A genetic bottleneck of mitochondrial DNA during human lymphocyte development

Mitochondria are essential organelles in eukaryotic cells that provide critical support for energetic and metabolic homeostasis. Mutations that accumulate in mitochondrial DNA (mtDNA) in somatic cells have been implicated in cancer, degenerative diseases, and the aging process. However, the mechanisms used by somatic cells to maintain proper functions despite their mtDNA mutation load are poorly understood. Here, we analyzed somatic mtDNA mutations in more than 30,000 human single peripheral and bone marrow mononuclear cells and observed a significant overrepresentation of homoplastic mtDNA mutations in B, T and NK lymphocytes despite their lower mutational burden than other hematopoietic cells. The characteristic mutational landscape of mtDNA in lymphocytes were validated with data from multiple platforms and individuals. Single-cell RNA-seq and computational modeling demonstrated a stringent mitochondrial bottleneck during lymphocyte development likely caused by lagging mtDNA replication relative to cell proliferation. These results illuminate a potential mechanism used by highly metabolically active immune cells for quality control of their mitochondrial genomes.

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Abstract 17097: Non-Synonymous Mitochondrial DNA Variants Are Common in Myocardial Tissue of Heart Failure Patients

Circulation ◽

10.1161/circ.142.suppl_3.17097 ◽

2020 ◽

Vol 142 (Suppl_3) ◽

Author(s):

Pappu Ananya ◽

Michael Binder ◽

Yang Wanjun ◽

Rebecca McClellan ◽

Brittney Murray ◽

...

Keyword(s):

Heart Failure ◽

Mitochondrial Dna ◽

Nuclear Dna ◽

Left Ventricular ◽

Individual Risk ◽

Myocardial Tissue ◽

Mtdna Mutation ◽

Mtdna Mutations ◽

Ventricular Tissue ◽

Mtdna Variants

Introduction: Mitochondrial heart disease due to pathogenic mitochondrial DNA (mtDNA) mutations can present as hypertrophic or dilated cardiomyopathy, ventricular arrhythmias and conduction disease. It is estimated that the mutation rate of mtDNA is 10 to 20-fold higher than that of nuclear DNA genes due to damage from reactive oxygen species released as byproducts during oxidative phosphorylation. When a new mtDNA mutation arises, it creates an intracellular heteroplasmic mixture of mutant and normal mtDNAs, called heteroplasmy. Heteroplasmy levels can vary in various tissues and examining mtDNA variants in blood may not be representative for the heart. The frequency of pathogenic mtDNA variants in myocardial tissues in unknown. Hypothesis: Human ventricular tissue may contain mtDNA mutations which can lead to alterations in mitochondrial function and increase individual risk for heart failure. Methods: Mitochondrial DNA was isolated from 61 left ventricular myocardial samples obtained from failing human hearts at the time of transplantation. mtDNA was sequenced with 23 primer pairs. In silico prediction of non-conservative missense variants was performed via PolyPhen-2. Heteroplasmy levels of variants predicted to be pathogenic were quantified using allele-specific ARMS-PCR. Results: We identified 21 mtDNA non-synonymous variants predicted to be pathogenic in 17 hearts. Notably, one heart contained four pathogenic mtDNA variants (ATP6: p.M104; ND5: p.P265S; ND4: p.N390S and p.L445F). Heteroplasmy levels exceeded 90% for all four variants in myocardial tissue and were significantly lower in blood. No pathogenic mtDNA variants were identified in 44 hearts. Hearts with mtDNA mutations had higher levels of myocardial GDF-15 (growth differentiation factor-15; 6.2±2.3 vs. 1.3±0.18, p=0.045), an established serum biomarker in various mitochondrial diseases. Conclusions: Non-synonymous mtDNA variants predicted to be pathogenic are common in human left ventricular tissue and may be an important modifier of the heart failure phenotype. Future studies are necessary to correlate myocardial mtDNA mutations with cardiovascular outcomes and to assess whether serum GDF-15 allows identifying patients with myocardial mtDNA mutations.

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What cost mitochondria? The maintenance of functional mitochondrial DNA within and across generations

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2013.0438 ◽

2014 ◽

Vol 369 (1646) ◽

pp. 20130438 ◽

Cited By ~ 24

Author(s):

Duur K. Aanen ◽

Johannes N. Spelbrink ◽

Madeleine Beekman

Keyword(s):

Mitochondrial Dna ◽

Somatic Growth ◽

Mtdna Mutations ◽

Specific Effects ◽

Age Related ◽

Mtdna Replication ◽

Mtdna Evolution ◽

Selection For ◽

Male Specific ◽

Mtdna Variants

The peculiar biology of mitochondrial DNA (mtDNA) potentially has detrimental consequences for organismal health and lifespan. Typically, eukaryotic cells contain multiple mitochondria, each with multiple mtDNA genomes. The high copy number of mtDNA implies that selection on mtDNA functionality is relaxed. Furthermore, because mtDNA replication is not strictly regulated, within-cell selection may favour mtDNA variants with a replication advantage, but a deleterious effect on cell fitness. The opportunities for selfish mtDNA mutations to spread are restricted by various organism-level adaptations, such as uniparental transmission, germline mtDNA bottlenecks, germline selection and, during somatic growth, regular alternation between fusion and fission of mitochondria. These mechanisms are all hypothesized to maintain functional mtDNA. However, the strength of selection for maintenance of functional mtDNA progressively declines with age, resulting in age-related diseases. Furthermore, organismal adaptations that most probably evolved to restrict the opportunities for selfish mtDNA create secondary problems. Owing to predominantly maternal mtDNA transmission, recombination among mtDNA from different individuals is highly restricted or absent, reducing the scope for repair. Moreover, maternal inheritance precludes selection against mtDNA variants with male-specific effects. We finish by discussing the consequences of life-history differences among taxa with respect to mtDNA evolution and make a case for the use of microorganisms to experimentally manipulate levels of selection.

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Associations of Mitochondrial DNA 3777-4679 region mutations with maternally inherited essential hypertensive subjects in China.

10.21203/rs.2.15696/v4 ◽

2020 ◽

Author(s):

Ye Zhu ◽

Jia You ◽

Chao Xu ◽

Xiang Gu

Keyword(s):

Mitochondrial Dna ◽

Essential Hypertension ◽

Fasting Blood Glucose ◽

Chinese Patients ◽

Abdominal Circumference ◽

Control Group ◽

Mtdna Mutation ◽

Mutation Site ◽

Genetic Characteristics ◽

Mtdna Mutations

Abstract Background: Nuclear genome or family mitochondrial screening system has become the hot focus of studies into essential hypertension. The role of mitochondrial DNA (mtDNA) in sporadic Chinese patients with hypertension has not been fully understood. The study was to evaluate the associations of mtDNA mutations with maternally inherited essential hypertensive subjects in China.Methods: From June 2009 to June 2016, a total of 800 gender-matched Chinese patients with maternally inherited essential hypertension (MIEH) and control group were 1:1 enrolled in this case-control study. Genomic DNA was extracted from each person's peripheral blood cells. The main mtDNA locations for MIEH were screened with oligodeoxynucleotides 3777-4679bp, analyzed and compared with the updated consensus Cambridge Sequence. Pathogenic mtDNA mutations were identified from the mitochondrial map.Results: MIEH subjects presented significantly higher values than those of control group in abdominal circumference(AC), waist circumference(WC), body mass index(BMI), fasting blood glucose(FBG), triglyceride(TG), low-density lipoprotein cholesterol (LDL) and renal function (P<0.05). MIEH subjects carried more amino acid changes and coding sequence variants (P<0.01) than control group. The allele frequencies of the eight single nucleotide polymorphisms(SNPs) were significantly different between the two groups, including m.3970 C>T, m.4048G>A, m.4071C>T, m.4086C>T, m. 4164A>G and m.4248T>C in ND1 gene, and m.4386T>C and m.4394C>T in tRNAGln gene(P<0.001). Fifty-five homoplasmic or heteroplasmic mutations were detected in 5 genes: ND1, tRNAIle, tRNAMet, tRNAGln and ND2 gene. The ND1 gene was the main mutation site, where the most mtDNA mutation was m.3970 C>T.Conclusions: The mtDNA mutations were involved in the process of MIEH. We identified mitochondrial genetic characteristics in MIEH patients in China. The present research serves as a solid foundation for further detailed research on the association between MIEH and mitochondrial dysfunction, and their causal relationship in Chinese and other populations with a similar lifestyle.

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Mitochondrial Dysfunction in Parkinson’s Disease: Focus on Mitochondrial DNA

Biomedicines ◽

10.3390/biomedicines8120591 ◽

2020 ◽

Vol 8 (12) ◽

pp. 591

Author(s):

Olga Buneeva ◽

Valerii Fedchenko ◽

Arthur Kopylov ◽

Alexei Medvedev

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Mitochondrial Dna ◽

Mitochondrial Dysfunction ◽

Nuclear Dna ◽

Good Evidence ◽

Inner Mitochondrial Membrane ◽

Mtdna Mutations ◽

Increased Risk ◽

Mtdna Replication

Mitochondria, the energy stations of the cell, are the only extranuclear organelles, containing their own (mitochondrial) DNA (mtDNA) and the protein synthesizing machinery. The location of mtDNA in close proximity to the oxidative phosphorylation system of the inner mitochondrial membrane, the main source of reactive oxygen species (ROS), is an important factor responsible for its much higher mutation rate than nuclear DNA. Being more vulnerable to damage than nuclear DNA, mtDNA accumulates mutations, crucial for the development of mitochondrial dysfunction playing a key role in the pathogenesis of various diseases. Good evidence exists that some mtDNA mutations are associated with increased risk of Parkinson’s disease (PD), the movement disorder resulted from the degenerative loss of dopaminergic neurons of substantia nigra. Although their direct impact on mitochondrial function/dysfunction needs further investigation, results of various studies performed using cells isolated from PD patients or their mitochondria (cybrids) suggest their functional importance. Studies involving mtDNA mutator mice also demonstrated the importance of mtDNA deletions, which could also originate from abnormalities induced by mutations in nuclear encoded proteins needed for mtDNA replication (e.g., polymerase γ). However, proteomic studies revealed only a few mitochondrial proteins encoded by mtDNA which were downregulated in various PD models. This suggests nuclear suppression of the mitochondrial defects, which obviously involve cross-talk between nuclear and mitochondrial genomes for maintenance of mitochondrial functioning.

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Associations of mitochondrial DNA 3777–4679 region mutations with maternally inherited essential hypertensive subjects in China

BMC Medical Genetics ◽

10.1186/s12881-020-01045-7 ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 3

Author(s):

Ye Zhu ◽

Jia You ◽

Chao Xu ◽

Xiang Gu

Keyword(s):

Mitochondrial Dna ◽

Essential Hypertension ◽

Fasting Blood Glucose ◽

Chinese Patients ◽

Abdominal Circumference ◽

Control Group ◽

Mtdna Mutation ◽

Mutation Site ◽

Genetic Characteristics ◽

Mtdna Mutations

Abstract Background Nuclear genome or family mitochondrial screening system has become the hot focus of studies into essential hypertension. The role of mitochondrial DNA (mtDNA) in sporadic Chinese patients with hypertension has not been fully understood. The study was to evaluate the associations of mtDNA mutations with maternally inherited essential hypertensive subjects in China. Methods From June 2009 to June 2016, a total of 800 gender-matched Chinese patients with maternally inherited essential hypertension (MIEH) and control group were 1:1 enrolled in this case-control study. Genomic DNA was extracted from each person’s peripheral blood cells. The main mtDNA locations for MIEH were screened with oligodeoxynucleotides 3777-4679 bp, analyzed and compared with the updated consensus Cambridge Sequence. Pathogenic mtDNA mutations were identified from the mitochondrial map. Results MIEH subjects presented significantly higher values than those of control group in abdominal circumference (AC), waist circumference (WC), body mass index (BMI), fasting blood glucose (FBG), triglyceride (TG), low-density lipoprotein cholesterol (LDL) and renal function (P < 0.05). MIEH subjects carried more amino acid changes and coding sequence variants (P < 0.01) than control group. The allele frequencies of the eight single nucleotide polymorphisms (SNPs) were significantly different between the two groups, including m.3970 C > T, m.4048G > A, m.4071C > T, m.4086C > T, m. 4164A > G and m.4248 T > C in ND1 gene, and m.4386 T > C and m.4394C > T in tRNAGln gene(P < 0.001). Fifty-five homoplasmic or heteroplasmic mutations were detected in 5 genes: ND1, tRNAIle, tRNAMet, tRNAGln and ND2 gene. The ND1 gene was the main mutation site, where the most mtDNA mutation was m.3970 C > T. Conclusions The mtDNA mutations were involved in the process of MIEH. We identified mitochondrial genetic characteristics in MIEH patients in China. The present research serves as a solid foundation for further detailed research on the association between MIEH and mitochondrial dysfunction, and their causal relationship in Chinese and other populations with a similar lifestyle.

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Mitochondrial DNA Mutation, Diseases, and Nutrient-Regulated Mitophagy

Annual Review of Nutrition ◽

10.1146/annurev-nutr-082018-124643 ◽

2019 ◽

Vol 39 (1) ◽

pp. 201-226 ◽

Cited By ~ 1

Author(s):

Xuan Yang ◽

Ruoyu Zhang ◽

Kiichi Nakahira ◽

Zhenglong Gu

Keyword(s):

Mitochondrial Dna ◽

Molecular Mechanisms ◽

Genetic Manipulation ◽

Wide Spectrum ◽

Human Diseases ◽

Nutrient Deficiencies ◽

Mtdna Mutation ◽

Mitochondrial Dna Mutation ◽

Mtdna Mutations ◽

Mitochondrial Homeostasis

A wide spectrum of human diseases, including cancer, neurodegenerative diseases, and metabolic disorders, have been shown to be associated with mitochondrial dysfunction through multiple molecular mechanisms. Mitochondria are particularly susceptible to nutrient deficiencies, and nutritional intervention is an essential way to maintain mitochondrial homeostasis. Recent advances in genetic manipulation and next-generation sequencing reveal the crucial roles of mitochondrial DNA (mtDNA) in various pathophysiological conditions. Mitophagy, a term coined to describe autophagy that targets dysfunctional mitochondria, has emerged as an important cellular process to maintain mitochondrial homeostasis and has been shown to be regulated by various nutrients and nutritional stresses. Given the high prevalence of mtDNA mutations in humans and their impact on mitochondrial function, it is important to investigate the mechanisms that regulate mtDNA mutation. Here, we discuss mitochondrial genetics and mtDNA mutations and their implications for human diseases. We also examine the role of mitophagy as a therapeutic target, highlighting how nutrients may eliminate mtDNA mutations through mitophagy.

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Growth Retardation in the Course of Fanconi Syndrome Caused by the 4977-bp Mitochondrial DNA Deletion: A Case Report

Children ◽

10.3390/children8100887 ◽

2021 ◽

Vol 8 (10) ◽

pp. 887

Author(s):

Ting Li ◽

Zhihong Lu ◽

Jingjing Wang ◽

Junyi Chen ◽

Haidong Fu ◽

...

Keyword(s):

Mitochondrial Dna ◽

Growth Retardation ◽

Fanconi Syndrome ◽

Mtdna Mutation ◽

Mitochondrial Dna Deletion ◽

Mtdna Mutations ◽

Mitochondrial Cytopathies ◽

Mtdna Deletion ◽

The Common ◽

Renal Tubular

Fanconi syndrome is one of the primary renal manifestations of mitochondrial cytopathies caused by mitochondrial DNA (mtDNA) mutation. The common 4977-bp mtDNA deletion has been reported to be associated with aging and diseases involving multiple extrarenal organs. Cases of Fanconi syndrome caused by the 4977-bp deletion were rarely reported previously. Here, we report a 6-year-old girl with growth retardation in the course of Fanconi syndrome. She had mild ptosis and pigmented retinopathy. Abnormal biochemical findings included low-molecular-weight proteinuria, normoglycemic glycosuria, increased urine phosphorus excretion, metabolic acidosis, and hypophosphatemia. Growth records showed that her body weight and height were normal in the first year and failed to thrive after the age of three. Using a highly sensitive mtDNA analysis methodology, she was identified to possess the common 4977-bp mtDNA deletion. The mutation rate was 84.7% in the urine exfoliated cells, 78.67% in the oral mucosal cells, and 23.99% in the blood sample. After three months of oral coenzyme Q10 and levocarnitine treatment in combination with standard electrolyte supplement, her condition was improved. This is a report of growth retardation as the initial major clinical presentation of Fanconi syndrome caused by the deletion of the 4977-bp fragment. Renal tubular abnormality without any other extrarenal dysfunction may be an initial clinical sign of mitochondrial disorders. Moreover, considering the heterogeneity of the phenotypes associated with mtDNA mutations, the risk of developing Kearns–Sayre syndrome (KSS) with age in this patient should be noted because she had ptosis, retinal involvement, and changes in the brain and skeletal muscle.

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Associations of Mitochondrial DNA 3777-4679 region mutations with maternally inherited essential hypertensive subjects in China.

10.21203/rs.2.15696/v1 ◽

2019 ◽

Author(s):

Ye Zhu ◽

Jia You ◽

Chao Xu ◽

Xiang Gu

Keyword(s):

Mitochondrial Dna ◽

Essential Hypertension ◽

Fasting Blood Glucose ◽

Chinese Patients ◽

Abdominal Circumference ◽

Control Group ◽

Mtdna Mutation ◽

Mutation Site ◽

Genetic Characteristics ◽

Mtdna Mutations

Abstract Background: Nuclear genome or family mitochondrial screening system has become the hot focus of studies into essential hypertension. The role of mitochondrial DNA (mtDNA) in sporadic Chinese patients with hypertension has not been fully understood. The study was to evaluate the associations of mtDNA mutations with maternally inherited essential hypertensive (MIEH) subjects in China. Methods: From June 2009 to June 2016, a total of 800 gender-matched Chinese patients with maternally inherited essential hypertension (MIEH) and control group were 1:1 enrolled in this case-control study. Genomic DNA was extracted from each person's peripheral blood cells. The main mtDNA locations for MIEH were screened with oligodeoxynucleotides 3777-4679bp, analyzed and compared with the updated consensus Cambridge Sequence. Pathogenic mtDNA mutations were identified from the mitochondrial map. Results: MIEH subjects presented significantly higher values than those of control group in abdominal circumference(AC), waist circumference(WC), body mass index(BMI), fasting blood glucose(FBG), triglyceride(TG), low-density lipoprotein cholesterol (LDL) and renal function ( P <0.05). MIEH subjects carried more amino acid changes and coding sequence variants ( P <0.01) than control group. The allele frequencies of the eight single nucleotide polymorphisms(SNPs) were significantly different between the two groups, including C3970T, G4048A, C4071T, C4086T, A4164G and T4248C in ND1 gene, and T4386C and C4394T in tRNA Gln gene( P <0.001). Fifty-five homoplasmic or heteroplasmic mutations were detected in 5 genes: ND1, tRNA Ile , tRNA Met , tRNA Gln and ND2 gene. The ND1 gene was the main mutation site, where the most mtDNA mutation was C3970T. Conclusions: The results convincingly proved that mtDNA mutations were involved in the process of MIEH. We identified mitochondrial genetic characteristics in MIEH patients in China. The present research serves as a solid foundation for further detailed research on the association between MIEH and mitochondrial dysfunction, and their causal relationship in Chinese and other populations with a similar lifestyle.

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Genetic mosaic analysis of a deleterious mitochondrial DNA mutation in Drosophila reveals novel aspects of mitochondrial regulation and function

Molecular Biology of the Cell ◽

10.1091/mbc.e14-11-1513 ◽

2015 ◽

Vol 26 (4) ◽

pp. 674-684 ◽

Cited By ~ 31

Author(s):

Zhe Chen ◽

Yun Qi ◽

Stephanie French ◽

Guofeng Zhang ◽

Raúl Covian Garcia ◽

...

Keyword(s):

Mitochondrial Dna ◽

Cytochrome C ◽

Cytochrome C Oxidase ◽

Mtdna Mutation ◽

Mitochondrial Dna Mutation ◽

Tissue Specific ◽

Dna Mutation ◽

Mtdna Mutations ◽

Genetic Mosaic ◽

Age Related

Various human diseases are associated with mitochondrial DNA (mtDNA) mutations, but heteroplasmy—the coexistence of mutant and wild-type mtDNA—complicates their study. We previously isolated a temperature-lethal mtDNA mutation in Drosophila, mt:CoIT300I, which affects the cytochrome c oxidase subunit I (CoI) locus. In the present study, we found that the decrease in cytochrome c oxidase (COX) activity was ascribable to a temperature-dependent destabilization of cytochrome a heme. Consistently, the viability of homoplasmic flies at 29°C was fully restored by expressing an alternative oxidase, which specifically bypasses the cytochrome chains. Heteroplasmic flies are fully viable and were used to explore the age-related and tissue-specific phenotypes of mt:CoIT300I. The proportion of mt:CoIT300I genome remained constant in somatic tissues along the aging process, suggesting a lack of quality control mechanism to remove defective mitochondria containing a deleterious mtDNA mutation. Using a genetic scheme that expresses a mitochondrially targeted restriction enzyme to induce tissue-specific homoplasmy in heteroplasmic flies, we found that mt:CoIT300I homoplasmy in the eye caused severe neurodegeneration at 29°C. Degeneration was suppressed by improving mitochondrial Ca2+ uptake, suggesting that Ca2+ mishandling contributed to mt:CoIT300I pathogenesis. Our results demonstrate a novel approach for Drosophila mtDNA genetics and its application in modeling mtDNA diseases.

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TBIO-12. THE SPECTRUM OF MITOCHONDRIAl DNA (mtDNA) MUTATIONS IN PEDIATRIC CENTRAL NERVOUS SYSTEM (CNS) TUMORS

Neuro-Oncology ◽

10.1093/neuonc/noaa222.839 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii468-iii469

Author(s):

Kristiyana Kaneva ◽

Petr Triska ◽

Daria Merkurjev ◽

Moiz Bootwalla ◽

Jennifer Cotter ◽

...

Keyword(s):

Mitochondrial Dna ◽

Cns Tumors ◽

Whole Genome Sequencing Data ◽

Low Grade ◽

Missense Mutations ◽

Loss Of Function ◽

Sequencing Data ◽

Mtdna Mutation ◽

Tumor Subtypes ◽

Mtdna Mutations

Abstract To explore the role of mitochondrial DNA mutations in pediatric CNS tumors, we analyzed 749 tumor-normal paired whole genome sequencing data sets from the Children’s Brain Tumor Tissue Consortium (CBTTC). We detected 307 somatic mtDNA mutations in 222 CNS tumors (29.6%). Most frequently observed were missense mutations (38.1%). We also detected 34 loss-of-function mutations. Different pediatric CNS tumor subtypes have distinct mtDNA mutation profiles. For categorical comparisons, we analyzed subtypes with at least 15 samples. The highest number of mtDNA mutations per tumor sample was in meningiomas (0.85), while atypical teratoid rhabdoid tumors (ATRTs) had the lowest number per sample (0.18). High-grade gliomas had a higher number of mtDNA mutations per sample than low-grade gliomas (0.56 vs. 0.31) (p = 0.0011), with almost twice as many missense mtDNA mutations per sample (0.22 vs. 0.13) (p < 0.001), and higher average heteroplasmy levels (11% vs. 9%). The average heteroplasmy was 10.1%, ranging from 15.6% in medulloblastoma to 6.36% in schwannoma suggesting that these are clonal alterations and not artifacts. Intriguingly, the two chordoma patients in the CBTTC database had an identical heteroplasmic m.10971G>A MT-ND4 nonsense mutation. Similarly, our patient with recurrent gliofibroma harbored the same somatic MT-ND4 synonymous variant (m.10700A>G) detected at 53% heteroplasmy in the initial tumor, 79% in the first recurrence, and 97% in the second recurrence. Although the functional consequences of these alterations are not yet understood, our findings suggest that sequencing the mtDNA genome may be used to characterize CNS tumors at diagnosis and monitor disease progression.

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