around the world and it may progress to cirrhosis and liver failure, increasing mortality risk. In hemodialysis (HD) patients, NAFLD may be a novel risk factor for their high cardiovascular mortality. Heightened oxidative stress is highly prevalent in HD patients. However, the relationship between oxidative stress and NAFLD in HD patients is not well defined.Methods. We studied seventy-one stable nondiabetic HD patients. Nineteen patients had the diagnosis of NAFLD by ultrasonography. Blood levels of oxidative stress markers were measured in each patient, including thiobarbituric acid reactive substances (TBARS), free thiols, superoxide dismutase (SOD) activities, and glutathione peroxidase (GPx) activity. The copy numbers of mitochondrial DNA (mtDNA) in peripheral leukocytes were also determined. Demographic, biochemistry, and hemogram data were recorded. The two groups of patients were compared in order to determine the factors associated with NAFLD in HD patients.Findings. Compared to those without NAFLD, nondiabetic HD patients with NAFLD had significantly higher mtDNA copy number and GPx levels. The two groups did not differ significantly in dialysis adequacy, hemoglobin, serum calcium, phosphorus, albumin, liver function tests, or lipid profiles. Regression analysis confirmed mtDNA copy numbers and GPx levels as two independent factors associated with NAFLD. Compared to those with polysulfone, patients dialyzed with cellulose membrane have significantly higher levels of TBARS. However, patients with or without NAFLD did not differ in their use of either dialysis membrane.Discussion. Oxidative stress (represented by antioxidant defense, GPx) and mitochondrial DNA copy numbers are independently associated with fatty liver disease in nondiabetic HD patients. The diagnostic and therapeutic implications of this key observation warrant further exploration.

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