bims-midmar 2022-02-20 papers

bims-midmar

Biomed News

on Mitochondrial DNA maintenance and replication

Issue of 2022–02–20
thirteen papers selected by
Flavia Söllner, Ludwig-Maximilians University

Mitochondrial Genome Editing to Treat Human Osteoarthritis-A Narrative Review.
Functional Role of Mitochondrial DNA in Cancer Progression.
Transcription Factor Movement and Exercise-Induced Mitochondrial Biogenesis in Human Skeletal Muscle: Current Knowledge and Future Perspectives.
LONP-1 and ATFS-1 sustain deleterious heteroplasmy by promoting mtDNA replication in dysfunctional mitochondria.
Metabolic Reprogramming in Response to Alterations of Mitochondrial DNA and Mitochondrial Dysfunction in Gastric Adenocarcinoma.
Mitochondrial DNA content reduction in the most fertile spermatozoa is accompanied by increased mitochondrial DNA rearrangement.
Neuralized-like protein 4 (NEURL4) mediates ADP-ribosylation of mitochondrial proteins.
A Method for Evaluation of the Level of Circulating Mitochondrial DNA by ND1 and ND2 Genes.
Single-cell mtDNA heteroplasmy in colorectal cancer.
The application of machine learning to predict genetic relatedness using human mtDNA hypervariable region I sequences.
Hijacking of host mitochondria by Toxoplasma gondii and SARS-CoV-2.
LONP-1 aids propagation of deleterious mtDNA.
Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system?

Int J Mol Sci. 2022 Jan 27. pii: 1467. [Epub ahead of print]23(3):

Mitochondrial Genome Editing to Treat Human Osteoarthritis-A Narrative Review.

Gang Zhong, Henning Madry, Magali Cucchiarini.

  Osteoarthritis (OA) is a severe, common chronic orthopaedic disorder characterised by a degradation of the articular cartilage with an incidence that increases over years. Despite the availability of various clinical options, none can stop the irreversible progression of the disease to definitely cure OA. Various mutations have been evidenced in the mitochondrial DNA (mtDNA) of cartilage cells (chondrocytes) in OA, leading to a dysfunction of the mitochondrial oxidative phosphorylation processes that significantly contributes to OA cartilage degeneration. The mitochondrial genome, therefore, represents a central, attractive target for therapy in OA, especially using genome editing procedures. In this narrative review article, we present and discuss the current advances and breakthroughs in mitochondrial genome editing as a potential, novel treatment to overcome mtDNA-related disorders such as OA. While still in its infancy and despite a number of challenges that need to be addressed (barriers to effective and site-specific mtDNA editing and repair), such a strategy has strong value to treat human OA in the future, especially using the groundbreaking clustered regularly interspaced short palindromic repeats (CRIPSR)/CRISPR-associated 9 (CRISPR/Cas9) technology and mitochondrial transplantation approaches.

Keywords:  genome editing; human osteoarthritis; mitochondria; mitochondrial DNA

DOI:  https://doi.org/10.3390/ijms23031467
Int J Mol Sci. 2022 Jan 31. pii: 1659. [Epub ahead of print]23(3):

Functional Role of Mitochondrial DNA in Cancer Progression.

Yang-Hsiang Lin, Siew-Na Lim, Cheng-Yi Chen, Hsiang-Cheng Chi, Chau-Ting Yeh, Wey-Ran Lin.

  Mitochondrial DNA (mtDNA) has been identified as a significant genetic biomarker in disease, cancer and evolution. Mitochondria function as modulators for regulating cellular metabolism. In the clinic, mtDNA variations (mutations/single nucleotide polymorphisms) and dysregulation of mitochondria-encoded genes are associated with survival outcomes among cancer patients. On the other hand, nuclear-encoded genes have been found to regulate mitochondria-encoded gene expression, in turn regulating mitochondrial homeostasis. These observations suggest that the crosstalk between the nuclear genome and mitochondrial genome is important for cellular function. Therefore, this review summarizes the significant mechanisms and functional roles of mtDNA variations (DNA level) and mtDNA-encoded genes (RNA and protein levels) in cancers and discusses new mechanisms of crosstalk between mtDNA and the nuclear genome.

Keywords:  SNP; cancer; mitochondria; mutation; ncRNA; prognostic marker

DOI:  https://doi.org/10.3390/ijms23031659
Int J Mol Sci. 2022 Jan 28. pii: 1517. [Epub ahead of print]23(3):

Transcription Factor Movement and Exercise-Induced Mitochondrial Biogenesis in Human Skeletal Muscle: Current Knowledge and Future Perspectives.

Dale F Taylor, David J Bishop.

  In response to exercise, the oxidative capacity of mitochondria within skeletal muscle increases through the coordinated expression of mitochondrial proteins in a process termed mitochondrial biogenesis. Controlling the expression of mitochondrial proteins are transcription factors-a group of proteins that regulate messenger RNA transcription from DNA in the nucleus and mitochondria. To fulfil other functions or to limit gene expression, transcription factors are often localised away from DNA to different subcellular compartments and undergo rapid movement or accumulation only when required. Although many transcription factors involved in exercise-induced mitochondrial biogenesis have been identified, numerous conflicting findings and gaps exist within our knowledge of their subcellular movement. This review aims to summarise and provide a critical analysis of the published literature regarding the exercise-induced movement of transcription factors involved in mitochondria biogenesis in skeletal muscle.

Keywords:  exercise; mitochondrial biogenesis; skeletal muscle; subcellular; transcription factors

DOI:  https://doi.org/10.3390/ijms23031517
Nat Cell Biol. 2022 Feb;24(2): 181-193

LONP-1 and ATFS-1 sustain deleterious heteroplasmy by promoting mtDNA replication in dysfunctional mitochondria.

Qiyuan Yang, Pengpeng Liu, Nadine S Anderson, Tomer Shpilka, YunGuang Du, Nandhitha Uma Naresh, Rui Li, Lihua Julie Zhu, Kevin Luk, Josh Lavelle, Rilee D Zeinert, Peter Chien, Scot A Wolfe, Cole M Haynes.

The accumulation of deleterious mitochondrial DNA (∆mtDNA) causes inherited mitochondrial diseases and ageing-associated decline in mitochondrial functions such as oxidative phosphorylation. Following mitochondrial perturbations, the bZIP protein ATFS-1 induces a transcriptional programme to restore mitochondrial function. Paradoxically, ATFS-1 is also required to maintain ∆mtDNAs in heteroplasmic worms. The mechanism by which ATFS-1 promotes ∆mtDNA accumulation relative to wild-type mtDNAs is unclear. Here we show that ATFS-1 accumulates in dysfunctional mitochondria. ATFS-1 is absent in healthy mitochondria owing to degradation by the mtDNA-bound protease LONP-1, which results in the nearly exclusive association between ATFS-1 and ∆mtDNAs in heteroplasmic worms. Moreover, we demonstrate that mitochondrial ATFS-1 promotes the binding of the mtDNA replicative polymerase (POLG) to ∆mtDNAs. Interestingly, inhibition of the mtDNA-bound protease LONP-1 increased ATFS-1 and POLG binding to wild-type mtDNAs. LONP-1 inhibition in Caenorhabditis elegans and human cybrid cells improved the heteroplasmy ratio and restored oxidative phosphorylation. Our findings suggest that ATFS-1 promotes mtDNA replication in dysfunctional mitochondria by promoting POLG-mtDNA binding, which is antagonized by LONP-1.

DOI: https://doi.org/10.1038/s41556-021-00840-5
Int J Mol Sci. 2022 Feb 06. pii: 1857. [Epub ahead of print]23(3):

Metabolic Reprogramming in Response to Alterations of Mitochondrial DNA and Mitochondrial Dysfunction in Gastric Adenocarcinoma.

Tzu-Ching Chang, Hui-Ting Lee, Siao-Cian Pan, Shih-Han Cho, Chieh Cheng, Liang-Hung Ou, Chia-I Lin, Chen-Sung Lin, Yau-Huei Wei.

  We used gastric cancer cell line AGS and clinical samples to investigate the roles of mitochondrial DNA (mtDNA) alterations and mitochondrial respiratory dysfunction in gastric adenocarcinoma (GAC). A total of 131 clinical samples, including 17 normal gastric mucosa (N-GM) from overweight patients who had received sleeve gastrectomy and 57 paired non-cancerous gastric mucosae (NC-GM) and GAC from GAC patients who had undergone partial/subtotal/total gastrectomy, were recruited to examine the copy number and D310 sequences of mtDNA. The gastric cancer cell line AGS was used with knockdown (KD) mitochondrial transcription factor A (TFAM) to achieve mitochondrial dysfunction through a decrease of mtDNA copy number. Parental (PT), null-target (NT), and TFAM-KD-(A/B/C) represented the parental, control, and TFAM knocked-down AGS cells, respectively. These cells were used to compare the parameters reflecting mitochondrial biogenesis, glycolysis, and cell migration activity. The median mtDNA copy numbers of 17 N-GM, 57 NC-GM, and 57 GAC were 0.058, 0.055, and 0.045, respectively. The trend of decrease was significant (p = 0.030). In addition, GAC had a lower mean mtDNA copy number of 0.055 as compared with the paired NC-GM of 0.078 (p < 0.001). The mean mtDNA copy number ratio (mtDNA copy number of GAC/mtDNA copy number of paired NC-GM) was 0.891. A total of 35 (61.4%) GAC samples had an mtDNA copy number ratio ≤0.804 (p = 0.017) and 27 (47.4%) harbored a D310 mutation (p = 0.047), and these patients had shorter survival time and poorer prognosis. After effective knockdown of TFAM, TFAM-KD-B/C cells expressed higher levels of hexokinase II (HK-II) and v-akt murine thymoma viral oncogene homolog 1 gene (AKT)-encoded AKT, but lower levels of phosphorylated pyruvate dehydrogenase (p-PDH) than did the NT/PT AGS cells. Except for a higher level of p-PDH, the expression levels of these proteins remained unchanged in TFAM-KD-A, which had a mild knockdown of TFAM. Compared to those of NT, TFAM-KD-C had not only a lower mtDNA copy number (p = 0.050), but also lower oxygen consumption rates (OCR), including basal respiration (OCRBR), ATP-coupled respiration (OCRATP), reserve capacity (OCRRC), and proton leak (OCRPL)(all with p = 0.050). In contrast, TFAM-KD-C expressed a higher extracellular acidification rate (ECAR)/OCRBR ratio (p = 0.050) and a faster wound healing migration at 6, 12, and 18 h, respectively (all with p = 0.050). Beyond a threshold, the decrease in mtDNA copy number, the mtDNA D310 mutation, and mitochondrial dysfunction were involved in the carcinogenesis and progression of GACs. Activation of PDH might be considered as compensation for the mitochondrial dysfunction in response to glucose metabolic reprogramming or to adjust mitochondrial plasticity in GAC.

Keywords:  D310 mutation; copy number; gastric adenocarcinoma (GAC); metabolic reprogramming; mitochondrial DNA (mtDNA); mitochondrial transcription factor A (TFAM); prognosis

DOI:  https://doi.org/10.3390/ijms23031857
Hum Reprod. 2022 Feb 12. pii: deac024. [Epub ahead of print]

Mitochondrial DNA content reduction in the most fertile spermatozoa is accompanied by increased mitochondrial DNA rearrangement.

M Boguenet, V Desquiret-Dumas, D Goudenège, C Bris, L Boucret, O Blanchet, V Procaccio, P E Bouet, P Reynier, P May-Panloup.

   STUDY QUESTION: Is there an association between male fertility and spermatozoa mitochondrial DNA (mtDNA) copy number and genome rearrangements?
SUMMARY ANSWER: Normal spermatozoa not only have a lower mtDNA copy number but also more DNA rearrangements than spermatozoa of men with severe oligoasthenospermia (SOA).
WHAT IS KNOWN ALREADY: While there is a consensus that mtDNA content is decreased in the most fertile spermatozoa, the role of mtDNA sequence alteration in male infertility is unclear. High-throughput sequencing, which allows an exhaustive analysis of mtDNA rearrangements and mutations, could be helpful in this context, but has yet to be used.
STUDY DESIGN, SIZE, DURATION: This is an observational study of semen samples obtained from 44 men undergoing ART at an academic infertility centre in France, from October 2018 to November 2020. The men were classified into two groups: 20 men in the SOA group and 24 men with normal semen parameters in the control group.
PARTICIPANTS/MATERIALS, SETTING, METHODS: For each patient and control, mtDNA was isolated from sperm fractions from the 40% and 90% layers of the density gradient. The average mtDNA content of each sample was assessed using digital PCR. Deep sequencing was performed using next-generation sequencing. Signal processing and base calling were performed via the embedded pre-processing pipeline, the variants were analysed using an in-house workflow and a dedicated tool, based on soft-clipping, was used to study large mtDNA rearrangements. The distribution and the type of rearrangements and variants were compared between patients with SOA and controls on one hand, and between the 40% and 90% gradient layers, on the other hand.
MAIN RESULTS AND THE ROLE OF CHANCE: The mtDNA content of spermatozoa in the SOA group was significantly higher than in the control group (P < 0.0001). Moreover, mtDNA content was significantly higher in spermatozoa from the 40% layer (the most fertile spermatozoa) compared to the 90% layer, both in the SOA (P = 0.02) and the control group (P < 0.0001). The frequency of large mtDNA deletions and duplications was significantly higher in the control group (P = 0.002). Most of these rearrangements are potentially related to DNA breaks and their number was reduced by the removal of the linear mtDNA from the samples. Heteroplasmic variants were found more frequently in the SOA group (P = 0.05) and in the 40% layer (P = 0.03), but none had any obvious functional consequence.
LIMITATIONS, REASONS FOR CAUTION: Our findings are novel and significant but should be verified in larger cohorts and other types of male infertility.
WIDER IMPLICATIONS OF THE FINDINGS: Our findings suggest that sperm mtDNA rearrangements are not necessarily associated with mitochondrial dysfunction and male infertility. Instead, they seem to be concomitant with the process of mtDNA content reduction in the most potentially fertile spermatozoa. Furthermore, they refute the hypothesis that, in the case of mtDNA alteration, a compensatory mechanism allows an increase in mtDNA copy number to rectify the energy deficit. The increased frequency of mtDNA rearrangements in the most fertile spermatozoa is a novel result that offers new insight into the relation between sperm quality and mtDNA.
STUDY FUNDING/COMPETING INTEREST(S): This work was supported by Angers University Hospital (grant AOI CHU Angers 2018), Angers University and the French national research centres INSERM and CNRS. There are no competing interests.
TRIAL REGISTRATION NUMBER: N/A.

Keywords:  copy number; digital PCR; male infertility; mitochondrial DNA; next-generation sequencing; oligoasthenospermia; rearrangements; spermatozoa

DOI:  https://doi.org/10.1093/humrep/deac024
J Cell Biol. 2022 03 07. pii: e202101021. [Epub ahead of print]221(3):

Neuralized-like protein 4 (NEURL4) mediates ADP-ribosylation of mitochondrial proteins.

Maria Dafne Cardamone, Yuan Gao, Julian Kwan, Vanessa Hayashi, Megan Sheeran, Junxiang Xu, Justin English, Joseph Orofino, Andrew Emili, Valentina Perissi.

ADP-ribosylation is a reversible post-translational modification where an ADP-ribose moiety is covalently attached to target proteins by ADP-ribosyltransferases (ARTs). Although best known for its nuclear roles, ADP-ribosylation is increasingly recognized as a key regulatory strategy across cellular compartments. ADP-ribosylation of mitochondrial proteins has been widely reported, but the exact nature of mitochondrial ART enzymes is debated. We have identified neuralized-like protein 4 (NEURL4) as a mitochondrial ART enzyme and show that most ART activity associated with mitochondria is lost in the absence of NEURL4. The NEURL4-dependent ADP-ribosylome in mitochondrial extracts from HeLa cells includes numerous mitochondrial proteins previously shown to be ADP-ribosylated. In particular, we show that NEURL4 is required for the regulation of mtDNA integrity via poly-ADP-ribosylation of mtLIG3, the rate-limiting enzyme for base excision repair (BER). Collectively, our studies reveal that NEURL4 acts as the main mitochondrial ART enzyme under physiological conditions and provide novel insights in the regulation of mitochondria homeostasis through ADP-ribosylation.

DOI: https://doi.org/10.1083/jcb.202101021
Bull Exp Biol Med. 2022 Feb 17.

A Method for Evaluation of the Level of Circulating Mitochondrial DNA by ND1 and ND2 Genes.

O B Ogarkov, E A Orlova, I V Malov, S N Zhdanova, S I Malov, P A Khromova, L A Stepanenko, V V Sinkov, L V Rychkova, L I Kolesnikova.

  The measurement of the level of mitochondrial DNA (mtDNA) in the blood is a difficult problem due to high variability of mitochondrial genes, deletions in the mitochondrial genome in some pathological conditions, different sources of mtDNA into the bloodstream (mtDNA from tissues, from blood cells, etc.). We designed primers and TaqMan probes for highly conserved regions of the ND1 and ND2 genes outside the mitochondrial deletions "hot zones". For standardizing the technique, the true concentration of low-molecular-weight mtDNA was determined by real-time PCR for two targets: a fragment of the ND2 gene (122 bp) and the ND1 and ND2 genes (1198 bp). The sensitivity and specificity of the developed approach were verified on a DNA pool isolated from the blood plasma of healthy donors of various nationalities. The concentration of low-molecular-weight mtDNA in the blood plasma of two patients with COVID-19 was monitored over two weeks of inpatient treatment. A significant increase in the content of low-molecular-weight mtDNA was observed during the first 5 days after hospitalization, followed by a drop to the level of healthy donors. The developed technique makes it possible to assess the blood level of low-molecular-weight mtDNA regardless of the quality of sampling and makes it possible to standardize this biological marker in a wide range of infectious and non-infectious pathologies.

Keywords:  COVID-19; ND1 and ND2 genes; circulating mitochondrial DNA (mtDNA); real-time PCR

DOI:  https://doi.org/10.1007/s10517-022-05421-6
Genomics. 2022 Feb 15. pii: S0888-7543(22)00060-X. [Epub ahead of print] 110315

Single-cell mtDNA heteroplasmy in colorectal cancer.

João Almeida, Andrés Pérez-Figueroa, João M Alves, Monica Valecha, Sonia Prado-López, Pilar Alvariño, José Manuel Cameselle-Teijeiro, Débora Chantada, Miguel M Fonseca, David Posada.

  Human mitochondria can be genetically distinct within the same individual, a phenomenon known as heteroplasmy. In cancer, this phenomenon seems exacerbated, and most mitochondrial mutations seem to be heteroplasmic. How this genetic variation is arranged within and among normal and tumor cells is not well understood. To address this question, here we sequenced single-cell mitochondrial genomes from multiple normal and tumoral locations in four colorectal cancer patients. Our results suggest that single cells, both normal and tumoral, can carry various mitochondrial haplotypes. Remarkably, this intra-cell heteroplasmy can arise before tumor development and be maintained afterward in specific tumoral cell subpopulations. At least in the colorectal patients studied here, the somatic mutations in the single-cells do not seem to have a prominent role in tumorigenesis.

Keywords:  Intracellular heteroplasmy; Single-cell mitochondrial genomics; mtDNA homoplasmy; scDNA-seq

DOI:  https://doi.org/10.1016/j.ygeno.2022.110315
PLoS One. 2022 ;17(2): e0263790

The application of machine learning to predict genetic relatedness using human mtDNA hypervariable region I sequences.

Priyanka Govender, Stephen Gbenga Fashoto, Leah Maharaj, Matthew A Adeleke, Elliot Mbunge, Jeremiah Olamijuwon, Boluwaji Akinnuwesi, Moses Okpeku.

Human identification of unknown samples following disaster and mass casualty events is essential, especially to bring closure to family and friends of the deceased. Unfortunately, victim identification is often challenging for forensic investigators as analysis becomes complicated when biological samples are degraded or of poor quality as a result of exposure to harsh environmental factors. Mitochondrial DNA becomes the ideal option for analysis, particularly for determining the origin of the samples. In such events, the estimation of genetic parameters plays an important role in modelling and predicting genetic relatedness and is useful in assigning unknown individuals to an ethnic group. Various techniques exist for the estimation of genetic relatedness, but the use of Machine learning (ML) algorithms are novel and presently the least used in forensic genetic studies. In this study, we investigated the ability of ML algorithms to predict genetic relatedness using hypervariable region I sequences; that were retrieved from the GenBank database for three race groups, namely African, Asian and Caucasian. Four ML classification algorithms; Support vector machines (SVM), Linear discriminant analysis (LDA), Quadratic discriminant analysis (QDA) and Random Forest (RF) were hybridised with one-hot encoding, Principal component analysis (PCA) and Bags of Words (BoW), and were compared for inferring genetic relatedness. The findings from this study on WEKA showed that genetic inferences based on PCA-SVM achieved an overall accuracy of 80-90% and consistently outperformed PCA-LDA, PCA-RF and PCA-QDA, while in Python BoW-PCA-RF achieved 94.4% accuracy which outperformed BoW-PCA-SVM, BoW-PCA-LDA and BoW-PCA-QDA respectively. ML results from the use of WEKA and Python software tools displayed higher accuracies as compared to the Analysis of molecular variance results. Given the results, SVM and RF algorithms are likely to also be useful in other sequence classification applications, making it a promising tool in genetics and forensic science. The study provides evidence that ML can be utilized as a supplementary tool for forensic genetics casework analysis.

DOI: https://doi.org/10.1371/journal.pone.0263790
Trends Parasitol. 2022 Feb 08. pii: S1471-4922(22)00032-0. [Epub ahead of print]

Hijacking of host mitochondria by Toxoplasma gondii and SARS-CoV-2.

Ruize Zhang, Jian Chen, Daowen Wang, Zheng Qing Fu.

  Mitochondria regulate energy production, cell cycle, and immune signaling. Li et al. recently reported that Toxoplasma gondii induces the shedding of mitochondrial outer membrane to promote its growth. Intriguingly, the hijacking of host mitochondria has been shown to play an essential role in the pathogenesis of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Keywords:  COVID-19; SARS-CoV-2; SPOTs; TOM70; TgMAF1; Toxoplasma gondii

DOI:  https://doi.org/10.1016/j.pt.2022.02.002
Nat Cell Biol. 2022 Feb;24(2): 127-128

LONP-1 aids propagation of deleterious mtDNA.

Ina Kirmes, Steven Zuryn.

DOI: https://doi.org/10.1038/s41556-021-00838-z
Bioessays. 2022 Feb 16. e2100283

Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system?

Sophie Breton, Donald T Stewart, Julie Brémaud, Justin C Havird, Chase H Smith, Walter R Hoeh.

  Animal and plant species exhibit an astonishing diversity of sexual systems, including environmental and genetic determinants of sex, with the latter including genetic material in the mitochondrial genome. In several hermaphroditic plants for example, sex is determined by an interaction between mitochondrial cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Specifically, CMS involves aberrant mitochondrial genes that prevent pollen development and specific nuclear genes that restore it, leading to a mixture of female (male-sterile) and hermaphroditic individuals in the population (gynodioecy). Such a mitochondrial-nuclear sex determination system is thought to be rare outside plants. Here, we present one possible case of CMS in animals. We hypothesize that the only exception to the strict maternal mtDNA inheritance in animals, the doubly uniparental inheritance (DUI) system in bivalves, might have originated as a mitochondrial-nuclear sex-determination system. We document and explore similarities that exist between DUI and CMS, and we propose various ways to test our hypothesis.

Keywords:  bivalves; mitochondria; mitonuclear interactions; plants; sex determination

DOI:  https://doi.org/10.1002/bies.202100283