bims-midmar 2022-01-16 papers

bims-midmar

Biomed News

on Mitochondrial DNA maintenance and replication

Issue of 2022–01–16
thirteen papers selected by
Flavia Söllner, Ludwig-Maximilians University

Ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression.
Therapeutic applications of mitochondrial transplantation.
Circulating cell-free mitochondrial DNA in pregnancy.
mitoDataclean: A machine learning approach for the accurate identification of cross-contamination-derived tumor mitochondrial DNA mutations.
Reduced Maternal Circulating Cell-Free Mitochondrial DNA Is Associated With the Development of Preeclampsia.
Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq.
Mitochondrial RNA processing defect caused by a SUPV3L1 mutation in two siblings with a novel neurodegenerative syndrome.
Clinical, Histological, and Genetic Features of 25 Patients with Autosomal Dominant Progressive External Ophthalmoplegia (ad-PEO)/PEO-Plus Due to TWNK Mutations.
Switching a conflicted bacterial DTD-tRNA code is essential for the emergence of mitochondria.
The RNA methyltransferase METTL8 installs m3C32 in mitochondrial tRNAsThr/Ser(UCN) to optimise tRNA structure and mitochondrial translation.
The Influence of Mitochondrial-DNA-Driven Inflammation Pathways on Macrophage Polarization: A New Perspective for Targeted Immunometabolic Therapy in Cerebral Ischemia-Reperfusion Injury.
Roles of host mitochondria in the development of COVID-19 pathology: Could mitochondria be a potential therapeutic target?
Mitochondrial Dysfunction as a Hallmark of Environmental Injury.

Nucleic Acids Res. 2022 Jan 08. pii: gkab1251. [Epub ahead of print]

Ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression.

Meenakshi Singh, Viktor Posse, Bradley Peter, Maria Falkenberg, Claes M Gustafsson.

Human mitochondria lack ribonucleotide excision repair pathways, causing misincorporated ribonucleotides (rNMPs) to remain embedded in the mitochondrial genome. Previous studies have demonstrated that human mitochondrial DNA polymerase γ can bypass a single rNMP, but that longer stretches of rNMPs present an obstacle to mitochondrial DNA replication. Whether embedded rNMPs also affect mitochondrial transcription has not been addressed. Here we demonstrate that mitochondrial RNA polymerase elongation activity is affected by a single, embedded rNMP in the template strand. The effect is aggravated at stretches with two or more consecutive rNMPs in a row and cannot be overcome by addition of the mitochondrial transcription elongation factor TEFM. Our findings lead us to suggest that impaired transcription may be of functional relevance in genetic disorders associated with imbalanced nucleotide pools and higher levels of embedded rNMPs.

DOI: https://doi.org/10.1093/nar/gkab1251
Biochimie. 2022 Jan 10. pii: S0300-9084(22)00002-5. [Epub ahead of print]

Therapeutic applications of mitochondrial transplantation.

Oner Ulger, Gokhan Burcin Kubat.

  This review aims to make a framework of exogenous healthy mitochondrial transplantation and to assemble present information for improving new therapeutic applications in a variety of diseases. Recently, the significance of mitochondrial transplantation has been emphasized in a variety of mitochondrial dysfunction-related diseases such as neurodegenerative diseases, toxic injury, ischemia, cardiovascular diseases. We describe the natural mitochondrial transfer mechanisms (ie. TNT, EVs, mitochondrial dynamics), mitochondrial isolation process for transplantation (ie. source of mitochondria, requirements for successful isolation), mitochondrial transplantation methods (in vivo, in vitro), the effects and limitations of mitochondrial transplantation. Since mitochondrial transplantation is seen as an innovative potential treatment for diseases that can not be treated at the desired level, we expect to represent how the mitochondrial transplantation methods can be used in different diseases.

Keywords:  Mitochondria dysfunction; Mitochondrial dynamics; Mitochondrial isolation; Mitochondrial transplantation

DOI:  https://doi.org/10.1016/j.biochi.2022.01.002
Physiology (Bethesda). 2022 Jan 10.

Circulating cell-free mitochondrial DNA in pregnancy.

Jessica L Bradshaw, Spencer C Cushen, Nicole R Phillips, Styliani Goulopoulou.

  Circulating cell-free mitochondrial DNA (ccf-mtDNA) released upon cell injury or death stimulates diverse pattern recognition receptors to activate innate immune responses and initiate systemic inflammation. In this review, we discuss the temporal changes of ccf-mtDNA during pregnancy and its potential contribution to adverse pregnancy outcomes in pregnancy complications.

Keywords:  circulating DNA; gestation; maternal; mitochondria; preeclampsia

DOI:  https://doi.org/10.1152/physiol.00037.2021
Int J Cancer. 2022 Jan 09.

mitoDataclean: A machine learning approach for the accurate identification of cross-contamination-derived tumor mitochondrial DNA mutations.

Liping Su, Shanshan Guo, Wenjie Guo, Xiaoying Ji, Yang Liu, Huanqin Zhang, Qichao Huang, Kaixiang Zhou, Xu Guo, Xiwen Gu, Jinliang Xing.

  Next-generation sequencing (NGS) of mitochondrial DNA (mtDNA) has widespread applications in aging and cancer studies. However, cross-contamination of mtDNA constitutes a major concern. Previous methods for the detection of mtDNA contamination mainly focus on haplogroup-level phylogeny, but neglect haplotype-level differences, leading to limited sensitivity and accuracy. In this study, we present mitoDataclean, a random-forest-based machine learning package for accurate identification of cross-contamination, evaluation of contamination levels and detection of contamination-derived variants in mtDNA NGS data. Comprehensive optimization of mitoDataclean revealed that training simulation with mixtures of small haplogroup distance and low polymorphic difference was critical for optimal modeling. Compared with existing methods, mitoDataclean exhibited significantly improved sensitivity and accuracy for the detection of sample contamination in simulated data. In addition, mitoDataclean achieved area under the curve values of 0.91 and 0.97 for discerning genuine and contamination-derived mtDNA variants in a simulated Western dataset and private sequencing contamination data, respectively, suggesting that this tool may be applicable for different populations and samples with different sources of contamination. Finally, mitoDataclean was further evaluated in several private and public datasets and showed a robust ability for contamination detection. Altogether, our study demonstrates that mitoDataclean may be used for accurate detection of contaminated samples and contamination-derived variants in mtDNA NGS data. This article is protected by copyright. All rights reserved.

Keywords:  machine learning; mitochondrial DNA; next-generation sequencing; sample cross-contamination

DOI:  https://doi.org/10.1002/ijc.33927
J Am Heart Assoc. 2022 Jan 11. e021726

Reduced Maternal Circulating Cell-Free Mitochondrial DNA Is Associated With the Development of Preeclampsia.

Spencer C Cushen, Contessa A Ricci, Jessica L Bradshaw, Talisa Silzer, Alexandra Blessing, Jie Sun, Zhengyang Zhou, Sabrina M Scroggins, Mark K Santillan, Donna A Santillan, Nicole R Phillips, Styliani Goulopoulou.

  Background Circulating cell-free mitochondrial DNA (ccf-mtDNA) is a damage-associated molecular pattern that reflects cell stress responses and tissue damage, but little is known about ccf-mtDNA in preeclampsia. The main objectives of this study were to determine (1) absolute concentrations of ccf-mtDNA in plasma and mitochondrial DNA content in peripheral blood mononuclear cells and (2) forms of ccf-mtDNA transport in blood from women with preeclampsia and healthy controls. In addition, we sought to establish the association between aberrance in circulating DNA-related metrics, including ccf-mtDNA and DNA clearance mechanisms, and the clinical diagnosis of preeclampsia using bootstrapped penalized logistic regression. Methods and Results Absolute concentrations of ccf-mtDNA were reduced in plasma from women with preeclampsia compared with healthy controls (P≤0.02), while mtDNA copy number in peripheral blood mononuclear cells did not differ between groups (P>0.05). While the pattern of reduced ccf-mtDNA in patients with preeclampsia remained, DNA isolation from plasma using membrane lysis buffer resulted in 1000-fold higher ccf-mtDNA concentrations in the preeclampsia group (P=0.0014) and 430-fold higher ccf-mtDNA concentrations in the control group (P<0.0001). Plasma from women with preeclampsia did not induce greater Toll-like receptor-9-induced nuclear factor kappa-light-chain enhancer of activated B cells-dependent responses in human embryonic kidney 293 cells overexpressing the human TLR-9 gene (P>0.05). Penalized regression analysis showed that women with preeclampsia were more likely to have lower concentrations of ccf-mtDNA as well as higher concentrations of nuclear DNA and DNase I compared with their matched controls. Conclusions Women with preeclampsia have aberrant circulating DNA dynamics, including reduced ccf-mtDNA concentrations and DNA clearance mechanisms, compared with gestational age-matched healthy pregnant women.

Keywords:  DNase I; cell‐free DNA; mitochondrial DNA; penalized regression analysis; preeclampsia

DOI:  https://doi.org/10.1161/JAHA.121.021726
Int J Legal Med. 2022 Jan 10.

Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq.

Hiroaki Nakanishi, Katsumi Yoneyama, Masaaki Hara, Aya Takada, Kentaro Sakai, Kazuyuki Saito.

  We tried to estimate individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq. The BAM files produced by MiSeq were viewed using Integrative Genomics Viewer (IGV) to verify mixed bases. By sorting the reads according to base type for each mixed base, partial haplotypes were determined. Then, the BAM files produced by MinKNOW were viewed using IGV. To determine haplotypes with IGV, only mixed bases determined by MiSeq were used as target bases. By sorting the reads according to base type for each target base, each contributor's haplotype was estimated. In mixed samples from two contributors, even a haplotype with a minor contribution of 5% could be distinguished from the haplotype of the major contributor. In mixed samples of three contributors (mixture ratios of 1:1:1 and 4:2:1), each haplotype could also be distinguished. Sequences of C-stretches were determined very inaccurately in the MinION analysis. Although the analysis method was simple, each haplotype was correctly detected in all mixed samples with two or three contributors in various mixture ratios by combining MinION and MiSeq. This should be useful for identifying contributors to mixed samples.

Keywords:  Contributor; MiSeq; MinION; Mitochondrial DNA; Mixed DNA sample

DOI:  https://doi.org/10.1007/s00414-021-02763-0
J Inherit Metab Dis. 2022 Jan 13.

Mitochondrial RNA processing defect caused by a SUPV3L1 mutation in two siblings with a novel neurodegenerative syndrome.

S L van Esveld, R J Rodenburg, F Al-Murshedi, E Al-Ajmi, S Al-Zuhaibi, M A Huynen, J N Spelbrink.

  SUPV3L1 encodes a helicase that is mainly localised in the mitochondria. It has been shown in vitro to possess both double-stranded RNA and DNA unwinding activity that is ATP-dependent. Here we report the first two patients for this gene who presented with a homozygous preliminary stop codon in the C-terminus of SUPV3L1. They presented with a characteristic phenotype of neurodegenerative nature with progressive spastic paraparesis, growth restriction, hypopigmentation, and predisposition to autoimmune disease. Ophthalmological examination showed severe photophobia with corneal erosions, optic atrophy, and pigmentary retinopathy, while neuroimaging showed atrophy of the optic chiasm and the pons with calcification of putamina, with intermittent and mild elevation of lactate. We show that the amino acids that are eliminated by the preliminary stop codon are highly conserved and are predicted to form an amphipathic helix. To investigate if the mutation causes mitochondrial dysfunction, we examined fibroblasts of the proband. We observed very low expression of the truncated protein, a reduction in the mature ND6 mRNA species as well as the accumulation of double stranded RNA. Lentiviral complementation with the full-length SUPV3L1 cDNA partly restored the observed RNA phenotypes, supporting that the SUPV3L1 mutation in these patients is pathogenic and the cause of the disease. This article is protected by copyright. All rights reserved.

Keywords:  SUPV3L1; degradosome; mitochondrial RNA processing; mitochondrial disease; mtDNA; neurodegenerative syndrome

DOI:  https://doi.org/10.1002/jimd.12476
J Clin Med. 2021 Dec 22. pii: 22. [Epub ahead of print]11(1):

Clinical, Histological, and Genetic Features of 25 Patients with Autosomal Dominant Progressive External Ophthalmoplegia (ad-PEO)/PEO-Plus Due to TWNK Mutations.

Laura Bermejo-Guerrero, Carlos Pablo de Fuenmayor-Fernández de la Hoz, Pablo Serrano-Lorenzo, Alberto Blázquez-Encinar, Gerardo Gutiérrez-Gutiérrez, Laura Martínez-Vicente, Lucía Galán-Dávila, Jorge García-García, Joaquín Arenas, Nuria Muelas, Aurelio Hernández-Laín, Cristina Domínguez-González, Miguel A Martín.

  Autosomal dominant mutations in the TWNK gene, which encodes a mitochondrial DNA helicase, cause adult-onset progressive external ophthalmoplegia (PEO) and PEO-plus presentations. In this retrospective observational study, we describe clinical and complementary data from 25 PEO patients with mutations in TWNK recruited from the Hospital 12 de Octubre Mitochondrial Disorders Laboratory Database. The mean ages of onset and diagnosis were 43 and 63 years, respectively. Family history was positive in 22 patients. Ptosis and PEO (92% and 80%) were the most common findings. Weakness was present in 48%, affecting proximal limbs, neck, and bulbar muscles. Exercise intolerance was present in 28%. Less frequent manifestations were cardiac (24%) and respiratory (4%) involvement, neuropathy (8%), ataxia (4%), and parkinsonism (4%). Only 28% had mild hyperCKemia. All 19 available muscle biopsies showed signs of mitochondrial dysfunction. Ten different TWNK mutations were identified, with c.1361T>G (p.Val454Gly) and c.1070G>C (p.Arg357Pro) being the most common. Before definitive genetic confirmation, 56% of patients were misdiagnosed (36% with myasthenia, 20% with oculopharyngeal muscle dystrophy). Accurate differential diagnosis and early confirmation with appropriately chosen complementary studies allow genetic counseling and the avoidance of unnecessary treatments. Thus, mitochondrial myopathies must be considered in PEO/PEO-plus presentations, and particularly, TWNK is an important cause when positive family history is present.

Keywords:  TWNK gene; mitochondrial dysfunction; mtDNA maintenance defects; progressive external ophthalmoplegia

DOI:  https://doi.org/10.3390/jcm11010022
Sci Adv. 2022 Jan 14. 8(2): eabj7307

Switching a conflicted bacterial DTD-tRNA code is essential for the emergence of mitochondria.

Jotin Gogoi, Akshay Bhatnagar, Kezia J Ann, Sambhavi Pottabathini, Raghvendra Singh, Mohd Mazeed, Santosh Kumar Kuncha, Shobha P Kruparani, Rajan Sankaranarayanan.

[Figure: see text].

DOI: https://doi.org/10.1126/sciadv.abj7307
Nat Commun. 2022 Jan 11. 13(1): 209

The RNA methyltransferase METTL8 installs m3C32 in mitochondrial tRNAsThr/Ser(UCN) to optimise tRNA structure and mitochondrial translation.

Nicole Kleiber, Nicolas Lemus-Diaz, Carina Stiller, Marleen Heinrichs, Mandy Mong-Quyen Mai, Philipp Hackert, Ricarda Richter-Dennerlein, Claudia Höbartner, Katherine E Bohnsack, Markus T Bohnsack.

Modified nucleotides in tRNAs are important determinants of folding, structure and function. Here we identify METTL8 as a mitochondrial matrix protein and active RNA methyltransferase responsible for installing m3C32 in the human mitochondrial (mt-)tRNAThr and mt-tRNASer(UCN). METTL8 crosslinks to the anticodon stem loop (ASL) of many mt-tRNAs in cells, raising the question of how methylation target specificity is achieved. Dissection of mt-tRNA recognition elements revealed U34G35 and t6A37/(ms2)i6A37, present concomitantly only in the ASLs of the two substrate mt-tRNAs, as key determinants for METTL8-mediated methylation of C32. Several lines of evidence demonstrate the influence of U34, G35, and the m3C32 and t6A37/(ms2)i6A37 modifications in mt-tRNAThr/Ser(UCN) on the structure of these mt-tRNAs. Although mt-tRNAThr/Ser(UCN) lacking METTL8-mediated m3C32 are efficiently aminoacylated and associate with mitochondrial ribosomes, mitochondrial translation is mildly impaired by lack of METTL8. Together these results define the cellular targets of METTL8 and shed new light on the role of m3C32 within mt-tRNAs.

DOI: https://doi.org/10.1038/s41467-021-27905-1
Int J Mol Sci. 2021 Dec 23. pii: 135. [Epub ahead of print]23(1):

The Influence of Mitochondrial-DNA-Driven Inflammation Pathways on Macrophage Polarization: A New Perspective for Targeted Immunometabolic Therapy in Cerebral Ischemia-Reperfusion Injury.

Sihang Yu, Jiaying Fu, Jian Wang, Yuanxin Zhao, Buhan Liu, Jiahang Wei, Xiaoyu Yan, Jing Su.

  Cerebral ischemia-reperfusion injury is related to inflammation driven by free mitochondrial DNA. At the same time, the pro-inflammatory activation of macrophages, that is, polarization in the M1 direction, aggravates the cycle of inflammatory damage. They promote each other and eventually transform macrophages/microglia into neurotoxic macrophages by improving macrophage glycolysis, transforming arginine metabolism, and controlling fatty acid synthesis. Therefore, we propose targeting the mtDNA-driven inflammatory response while controlling the metabolic state of macrophages in brain tissue to reduce the possibility of cerebral ischemia-reperfusion injury.

Keywords:  STING; cerebral ischemia-reperfusion; immune metabolism; inflammation; macrophages; mtDNA

DOI:  https://doi.org/10.3390/ijms23010135
Mol Biomed. 2021 Nov 23. 2(1): 38

Roles of host mitochondria in the development of COVID-19 pathology: Could mitochondria be a potential therapeutic target?

Kavya Srinivasan, Ashutosh Kumar Pandey, Ashlena Livingston, Sundararajan Venkatesh.

  The recent emergence of severe acute respiratory syndrome-Corona Virus 2 (SARS-CoV-2) in late 2019 and its spread worldwide caused an acute pandemic of Coronavirus disease 19 (COVID-19). Since then, COVID-19 has been under intense scrutiny as its outbreak led to significant changes in healthcare, social activities, and economic settings worldwide. Although angiotensin-converting enzyme-2 (ACE-2) receptor is shown to be the primary port of SARS-CoV-2 entry in cells, the mechanisms behind the establishment and pathologies of COVID-19 are poorly understood. As recent studies have shown that host mitochondria play an essential role in virus-mediated innate immune response, pathologies, and infection, in this review, we will discuss in detail the entry and progression of SARS-CoV-2 and how mitochondria could play roles in COVID-19 disease. We will also review the potential interactions between SARS-CoV-2 and mitochondria and discuss possible treatments, including whether mitochondria as a potential therapeutic target in COVID-19. Understanding SARS-CoV-2 and mitochondrial interactions mediated virus establishment, inflammation, and other consequences may provide a unique mechanism and conceptual advancement in finding a novel treatment for COVID-19.

Keywords:  ACE-2 receptor; COVID-19; Cytokine storm; Inflammation; Mitochondria; SARS-CoV-2

DOI:  https://doi.org/10.1186/s43556-021-00060-1
Cells. 2021 Dec 30. pii: 110. [Epub ahead of print]11(1):

Mitochondrial Dysfunction as a Hallmark of Environmental Injury.

Carolina Duarte-Hospital, Arnaud Tête, François Brial, Louise Benoit, Meriem Koual, Céline Tomkiewicz, Min Ji Kim, Etienne B Blanc, Xavier Coumoul, Sylvie Bortoli.

  Environmental factors including diet, sedentary lifestyle and exposure to pollutants largely influence human health throughout life. Cellular and molecular events triggered by an exposure to environmental pollutants are extremely variable and depend on the age, the chronicity and the doses of exposure. Only a fraction of all relevant mechanisms involved in the onset and progression of pathologies in response to toxicants has probably been identified. Mitochondria are central hubs of metabolic and cell signaling responsible for a large variety of biochemical processes, including oxidative stress, metabolite production, energy transduction, hormone synthesis, and apoptosis. Growing evidence highlights mitochondrial dysfunction as a major hallmark of environmental insults. Here, we present mitochondria as crucial organelles for healthy metabolic homeostasis and whose dysfunction induces critical adverse effects. Then, we review the multiple mechanisms of action of pollutants causing mitochondrial toxicity in link with chronic diseases. We propose the Aryl hydrocarbon Receptor (AhR) as a model of "exposome receptor", whose activation by environmental pollutants leads to various toxic events through mitochondrial dysfunction. Finally, we provide some remarks related to mitotoxicity and risk assessment.

Keywords:  environmental pollutants; mitotoxicity; xenobiotics

DOI:  https://doi.org/10.3390/cells11010110