bims-midmar 2021-10-03 papers

bims-midmar

Biomed News

on Mitochondrial DNA maintenance and replication

Issue of 2021–10–03
fourteen papers selected by
Flavia Söllner, Ludwig-Maximilians University

Advances in mitochondrial medicine and translational research.
Mitochondrial DNA and MitomiR Variations in Pancreatic Cancer: Potential Diagnostic and Prognostic Biomarkers.
Live-Cell Probe for In Situ Single-Cell Monitoring of Mitochondrial DNA Methylation.
The Role of Mitochondria in Oocyte Maturation.
Mitochondria and Mitochondrial DNA: Key Elements in the Pathogenesis and Exacerbation of the Inflammatory State Caused by COVID-19.
MicroRNAs as Factors in Bidirectional Crosstalk Between Mitochondria and the Nucleus During Cellular Senescence.
Higher DNA repair in mitochondria of long-lived species.
Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications.
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects.
A bright, red-emitting water-soluble BODIPY fluorophore as an alternative to the commercial Mito Tracker Red for high-resolution mitochondrial imaging.
Mitochondria: From Physiology to Pathology.
Denaturing cross-linking immunoprecipitation to identify footprints for RNA-binding proteins.
Can the Mitochondrial Metabolic Theory Explain Better the Origin and Management of Cancer than Can the Somatic Mutation Theory?
MitoLink: A Generic Integrated Web-based Workflow System to Evaluate Genotype-Phenotype Correlations in Human Mitochondrial Diseases: Observations from The GenomeAsia Pilot Project.

Mitochondrion. 2021 Sep 24. pii: S1567-7249(21)00134-3. [Epub ahead of print]

Advances in mitochondrial medicine and translational research.

Raviprasad Kuthethur, Keshava Prasad, Sanjiban Chakrabarty, Shama Prasada Kabekkodu, Keshav K Singh, Kumarasamy Thangaraj, Kapaettu Satyamoorthy.

  Current knowledge of mitochondrial biology and function has provided tools and technologies that helped a better understanding of the molecular etiology of complex mitochondrial disorders. Dual genetic control of this subcellular organelle function regulates various signaling mechanisms which are essential for metabolism, bioenergetics, fatty acid biosynthesis, and DNA replication & repair. Understanding nuclear mitochondrial crosstalk through advanced genomics as well as clinical perspectives is the overall basis of mitochondrial research and medicine, also the sole objective of Society for Mitochondrial Medicine and Research (SMRM) - India. The eighth virtual international conference on 'Advances in Mitochondrial Medicine and Translational Research' was organized at the Manipal School of Life Sciences, MAHE, Manipal, India, during 6 - 7 November 2020. The aim of the virtual conference was to highlight the recent advances and future perspectives that represent comprehensive clinical and fundamental research interests in the area of mitochondrial biology of human diseases. To systematically present the various findings in mitochondrial biology, the meeting was themed with specific aspects comprising (a) mitochondrial disorders: clinical & genomic perspectives, (b) mitochondria in cancer, (c) mitochondrial metabolism & disorders, and (d) mitochondrial diseases & therapy. This report provides an overview of the recent advancements in the area of mitochondrial biology and medicine that was discussed at the conference.

Keywords:  Anterograde and retrograde signaling; Cancer and mitochondria; Mitochondrial disorders; Mitochondrial metabolism; Therapeutics and mitochondria; miRNAs and mitochondria

DOI:  https://doi.org/10.1016/j.mito.2021.09.008
Int J Mol Sci. 2021 Sep 07. pii: 9692. [Epub ahead of print]22(18):

Mitochondrial DNA and MitomiR Variations in Pancreatic Cancer: Potential Diagnostic and Prognostic Biomarkers.

Loredana Moro.

  Pancreatic cancer is an aggressive disease with poor prognosis. Only about 15-20% of patients diagnosed with pancreatic cancer can undergo surgical resection, while the remaining 80% are diagnosed with locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). In these cases, chemotherapy and radiotherapy only confer marginal survival benefit. Recent progress has been made in understanding the pathobiology of pancreatic cancer, with a particular effort in discovering new diagnostic and prognostic biomarkers, novel therapeutic targets, and biomarkers that can predict response to chemo- and/or radiotherapy. Mitochondria have become a focus in pancreatic cancer research due to their roles as powerhouses of the cell, important subcellular biosynthetic factories, and crucial determinants of cell survival and response to chemotherapy. Changes in the mitochondrial genome (mtDNA) have been implicated in chemoresistance and metastatic progression in some cancer types. There is also growing evidence that changes in microRNAs that regulate the expression of mtDNA-encoded mitochondrial proteins (mitomiRs) or nuclear-encoded mitochondrial proteins (mitochondria-related miRs) could serve as diagnostic and prognostic cancer biomarkers. This review discusses the current knowledge on the clinical significance of changes of mtDNA, mitomiRs, and mitochondria-related miRs in pancreatic cancer and their potential role as predictors of cancer risk, as diagnostic and prognostic biomarkers, and as molecular targets for personalized cancer therapy.

Keywords:  mitochondrial genome; mitochondrial microRNAs; pancreatic cancer

DOI:  https://doi.org/10.3390/ijms22189692
ACS Sens. 2021 Sep 29.

Live-Cell Probe for In Situ Single-Cell Monitoring of Mitochondrial DNA Methylation.

Han Zhao, Donghan Ma, Junkai Xie, Oscar Sanchez, Fang Huang, Chongli Yuan.

  Mitochondria, as the center of energy production, play an important role in cell homeostasis by regulating the cellular metabolism and mediating the cellular response to stress. Epigenetic changes such as DNA and histone methylation have been increasingly recognized to play a significant role in homeostasis and stress response. The cross-talking between the metabolome and the epigenome has attracted significant attention in recent years but with a major focus on how metabolism contributes to epigenomic changes. Few studies have focused on how epigenetic modifications may alter the mitochondrial composition and activity. In this work, we designed a novel probe targeting methylated CpGs of mitochondrial DNA (mtDNA). We demonstrated the capability of our probe to reveal the spatial distribution of methylated mtDNA and capture the mtDNA methylation changes at a single-cell level. We were also able to track single-cell mtDNA and nDNA methylation simultaneously and discovered the unsynchronized dynamics of the nucleus and mitochondria. Our tool offers a unique opportunity to understand the epigenetic regulation of mtDNA and its dynamic response to the microenvironment and cellular changes.

Keywords:  DNA CpG methylation; epigenetics; live-cell probe; mitochondria; super-resolution microscopy

DOI:  https://doi.org/10.1021/acssensors.1c00731
Cells. 2021 Sep 19. pii: 2484. [Epub ahead of print]10(9):

The Role of Mitochondria in Oocyte Maturation.

Anastasia Kirillova, Johan E J Smitz, Gennady T Sukhikh, Ilya Mazunin.

  With the nucleus as an exception, mitochondria are the only animal cell organelles containing their own genetic information, called mitochondrial DNA (mtDNA). During oocyte maturation, the mtDNA copy number dramatically increases and the distribution of mitochondria changes significantly. As oocyte maturation requires a large amount of ATP for continuous transcription and translation, the availability of the right number of functional mitochondria is crucial. There is a correlation between the quality of oocytes and both the amount of mtDNA and the amount of ATP. Suboptimal conditions of in vitro maturation (IVM) might lead to changes in the mitochondrial morphology as well as alternations in the expression of genes encoding proteins associated with mitochondrial function. Dysfunctional mitochondria have a lower ability to counteract reactive oxygen species (ROS) production which leads to oxidative stress. The mitochondrial function might be improved with the application of antioxidants and significant expectations are laid on the development of new IVM systems supplemented with mitochondria-targeted reagents. Different types of antioxidants have been tested already on animal models and human rescue IVM oocytes, showing promising results. This review focuses on the recent observations on oocytes' intracellular mitochondrial distribution and on mitochondrial genomes during their maturation, both in vivo and in vitro. Recent mitochondrial supplementation studies, aiming to improve oocyte developmental potential, are summarized.

Keywords:  IVM; mitochondria distribution; mitochondrial supplementation reagents; mtDNA copy number; oocyte maturation

DOI:  https://doi.org/10.3390/cells10092484
Medicina (Kaunas). 2021 Sep 03. pii: 928. [Epub ahead of print]57(9):

Mitochondria and Mitochondrial DNA: Key Elements in the Pathogenesis and Exacerbation of the Inflammatory State Caused by COVID-19.

José J Valdés-Aguayo, Idalia Garza-Veloz, José I Badillo-Almaráz, Sofia Bernal-Silva, Maria C Martínez-Vázquez, Vladimir Juárez-Alcalá, José R Vargas-Rodríguez, María L Gaeta-Velasco, Carolina González-Fuentes, Lorena Ávila-Carrasco, Margarita L Martinez-Fierro.

  Background and Objectives. The importance of mitochondria in inflammatory pathologies, besides providing energy, is associated with the release of mitochondrial damage products, such as mitochondrial DNA (mt-DNA), which may perpetuate inflammation. In this review, we aimed to show the importance of mitochondria, as organelles that produce energy and intervene in multiple pathologies, focusing mainly in COVID-19 and using multiple molecular mechanisms that allow for the replication and maintenance of the viral genome, leading to the exacerbation and spread of the inflammatory response. The evidence suggests that mitochondria are implicated in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which forms double-membrane vesicles and evades detection by the cell defense system. These mitochondrion-hijacking vesicles damage the integrity of the mitochondrion's membrane, releasing mt-DNA into circulation and triggering the activation of innate immunity, which may contribute to an exacerbation of the pro-inflammatory state. Conclusions. While mitochondrial dysfunction in COVID-19 continues to be studied, the use of mt-DNA as an indicator of prognosis and severity is a potential area yet to be explored.

Keywords:  COVID-19; SARS-CoV-2; mitochondrial DNA; mitochondrial dysfunction

DOI:  https://doi.org/10.3390/medicina57090928
Front Physiol. 2021 ;12 734976

MicroRNAs as Factors in Bidirectional Crosstalk Between Mitochondria and the Nucleus During Cellular Senescence.

Chiara Giordani, Andrea Silvestrini, Angelica Giuliani, Fabiola Olivieri, Maria Rita Rippo.

  Mitochondria are essential organelles that generate most of the chemical energy to power the cell through ATP production, thus regulating cell homeostasis. Although mitochondria have their own independent genome, most of the mitochondrial proteins are encoded by nuclear genes. An extensive bidirectional communication network between mitochondria and the nucleus has been discovered, thus making them semi-autonomous organelles. The nucleus-to-mitochondria signaling pathway, called Anterograde Signaling Pathway can be deduced, since the majority of mitochondrial proteins are encoded in the nucleus, less is known about the opposite pathway, the so-called mitochondria-to-nucleus retrograde signaling pathway. Several studies have demonstrated that non-coding RNAs are essential "messengers" of this communication between the nucleus and the mitochondria and that they might have a central role in the coordination of important mitochondrial biological processes. In particular, the finding of numerous miRNAs in mitochondria, also known as mitomiRs, enabled insights into their role in mitochondrial gene transcription. MitomiRs could act as important mediators of this complex crosstalk between the nucleus and the mitochondria. Mitochondrial homeostasis is critical for the physiological processes of the cell. Disruption at any stage in their metabolism, dynamics and bioenergetics could lead to the production of considerable amounts of reactive oxygen species and increased mitochondrial permeability, which are among the hallmarks of cellular senescence. Extensive changes in mitomiR expression and distribution have been demonstrated in senescent cells, those could possibly lead to an alteration in mitochondrial homeostasis. Here, we discuss the emerging putative roles of mitomiRs in the bidirectional communication pathways between mitochondria and the nucleus, with a focus on the senescence-associated mitomiRs.

Keywords:  microRNA; mitochondria; mitomiRs; mitonuclear communication; senescence

DOI:  https://doi.org/10.3389/fphys.2021.734976
Aging (Albany NY). 2021 Sep 27. undefined(undefined):

Higher DNA repair in mitochondria of long-lived species.

Gustavo Barja.



Keywords:  DNA repair; aging rate; base excision repair; longevity; mitochondria

DOI:  https://doi.org/10.18632/aging.203595
Pharmacol Ther. 2021 Sep 27. pii: S0163-7258(21)00197-2. [Epub ahead of print] 107995

Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications.

Brian Li, Pola Kalinowski, BaRun Kim, Andrew Pauls, Damon Poburko.

  The past thirty years have seen a surge in interest in pathophysiological roles of mitochondrial, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 - 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should future clinical applications of mCN measurements.

Keywords:  Cancer; Cardiovascular disease; Digital PCR; High throughput sequencing; Mitochondria; Mitochondrial DNA

DOI:  https://doi.org/10.1016/j.pharmthera.2021.107995
BMC Bioinformatics. 2021 Sep 28. 22(1): 468

rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects.

Manon Geerts, Achim Schnaufer, Frederik Van den Broeck.

   BACKGROUND: The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been generated and analyzed, information about the diversity, structure and evolution of their mitochondrial genomes remains fragmentary, mainly because of their extraordinary complexity. Indeed, unicellular flagellates of the order Kinetoplastida contain structurally the most complex mitochondrial genome of all eukaryotes, organized as a giant network of homogeneous maxicircles and heterogeneous minicircles. We recently developed KOMICS, an analysis toolkit that automates the assembly and circularization of the mitochondrial genomes of Kinetoplastid parasites. While this tool overcomes the limitation of extracting mitochondrial assemblies from Next-Generation Sequencing datasets, interpreting and visualizing the genetic (dis)similarity within and between samples remains a time-consuming process.
RESULTS: Here, we present a new analysis toolkit-rKOMICS-to streamline the analyses of minicircle sequence diversity in population-scale genome projects. rKOMICS is a user-friendly R package that has simple installation requirements and that is applicable to all 27 trypanosomatid genera. Once minicircle sequence alignments are generated, rKOMICS allows to examine, summarize and visualize minicircle sequence diversity within and between samples through the analyses of minicircle sequence clusters. We showcase the functionalities of the (r)KOMICS tool suite using a whole-genome sequencing dataset from a recently published study on the history of diversification of the Leishmania braziliensis species complex in Peru. Analyses of population diversity and structure highlighted differences in minicircle sequence richness and composition between Leishmania subspecies, and between subpopulations within subspecies.
CONCLUSION: The rKOMICS package establishes a critical framework to manipulate, explore and extract biologically relevant information from mitochondrial minicircle assemblies in tens to hundreds of samples simultaneously and efficiently. This should facilitate research that aims to develop new molecular markers for identifying species-specific minicircles, or to study the ancestry of parasites for complementary insights into their evolutionary history.

Keywords:  Assembly; Clustering; Kinetoplast; Leishmania; Minicircles; Parasites; Sequencing; Trypanosoma

DOI:  https://doi.org/10.1186/s12859-021-04384-1
J Mater Chem B. 2021 Sep 29.

A bright, red-emitting water-soluble BODIPY fluorophore as an alternative to the commercial Mito Tracker Red for high-resolution mitochondrial imaging.

Jiang-Lin Wang, Lu Zhang, Lian-Xun Gao, Ji-Lei Chen, Te Zhou, Yi Liu, Feng-Lei Jiang.

With the emergence and rapid development of super-resolution fluorescence microscopy, monitoring of mitochondrial morphological changes has aroused great interest for exploring the role of mitochondria in the process of cell metabolism. However, in the absence of water-soluble, photostable and low-toxicity fluorescent dyes, ultra-high-resolution mitochondrial imaging is still challenging. Herein, we designed two fluorescent BODIPY dyes, namely Mito-BDP 630 and Mito-BDP 760, for mitochondrial imaging. The results proved that Mito-BDP 760 underwent aggregation-caused quenching (ACQ) in the aqueous matrix owing to its hydrophobicity and was inaccessible to the cells, which restricted its applications in mitochondrial imaging. In stark contrast, water-soluble Mito-BDP 630 readily penetrated cellular and mitochondrial membranes for mitochondrial imaging with high dye densities under wash-free conditions as driven by membrane potential. As a comparison, Mito Tracker Red presented high photobleaching (the fluorescence intensity dropped by nearly 50%) and high phototoxicity after irradiation by a laser for 30 min. However, Mito-BDP 630 possessed excellent biocompatibility, photostability and chemical stability. Furthermore, clear and bright mitochondria distribution in living HeLa cells after incubation with Mito-BDP 630 could be observed by CLSM. Convincingly, the morphology and cristae of mitochondria could be visualized using an ultra-high-resolution microscope. In short, Mito-BDP 630 provided a powerful and convenient tool for monitoring mitochondrial morphologies in living cells. Given the facile synthesis, photobleaching resistance and low phototoxicity of Mito-BDP 630, it is an alternative to the commercial Mito Tracker Red.

DOI: https://doi.org/10.1039/d1tb01585k
Life (Basel). 2021 Sep 21. pii: 991. [Epub ahead of print]11(9):

Mitochondria: From Physiology to Pathology.

Francesco Bruni.

Over the past decade, the role of mitochondria has extended beyond those tasks for which these organelles are historically known [...].

DOI: https://doi.org/10.3390/life11090991
STAR Protoc. 2021 Dec 17. 2(4): 100819

Denaturing cross-linking immunoprecipitation to identify footprints for RNA-binding proteins.

Michael Rosenberg, Vered Levy, Verena K Maier, Barry Kesner, Roy Blum, Jeannie T Lee.

  The isolation of protein-RNA complexes in the "denaturing cross-linked RNA immunoprecipitation" (dCLIP) protocol is based on biotin-tagging proteins of interest, UV cross-linking RNA to protein in vivo, RNase protection assay, and isolating RNA-protein complexes under denaturing conditions over a streptavidin column. Insofar as conventional antibody-based CLIP assays have been challenging to apply to Polycomb complexes, dCLIP has been applied successfully and yields small RNA footprints from which de novo motif analysis can be performed to identify RNA binding motifs. For complete details on the use and execution of this protocol, please refer to Rosenberg et al. (2017).

Keywords:  Genetics; Genomics; Molecular Biology; Molecular/Chemical Probes; Protein Biochemistry; Systems biology

DOI:  https://doi.org/10.1016/j.xpro.2021.100819
Metabolites. 2021 Aug 25. pii: 572. [Epub ahead of print]11(9):

Can the Mitochondrial Metabolic Theory Explain Better the Origin and Management of Cancer than Can the Somatic Mutation Theory?

Thomas N Seyfried, Christos Chinopoulos.

  A theory that can best explain the facts of a phenomenon is more likely to advance knowledge than a theory that is less able to explain the facts. Cancer is generally considered a genetic disease based on the somatic mutation theory (SMT) where mutations in proto-oncogenes and tumor suppressor genes cause dysregulated cell growth. Evidence is reviewed showing that the mitochondrial metabolic theory (MMT) can better account for the hallmarks of cancer than can the SMT. Proliferating cancer cells cannot survive or grow without carbons and nitrogen for the synthesis of metabolites and ATP (Adenosine Triphosphate). Glucose carbons are essential for metabolite synthesis through the glycolysis and pentose phosphate pathways while glutamine nitrogen and carbons are essential for the synthesis of nitrogen-containing metabolites and ATP through the glutaminolysis pathway. Glutamine-dependent mitochondrial substrate level phosphorylation becomes essential for ATP synthesis in cancer cells that over-express the glycolytic pyruvate kinase M2 isoform (PKM2), that have deficient OxPhos, and that can grow in either hypoxia (0.1% oxygen) or in cyanide. The simultaneous targeting of glucose and glutamine, while elevating levels of non-fermentable ketone bodies, offers a simple and parsimonious therapeutic strategy for managing most cancers.

Keywords:  IDH1; chimpanzees; evolution; fermentation; glutaminolysis; glycolysis; ketogenic metabolic therapy; metastasis; mitochondrial substrate level phosphorylation; mutations; oncogenes; respiration

DOI:  https://doi.org/10.3390/metabo11090572
Mitochondrion. 2021 Sep 24. pii: S1567-7249(21)00131-8. [Epub ahead of print]

MitoLink: A Generic Integrated Web-based Workflow System to Evaluate Genotype-Phenotype Correlations in Human Mitochondrial Diseases: Observations from The GenomeAsia Pilot Project.

Rakesh Kumar, Neeraj K Rajput, Bani Jolly, Amol Narwade, Anshu Bhardwaj.

  MitoLink is a generic, scalable and modular web-based workflow system developed to study genotype-phenotype correlations in human mitochondrial diseases. MitoLink integrates applications for assessment of genomic variation and currently houses genome-wide datasets from GenomeAsia Pilot project, gnomAD, ClinVar and DisGenNet. In this study, a reference list of nearly 3975 proteins (both nuclear and mitochondrial encoded) with mitochondrial function is reported. This protein set is mapped to disease associated variants in the GenomeAsia Project and DisGenNet and evaluated for pathogenicity as defined by ClinVar. Observations of shared genetic components in potential comorbidities are discussed from gene-disease network in Asian population, however, the platform is generic and can be applied to any population dataset. MitoLink is a unique customized workflow system that allows for systematic storage, extraction, analysis and visualization of genomic variation to understand genotype-phenotype correlations for mitochondrial diseases. Given the modularity of tool and data integration, MitoLink is a scalable system that can accommodate a diverse set of applications linked via standard data structure within the framework of Galaxy. MitoLink is built on FAIR principles and supports creation of reproducible workflows towards understanding genotype-phenotype correlations across several disease phenotypes globally.

Keywords:  NGS; galaxy workflow; genome Asia; genome variation; genotype-phenotype; mitochondrial diseases

DOI:  https://doi.org/10.1016/j.mito.2021.09.005