bims-midmar Biomed News
on Mitochondrial DNA maintenance and replication
Issue of 2021‒12‒05
ten papers selected by
Flavia Söllner
Ludwig-Maximilians University
  1. The potential of mitochondrial genome engineering.
  2. Fluorescence Imaging of Mitochondrial DNA Base Excision Repair Reveals Dynamics of Oxidative Stress Responses.
  3. Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues.
  4. The FusX TALE Base Editor (FusXTBE) for Rapid Mitochondrial DNA Programming of Human Cells In Vitro and Zebrafish Disease Models In Vivo.
  5. Mitochondrial DNA and TLR9 activation contribute to SARS-CoV-2-induced endothelial cell damage.
  6. Mitochondrial TFAM as a Signaling Regulator between Cellular Organelles: A Perspective on Metabolic Diseases.
  7. Mitochondrial DNA and Alzheimer's disease: a first case-control study of the Tunisian population.
  8. METTLing in the right place: METTL8 is a mitochondrial tRNA-specific methyltransferase.
  9. Pediatric single large-scale mtDNA deletion syndromes: The power of patient reported outcomes.
  10. Mitochondrial homeostasis is maintained in the absence of autophagy.
  1. Nat Rev Genet. 2021 Dec 02.
    The potential of mitochondrial genome engineering.
    Pedro Silva-Pinheiro, Michal Minczuk.
      Mitochondria are subject to unique genetic control by both nuclear DNA and their own genome, mitochondrial DNA (mtDNA), of which each mitochondrion contains multiple copies. In humans, mutations in mtDNA can lead to devastating, heritable, multi-system diseases that display different tissue-specific presentation at any stage of life. Despite rapid advances in nuclear genome engineering, for years, mammalian mtDNA has remained resistant to genetic manipulation, hampering our ability to understand the mechanisms that underpin mitochondrial disease. Recent developments in the genetic modification of mammalian mtDNA raise the possibility of using genome editing technologies, such as programmable nucleases and base editors, for the treatment of hereditary mitochondrial disease.
    DOI:  https://doi.org/10.1038/s41576-021-00432-x
  2. Angew Chem Int Ed Engl. 2021 Dec 01.
    Fluorescence Imaging of Mitochondrial DNA Base Excision Repair Reveals Dynamics of Oxidative Stress Responses.
    Yong Woong Jun, Eddy Albarran, David L Wilson, Jun Ding, Eric T Kool.
      Mitochondrial function in cells declines with aging and with neurodegeneration, due in large part to accumulated mutations in mitochondrial DNA (mtDNA) that arise from deficient DNA repair. However, measuring this repair activity is challenging. Here we employ a molecular approach for visualizing mitochondrial base excision repair (BER) activity in situ by use of a fluorescent probe ( UBER ) that reacts rapidly with AP sites resulting from BER activity. Administering the probe to cultured cells revealed signals that were localized to mitochondria, enabling selective observation of mtDNA BER intermediates. The probe showed elevated DNA repair activity under oxidative stress, and responded to suppression of glycosylase activity. Furthermore, the probe illuminated the time lag between the initiation of oxidative stress and the initial step of BER. Absence of MTH1 in cells resulted in elevated demand for BER activity upon extended oxidative stress, while the absence of OGG1 activity limited glycosylation capacity.
    Keywords:  DNA damage and repair; dynamics; fluorescence probes; mitochondrial DNA
    DOI:  https://doi.org/10.1002/anie.202111829
  3. Nucleic Acids Res. 2021 Nov 29. pii: gkab1179. [Epub ahead of print]
    Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues.
    Iacopo Bicci, Claudia Calabrese, Zoe J Golder, Aurora Gomez-Duran, Patrick F Chinnery.
      Methylation on CpG residues is one of the most important epigenetic modifications of nuclear DNA, regulating gene expression. Methylation of mitochondrial DNA (mtDNA) has been studied using whole genome bisulfite sequencing (WGBS), but recent evidence has uncovered technical issues which introduce a potential bias during methylation quantification. Here, we validate the technical concerns of WGBS, and develop and assess the accuracy of a new protocol for mtDNA nucleotide variant-specific methylation using single-molecule Oxford Nanopore Sequencing (ONS). Our approach circumvents confounders by enriching for full-length molecules over nuclear DNA. Variant calling analysis against showed that 99.5% of homoplasmic mtDNA variants can be reliably identified providing there is adequate sequencing depth. We show that some of the mtDNA methylation signal detected by ONS is due to sequence-specific false positives introduced by the technique. The residual signal was observed across several human primary and cancer cell lines and multiple human tissues, but was always below the error threshold modelled using negative controls. We conclude that there is no evidence for CpG methylation in human mtDNA, thus resolving previous controversies. Additionally, we developed a reliable protocol to study epigenetic modifications of mtDNA at single-molecule and single-base resolution, with potential applications beyond CpG methylation.
    DOI:  https://doi.org/10.1093/nar/gkab1179
  4. CRISPR J. 2021 Nov 30.
    The FusX TALE Base Editor (FusXTBE) for Rapid Mitochondrial DNA Programming of Human Cells In Vitro and Zebrafish Disease Models In Vivo.
    Ankit Sabharwal, Bibekananda Kar, Santiago Restrepo-Castillo, Shannon R Holmberg, Neal D Mathew, Benjamin Luke Kendall, Ryan P Cotter, Zachary WareJoncas, Christoph Seiler, Eiko Nakamaru-Ogiso, Karl J Clark, Stephen C Ekker.
      Functional analyses of mitochondria have been hampered by few effective approaches to manipulate mitochondrial DNA (mtDNA) and a lack of existing animal models. Recently a TALE-derived base editor was shown to induce C-to-T (or G-to-A) sequence changes in mtDNA. We report here the FusX TALE Base Editor (FusXTBE) to facilitate broad-based access to TALE mitochondrial base editing technology. TALE Writer is a de novo in silico design tool to map potential mtDNA base editing sites. FusXTBE was demonstrated to function with comparable activity to the initial base editor in human cells in vitro. Zebrafish embryos were used as a pioneering in vivo test system, with FusXTBE inducing 90+% editing efficiency in mtDNA loci as an example of near-complete induction of mtDNA heteroplasmy in vivo. Gene editing specificity as precise as a single nucleotide was observed for a protein-coding gene. Nondestructive genotyping enables single-animal mtDNA analyses for downstream biological functional genomic applications. FusXTBE is a new gene editing toolkit for exploring important questions in mitochondrial biology and genetics.
    DOI:  https://doi.org/10.1089/crispr.2021.0061
  5. Vascul Pharmacol. 2021 Nov 24. pii: S1537-1891(21)00118-X. [Epub ahead of print] 106946
    Mitochondrial DNA and TLR9 activation contribute to SARS-CoV-2-induced endothelial cell damage.
    Tiago J Costa, Simone R Potje, Thais F C Fraga-Silva, Júlio A da Silva-Neto, Paula R Barros, Daniel Rodrigues, Mirele R Machado, Ronaldo B Martins, Rosangela A Santos-Eichler, Maira N Benatti, Keyla S G de Sá, Carlos Eduardo L Almado, Ítalo A Castro, Marjorie C Pontelli, Leonardo La Serra, Fernando S Carneiro, Christiane Becari, Paulo Louzada-Junior, Rene D R Oliveira, Dario S Zamboni, Eurico Arruda, Maria Auxiliadora-Martins, Fernanda R C Giachini, Vânia L D Bonato, Natasha E Zachara, Gisele F Bomfim, Rita C Tostes.
      BACKGROUND AND PURPOSE: Mitochondria play a central role in the host response to viral infection and immunity, being key to antiviral signaling and exacerbating inflammatory processes. Mitochondria and Toll-like receptor (TLR) have been suggested as potential targets in SARS-CoV-2 infection. However, the involvement of TLR9 in SARS-Cov-2-induced endothelial dysfunction and potential contribution to cardiovascular complications in COVID-19 have not been demonstrated. This study determined whether infection of endothelial cells by SARS-CoV-2 affects mitochondrial function and induces mitochondrial DNA (mtDNA) release. We also questioned whether TLR9 signaling mediates the inflammatory responses induced by SARS-CoV-2 in endothelial cells.EXPERIMENTAL APPROACH: Human umbilical vein endothelial cells (HUVECs) were infected by SARS-CoV-2 and immunofluorescence was used to confirm the infection. Mitochondrial function was analyzed by specific probes and mtDNA levels by real-time polymerase chain reaction (RT-PCR). Inflammatory markers were measured by ELISA, protein expression by western blot, intracellular calcium (Ca2+) by FLUOR-4, and vascular reactivity with a myography.
    KEY RESULTS: SARS-CoV-2 infected HUVECs, which express ACE2 and TMPRSS2 proteins, and promoted mitochondrial dysfunction, i.e. it increased mitochondria-derived superoxide anion, mitochondrial membrane potential, and mtDNA release, leading to activation of TLR9 and NF-kB, and release of cytokines. SARS-CoV-2 also decreased nitric oxide synthase (eNOS) expression and inhibited Ca2+ responses in endothelial cells. TLR9 blockade reduced SARS-CoV-2-induced IL-6 release and prevented decreased eNOS expression. mtDNA increased vascular reactivity to endothelin-1 (ET-1) in arteries from wild type, but not TLR9 knockout mice. These events were recapitulated in serum samples from COVID-19 patients, that exhibited increased levels of mtDNA compared to sex- and age-matched healthy subjects and patients with comorbidities.
    CONCLUSION AND APPLICATIONS: SARS-CoV-2 infection impairs mitochondrial function and activates TLR9 signaling in endothelial cells. TLR9 triggers inflammatory responses that lead to endothelial cell dysfunction, potentially contributing to the severity of symptoms in COVID-19. Targeting mitochondrial metabolic pathways may help to define novel therapeutic strategies for COVID-19.
    Keywords:  Endothelial dysfunction; Mitochondria; SARS-CoV-2; Toll like receptor 9
    DOI:  https://doi.org/10.1016/j.vph.2021.106946
  6. Diabetes Metab J. 2021 Nov;45(6): 853-865
    Mitochondrial TFAM as a Signaling Regulator between Cellular Organelles: A Perspective on Metabolic Diseases.
    Jin-Ho Koh, Yong-Woon Kim, Dae-Yun Seo, Tae-Seo Sohn.
      Tissues actively involved in energy metabolism are more likely to face metabolic challenges from bioenergetic substrates and are susceptible to mitochondrial dysfunction, leading to metabolic diseases. The mitochondria receive signals regarding the metabolic states in cells and transmit them to the nucleus or endoplasmic reticulum (ER) using calcium (Ca2+) for appropriate responses. Overflux of Ca2+ in the mitochondria or dysregulation of the signaling to the nucleus and ER could increase the incidence of metabolic diseases including insulin resistance and type 2 diabetes mellitus. Mitochondrial transcription factor A (Tfam) may regulate Ca2+ flux via changing the mitochondrial membrane potential and signals to other organelles such as the nucleus and ER. Since Tfam is involved in metabolic function in the mitochondria, here, we discuss the contribution of Tfam in coordinating mitochondria-ER activities for Ca2+ flux and describe the mechanisms by which Tfam affects mitochondrial Ca2+ flux in response to metabolic challenges.
    Keywords:  Calcium; Cell nucleus; Diabetes mellitus, type 2; Endoplasmic reticulum; Mitochondria; TFAM protein
    DOI:  https://doi.org/10.4093/dmj.2021.0138
  7. Mol Biol Rep. 2021 Dec 01.
    Mitochondrial DNA and Alzheimer's disease: a first case-control study of the Tunisian population.
    Nesrine Ben Salem, Sami Boussetta, Itziar de Rojas, Sonia Moreno-Grau, Laura Montrreal, Narjes Mokni, Imene Mahmoud, Samia Younes, Nizar Daouassi, Mahbouba Frih-Ayed, Afef Hammami, Amel Ben Ammar Elgaaied, Agustín Ruiz, Lotfi Cherni.
      BACKGROUND: Alzheimer's disease (AD) is the most common neurodegenerative disorder in humans and presents a major health problem throughout the world. The etiology of AD is complex, and many factors are implicated, including mitochondria. Mitochondrial alteration has been proposed as a possible cause of AD. Therefore, several studies have focused on finding an association between inherited mitochondrial DNA variants and AD onset.METHODS: In this study, we looked, for the first time, for a potential association between mitochondrial haplogroups or polymorphisms and AD in the Tunisian population. We also evaluated the distribution of the major genetic risk factor for AD, the apolipoprotein E epsilon 4 (APOE ε4), in this population. In total, 159 single-nucleotide polymorphisms (SNPs) of mitochondrial DNA haplogroups were genotyped in 254 individuals (58 patients and 196 controls). An additional genotyping of APOE ε4 was performed.
    RESULTS: No significant association between mitochondrial haplogroups and AD was found. However, two individual SNPs, A5656G (p = 0.03821, OR = 10.46) and A13759G (p = 0.03719, OR = 10.78), showed a significant association with AD. APOE 4 was confirmed as a risk factor for AD (p = 0.000014).
    CONCLUSION: Our findings may confirm the absence of a relation between mitochondrial haplogroups and AD and support the possible involvement of some inherited variants in the pathogenicity of AD.
    Keywords:  Alzheimer’s disease (AD); Genetic diversity; Mitochondrial SNPs; Tunisian population; mtDNA haplogroups
    DOI:  https://doi.org/10.1007/s11033-021-06978-7
  8. Mol Cell. 2021 Dec 02. pii: S1097-2765(21)00978-3. [Epub ahead of print]81(23): 4765-4767
    METTLing in the right place: METTL8 is a mitochondrial tRNA-specific methyltransferase.
    Eva Kowalinski, Juan D Alfonzo.
      Schöller et al. (2021) discovered that METTL8, thought of as an mRNA modifier, is a tRNA-specific mitochondrial enzyme important for mitochondrial translation and function. Paradoxically, increased expression of METTL8 is associated with high respiratory rates in pancreatic cancers.
    DOI:  https://doi.org/10.1016/j.molcel.2021.11.009
  9. Mol Genet Metab. 2021 Nov 14. pii: S1096-7192(21)00822-2. [Epub ahead of print]
    Pediatric single large-scale mtDNA deletion syndromes: The power of patient reported outcomes.
    Elizabeth Reynolds, Matthew Byrne, Rebecca Ganetzky, Sumit Parikh.
      There is a limited understanding of system-level clinical outcomes and interventions associated with single large-scale mitochondrial DNA deletion syndromes (SLSMDS). Additionally, no research exists that describes patient reported outcomes (PROs) of children with SLSMDS. A global and observational registry was established to understand the multi-systemic course of SLSMDS and track clinical outcomes. The development and design of the registry is described. Demographic characteristics, history and diagnoses, and system level prevalence of problems and interventions are reported for 42 children. System level problems and interventions include information on the following body systems: audiology, cardiac, endocrine, gastrointestinal (including pancreatic and hepatobiliary system), hematological, metabolic, neurological (including autonomic, mobility, & learning), ophthalmic, psychiatric, renal, and respiratory. Results emphasize the need of patient registries and suggest that the diagnostic odyssey and burden of disease for children with SLSMDS is significant. System-level findings may help families and clinical providers with diagnosis, prognostication, and treatment. A multidisciplinary team of clinical experts with a central coordinating specialist for children with SLSMDS is recommended.
    Keywords:  Kearns-Sayre syndrome; Pearson syndrome; Rare disease registry; Single large-scale mitochondrial deletion syndromes; mtDNA
    DOI:  https://doi.org/10.1016/j.ymgme.2021.11.004
  10. Mol Cell Oncol. 2021 ;8(5): 1984162
    Mitochondrial homeostasis is maintained in the absence of autophagy.
    Christina G Towers.
      Autophagy is a central recycling process, and it plays a complex role in cancer. We discovered that when autophagy is blocked, cancer cells compensate by increasing mitochondrial-derived vesicles. However, there are many unanswered questions remaining, particularly in the context of the dual roles of autophagy in cancer.
    Keywords:  Autophagy; cancer; mitochondria; mitochondrial derived vesicles; mitophagy
    DOI:  https://doi.org/10.1080/23723556.2021.1984162
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