bims-mitmed 2022-10-16 papers

bims-mitmed

Biomed News

on Mitochondrial medicine

Issue of 2022‒10‒16
thirty papers selected by
Dario Brunetti
Fondazione IRCCS Istituto Neurologico

Enhanced mitochondrial DNA editing in mice using nuclear-exported TALE-linked deaminases and nucleases.
Precision mitochondrial DNA editing with high-fidelity DddA-derived base editors.
Congenital Hypermetabolism and Uncoupled Oxidative Phosphorylation.
PGC-1α activity and mitochondrial dysfunction in preterm infants.
Neuronal induction of BNIP3-mediated mitophagy slows systemic aging in Drosophila.
Manganese-driven CoQ deficiency.
Computation of the mitochondrial age distribution along the axon length.
The role of mitochondrial genome abundance in Alzheimer's disease.
Mitochondrial VDAC1: A Potential Therapeutic Target of Inflammation-Related Diseases and Clinical Opportunities.
Evaluation of Mitochondrial Turnover Using Fluorescence Microscopy in Drosophila.
Mitochondrial and Endoplasmic Reticulum Alterations in a Case of Amyotrophic Lateral Sclerosis Caused by TDP-43 A382T Mutation.
Case report: Thirty-year progression of an EMPF1 encephalopathy due to defective mitochondrial and peroxisomal fission caused by a novel de novo heterozygous DNM1L variant.
CERKL, a Retinal Dystrophy Gene, Regulates Mitochondrial Transport and Dynamics in Hippocampal Neurons.
Mitochondrial Dysfunction in Polycystic Ovary Syndrome.
Mitochondrial DNA Repair in Neurodegenerative Diseases and Ageing.
Mitochondrial network configuration influences sarcomere and myosin filament structure in striated muscles.
Rapid fractionation of mitochondria from mouse liver and heart reveals in vivo metabolite compartmentation.
Pathological Features in Paediatric Patients with TK2 Deficiency.
Universal dynamics of mitochondrial networks: a finite-size scaling analysis.
Knockdown of TMEM160 leads to an increase in reactive oxygen species generation and the induction of the mitochondrial unfolded protein response.
Early loss of endogenous NAD+ following rotenone treatment leads to mitochondrial dysfunction and Sarm1 induction that is ameliorated by PARP inhibition.
Senescent cells in the brain and where to find them.
BNIP3L/NIX regulates both mitophagy and pexophagy.
Effects of Noonan Syndrome-Germline Mutations on Mitochondria and Energy Metabolism.
An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.
Mitochondrial network expansion and dynamic redistribution during islet morphogenesis in zebrafish larvae.
Adults with spinal muscular atrophy: a large-scale natural history study shows gender effect on disease.
PKAN pathogenesis and treatment.
Cross-species evolution of a highly potent AAV variant for therapeutic gene transfer and genome editing.
Generation of iMyoblasts from Human Induced Pluripotent Stem Cells.

Genome Biol. 2022 Oct 12. 23(1): 211

Enhanced mitochondrial DNA editing in mice using nuclear-exported TALE-linked deaminases and nucleases.

Seonghyun Lee, Hyunji Lee, Gayoung Baek, Eunji Namgung, Joo Min Park, Sanghun Kim, Seongho Hong, Jin-Soo Kim.

  We present two methods for enhancing the efficiency of mitochondrial DNA (mtDNA) editing in mice with DddA-derived cytosine base editors (DdCBEs). First, we fused DdCBEs to a nuclear export signal (DdCBE-NES) to avoid off-target C-to-T conversions in the nuclear genome and improve editing efficiency in mtDNA. Second, mtDNA-targeted TALENs (mitoTALENs) are co-injected into mouse embryos to cleave unedited mtDNA. We generated a mouse model with the m.G12918A mutation in the MT-ND5 gene, associated with mitochondrial genetic disorders in humans. The mutant mice show hunched appearances, damaged mitochondria in kidney and brown adipose tissues, and hippocampal atrophy, resulting in premature death.

Keywords:  DdCBE; Mitochondrial DNA editing; NES; mitoTALEN; mtDNA

DOI:  https://doi.org/10.1186/s13059-022-02782-z
Nat Biotechnol. 2022 Oct 13.

Precision mitochondrial DNA editing with high-fidelity DddA-derived base editors.

Seonghyun Lee, Hyunji Lee, Gayoung Baek, Jin-Soo Kim.

Bacterial toxin DddA-derived cytosine base editors (DdCBEs)-composed of split DddAtox (a cytosine deaminase specific to double-stranded DNA), custom-designed TALE (transcription activator-like effector) DNA-binding proteins, and a uracil glycosylase inhibitor-enable mitochondrial DNA (mtDNA) editing in human cells, which may pave the way for therapeutic correction of pathogenic mtDNA mutations in patients. The utility of DdCBEs has been limited by off-target activity, which is probably caused by spontaneous assembly of the split DddAtox deaminase enzyme, independent of DNA-binding interactions. We engineered high-fidelity DddA-derived cytosine base editors (HiFi-DdCBEs) with minimal off-target activity by substituting alanine for amino acid residues at the interface between the split DddAtox halves. The resulting domains cannot form a functional deaminase without binding of their linked TALE proteins at adjacent sites on DNA. Whole mitochondrial genome sequencing shows that, unlike conventional DdCBEs, which induce hundreds of unwanted off-target C-to-T conversions in human mtDNA, HiFi-DdCBEs are highly efficient and precise, avoiding collateral off-target mutations, and as such, they will probably be desirable for therapeutic applications.

DOI: https://doi.org/10.1038/s41587-022-01486-w
N Engl J Med. 2022 Oct 13. 387(15): 1395-1403

Congenital Hypermetabolism and Uncoupled Oxidative Phosphorylation.

Rebecca D Ganetzky, Andrew L Markhard, Irene Yee, Sheila Clever, Alan Cahill, Hardik Shah, Zenon Grabarek, Tsz-Leung To, Vamsi K Mootha.

We describe the case of identical twin boys who presented with low body weight despite excessive caloric intake. An evaluation of their fibroblasts showed elevated oxygen consumption and decreased mitochondrial membrane potential. Exome analysis revealed a de novo heterozygous variant in ATP5F1B, which encodes the β subunit of mitochondrial ATP synthase (also called complex V). In yeast, mutations affecting the same region loosen coupling between the proton motive force and ATP synthesis, resulting in high rates of mitochondrial respiration. Expression of the mutant allele in human cell lines recapitulates this phenotype. These data support an autosomal dominant mitochondrial uncoupling syndrome with hypermetabolism. (Funded by the National Institutes of Health.).

DOI: https://doi.org/10.1056/NEJMoa2202949
Front Physiol. 2022 ;13 997619

PGC-1α activity and mitochondrial dysfunction in preterm infants.

Atefeh Mohammadi, Randa Higazy, Estelle B Gauda.

  Extremely low gestational age neonates (ELGANs) are born in a relatively hyperoxic environment with weak antioxidant defenses, placing them at high risk for mitochondrial dysfunction affecting multiple organ systems including the nervous, respiratory, ocular, and gastrointestinal systems. The brain and lungs are highly affected by mitochondrial dysfunction and dysregulation in the neonate, causing white matter injury (WMI) and bronchopulmonary dysplasia (BPD), respectively. Adequate mitochondrial function is important in providing sufficient energy for organ development as it relates to alveolarization and axonal myelination and decreasing oxidative stress via reactive oxygen species (ROS) and reactive nitrogen species (RNS) detoxification. Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) is a master regulator of mitochondrial biogenesis and function. Since mitochondrial dysfunction is at the root of WMI and BPD pathobiology, exploring therapies that can regulate PGC-1α activity may be beneficial. This review article describes several promising therapeutic agents that can mitigate mitochondrial dysfunction through direct and indirect activation and upregulation of the PGC-1α pathway. Metformin, resveratrol, omega 3 fatty acids, montelukast, L-citrulline, and adiponectin are promising candidates that require further pre-clinical and clinical studies to understand their efficacy in decreasing the burden of disease from WMI and BPD in preterm infants.

Keywords:  PGC-1α; bronchopulmonary dysplasia; mitochondrial dysfunction; oxidative stress; reactive oxygen species; white matter injury

DOI:  https://doi.org/10.3389/fphys.2022.997619
Nat Aging. 2022 Jun;2(6): 494-507

Neuronal induction of BNIP3-mediated mitophagy slows systemic aging in Drosophila.

Edward T Schmid, Jung-Hoon Pyo, David W Walker.

  The effects of aging on the brain are widespread and can have dramatic implications on the overall health of an organism. Mitochondrial dysfunction is a hallmark of brain aging, but, the interplay between mitochondrial quality control, neuronal aging, and organismal health is not well understood. Here, we show that aging leads to a decline in mitochondrial autophagy (mitophagy) in the Drosophila brain with a concomitant increase in mitochondrial content. We find that induction of BCL2-interacting protein 3 (BNIP3), a mitochondrial outer membrane protein, in the adult nervous system induces mitophagy and prevents the accumulation of dysfunctional mitochondria in the aged brain. Importantly, neuronal induction of BNIP3-mediated mitophagy increases organismal longevity and healthspan. Furthermore, BNIP3-mediated mitophagy in the nervous system improves muscle and intestinal homeostasis in aged flies, indicating cell non-autonomous effects. Our findings identify BNIP3 as a therapeutic target to counteract brain aging and prolong overall organismal health with age.

Keywords:  Autophagy; Intestinal barrier dysfunction; Intestinal stem cell; Mito-QC; Mitophagy; Muscle aging; Neuronal aging

DOI:  https://doi.org/10.1038/s43587-022-00214-y
Nat Commun. 2022 Oct 13. 13(1): 6061

Manganese-driven CoQ deficiency.

Jutta Diessl, Jens Berndtsson, Filomena Broeskamp, Lukas Habernig, Verena Kohler, Carmela Vazquez-Calvo, Arpita Nandy, Carlotta Peselj, Sofia Drobysheva, Ludovic Pelosi, F-Nora Vögtle, Fabien Pierrel, Martin Ott, Sabrina Büttner.

Overexposure to manganese disrupts cellular energy metabolism across species, but the molecular mechanism underlying manganese toxicity remains enigmatic. Here, we report that excess cellular manganese selectively disrupts coenzyme Q (CoQ) biosynthesis, resulting in failure of mitochondrial bioenergetics. While respiratory chain complexes remain intact, the lack of CoQ as lipophilic electron carrier precludes oxidative phosphorylation and leads to premature cell and organismal death. At a molecular level, manganese overload causes mismetallation and proteolytic degradation of Coq7, a diiron hydroxylase that catalyzes the penultimate step in CoQ biosynthesis. Coq7 overexpression or supplementation with a CoQ headgroup analog that bypasses Coq7 function fully corrects electron transport, thus restoring respiration and viability. We uncover a unique sensitivity of a diiron enzyme to mismetallation and define the molecular mechanism for manganese-induced bioenergetic failure that is conserved across species.

DOI: https://doi.org/10.1038/s41467-022-33641-x
Comput Methods Biomech Biomed Engin. 2022 Oct 13. 1-13

Computation of the mitochondrial age distribution along the axon length.

Ivan A Kuznetsov, Andrey V Kuznetsov.

  We describe a compartmental model of mitochondrial transport in axons, which we apply to compute mitochondrial age at different distances from the soma. The model predicts that at the tip of an axon that has a length of 1 cm, the average mitochondrial age is approximately 22 h. The mitochondria are youngest closest to the soma and their age scales approximately linearly with distance from the soma. To the best of the authors' knowledge, this is the first attempt to predict the spatial distribution of mitochondrial age within an axon. A sensitivity study of the mean age of mitochondria to various model parameters is also presented.

Keywords:  Neurons; axonal transport; mathematical modeling; mean age; organelles

DOI:  https://doi.org/10.1080/10255842.2022.2128784
Alzheimers Dement. 2022 Oct 12.

The role of mitochondrial genome abundance in Alzheimer's disease.

Nadia V Harerimana, Devashi Paliwali, Carmen Romero-Molina, David A Bennett, Judy Pa, Alison Goate, Russell H Swerdlow, Shea J Andrews.

  Mitochondrial dysfunction is an early and prominent feature of Alzheimer's disease (AD), with impaired energy metabolism preceding the onset of clinical symptoms. Here we propose an update to the mitochondrial dysfunction hypothesis of AD based on recent results examining the role of mitochondrial genome abundance in AD. In a large post mortem study, we show that lower brain mitochondrial genome abundance is associated with a greater odds of AD neuropathological change and worse cognitive performance. We hypothesize that lower mitochondrial genome abundance impairs mitochondrial function by reducing mitochondrial bioenergetics, thereby impacting neuronal and glial cell function. However, it remains to be determined if mitochondrial dysfunction causes, mediates, or is a by-product of AD pathogenesis. Additional support for this hypothesis will be generated by linking peripheral blood mitochondrial genome abundance to AD and establishing clinical trials of compounds that upregulate total mitochondrial genome abundance or boost mitochondrial mass.

Keywords:  Alzheimer's disease; haplogroup; mitochondrial DNA copy number; mitochondrial dysfunction; mitochondrial genome abundance; mitochondrial heteroplasmy

DOI:  https://doi.org/10.1002/alz.12812
Cells. 2022 Oct 10. pii: 3174. [Epub ahead of print]11(19):

Mitochondrial VDAC1: A Potential Therapeutic Target of Inflammation-Related Diseases and Clinical Opportunities.

Hang Hu, Linlin Guo, Jay Overholser, Xing Wang.

  The multifunctional protein, voltage-dependent anion channel 1 (VDAC1), is located on the mitochondrial outer membrane. It is a pivotal protein that maintains mitochondrial function to power cellular bioactivities via energy generation. VDAC1 is involved in regulating energy production, mitochondrial oxidase stress, Ca2+ transportation, substance metabolism, apoptosis, mitochondrial autophagy (mitophagy), and many other functions. VDAC1 malfunction is associated with mitochondrial disorders that affect inflammatory responses, resulting in an up-regulation of the body's defensive response to stress stimulation. Overresponses to inflammation may cause chronic diseases. Mitochondrial DNA (mtDNA) acts as a danger signal that can further trigger native immune system activities after its secretion. VDAC1 mediates the release of mtDNA into the cytoplasm to enhance cytokine levels by activating immune responses. VDAC1 regulates mitochondrial Ca2+ transportation, lipid metabolism and mitophagy, which are involved in inflammation-related disease pathogenesis. Many scientists have suggested approaches to deal with inflammation overresponse issues via specific targeting therapies. Due to the broad functionality of VDAC1, it may become a useful target for therapy in inflammation-related diseases. The mechanisms of VDAC1 and its role in inflammation require further exploration. We comprehensively and systematically summarized the role of VDAC1 in the inflammatory response, and hope that our research will lead to novel therapeutic strategies that target VDAC1 in order to treat inflammation-related disorders.

Keywords:  Ca2+; VDAC1; inflammation; metabolism; mitochondria; mitophagy

DOI:  https://doi.org/10.3390/cells11193174
Bio Protoc. 2022 Sep 05. pii: e4498. [Epub ahead of print]12(17):

Evaluation of Mitochondrial Turnover Using Fluorescence Microscopy in Drosophila.

Felipe Martelli.

  Mitochondrial dysfunction is associated with perturbations in the cellular oxidative status, changes in energy production and metabolic rate, and the onset of pathological processes. Classic methods of assessing mitochondrial dysfunction rely on indirect measures, such as evaluating mitochondrial DNA copy numbers, or direct but more costly and skilled techniques, such as electron microscopy. The protocol presented here was recently implemented to evaluate mitochondrial dysfunction in response to insecticide exposure in Drosophila melanogaster larvae, and it relies on the use of a previously established MitoTimer mutant strain. MitoTimer is a genetically engineered mitochondrial protein that shows green fluorescence when newly synthetized, irreversibly turning into red as mitochondria age. The protocol described here allows for the easy and direct assessment of shifts in mitochondrial turnover, with tissue-specific accuracy. This protocol can be adapted to assess changes in mitochondrial turnover in response to drugs, rearing conditions, and/or mutations in larva, pupa, or adult fruit flies.

Keywords:   Dissection ; Drosophila ; Fluorescence microscopy ; Insecticide ; Mitochondria ; Mitochondrial turnover ; Oxidative stress ; Tissue imaging

DOI:  https://doi.org/10.21769/BioProtoc.4498
Int J Mol Sci. 2022 Oct 06. pii: 11881. [Epub ahead of print]23(19):

Mitochondrial and Endoplasmic Reticulum Alterations in a Case of Amyotrophic Lateral Sclerosis Caused by TDP-43 A382T Mutation.

Giada Zanini, Valentina Selleri, Milena Nasi, Anna De Gaetano, Ilaria Martinelli, Giulia Gianferrari, Francesco Demetrio Lofaro, Federica Boraldi, Jessica Mandrioli, Marcello Pinti.

  Amyotrophic lateral sclerosis is the most common form of motor neuron disease. Mutations in TARDBP, the gene encoding the RNA-binding protein TDP-43, are responsible for about 5% of familial ALS. Here we report the clinical and biological features of an ALS patients with pA382T mutation in TPD-43 protein. Disease began with right hand muscles weakness, and equally involved upper and lower motor neuron with a classic phenotype, without cognitive impairment. While a family history of neurological diseases was reported, there was no evidence of familial frontotemporal dementia. Cultured fibroblasts from the patient were characterized by profound alterations of cell proteome, which impacts particularly the mitochondrial metabolic pathways and the endoplasmic reticulum. TDP-43 levels were similar to control, healthy fibroblasts, but a higher fraction localized in mitochondria. Mitochondrial network appeared fragmented, and the organelles smaller and more spheric. In agreement with impaired proteome and morphology of mitochondria, basal cell respiration was reduced. Mitochondrial DNA levels appeared normal. However, a higher amount of mitochondrial DNA was present in the cytosol, suggesting a pronounced mitochondrial DNA misplacement which can promote a pro-inflammatory response mediating by cGAS/STING. Thus, this case report further expands the clinical and pathological phenotype of A382T mutation.

Keywords:  TDP-43; amyotrophic lateral sclerosis; mitochondria; mtDNA

DOI:  https://doi.org/10.3390/ijms231911881
Front Neurol. 2022 ;13 937885

Case report: Thirty-year progression of an EMPF1 encephalopathy due to defective mitochondrial and peroxisomal fission caused by a novel de novo heterozygous DNM1L variant.

Charlène Lhuissier, Bart E Wagner, Amy Vincent, Gaëtan Garraux, Olivier Hougrand, Rudy Van Coster, Valerie Benoit, Deniz Karadurmus, Guy Lenaers, Naïg Gueguen, Arnaud Chevrollier, Isabelle Maystadt.

  Mutations in DNM1L (DRP1), which encode a key player of mitochondrial and peroxisomal fission, have been reported in patients with the variable phenotypic spectrum, ranging from non-syndromic optic atrophy to lethal infantile encephalopathy. Here, we report a case of an adult female patient presenting with a complex neurological phenotype that associates axonal sensory neuropathy, spasticity, optic atrophy, dysarthria, dysphasia, dystonia, and ataxia, worsening with aging. Whole-exome sequencing revealed a heterozygous de novo variant in the GTPase domain of DNM1L [NM_001278464.1: c.176C>A p.(Thr59Asn)] making her the oldest patient suffering from encephalopathy due to defective mitochondrial and peroxisomal fission-1. In silico analysis suggested a protein destabilization effect of the variant Thr59Asn. Unexpectedly, Western blotting disclosed profound decrease of DNM1L expression, probably related to the degradation of DNM1L complexes. A detailed description of mitochondrial and peroxisomal anomalies in transmission electron and 3D fluorescence microscopy studies confirmed the exceptional phenotype of this patient.

Keywords:  DNM1L; DRP1; EMPF1; encephalopathy; mitochondrial fission

DOI:  https://doi.org/10.3389/fneur.2022.937885
Int J Mol Sci. 2022 Sep 30. pii: 11593. [Epub ahead of print]23(19):

CERKL, a Retinal Dystrophy Gene, Regulates Mitochondrial Transport and Dynamics in Hippocampal Neurons.

Rocío García-Arroyo, Gemma Marfany, Serena Mirra.

  Mutations in the Ceramide Kinase-like (CERKL) gene cause retinal dystrophies, characterized by progressive degeneration of retinal neurons, which eventually lead to vision loss. Among other functions, CERKL is involved in the regulation of autophagy, mitochondrial dynamics, and metabolism in the retina. However, CERKL is nearly ubiquitously expressed, and it has been recently described to play a protective role against brain injury. Here we show that Cerkl is expressed in the hippocampus, and we use mouse hippocampal neurons to explore the impact of either overexpression or depletion of CERKL on mitochondrial trafficking and dynamics along axons. We describe that a pool of CERKL localizes at mitochondria in hippocampal axons. Importantly, the depletion of CERKL in the CerklKD/KO mouse model is associated with changes in the expression of fusion/fission molecular regulators, induces mitochondrial fragmentation, and impairs axonal mitochondrial trafficking. Our findings highlight the role of CERKL, a retinal dystrophy gene, in the regulation of mitochondrial health and homeostasis in central nervous system anatomic structures other than the retina.

Keywords:  CERKL; hippocampus; mitochondria; mitochondrial dysfunction; mitochondrial trafficking; neurons

DOI:  https://doi.org/10.3390/ijms231911593
Reprod Sci. 2022 Oct 11.

Mitochondrial Dysfunction in Polycystic Ovary Syndrome.

Josef Finsterer.

  Polycystic ovary syndrome (PCOS) is a multi-causal condition. Among the genetic causes, variations in the mitochondrial DNA (mtDNA) are increasingly recognised as causative. PCOS not only occurs in known syndromic mitochondrial disorders due to pathogenic variants in the mtDNA but also in non-syndromic mitochondrial disorders. Additionally, mtDNA variants not causing a multi-system mitochondrial disorder but exclusively PCOS have been reported. Among the syndromic mitochondrial disorders, PCOS has been described in myoclonic epilepsy with ragged-red fibre (MERRF) syndrome. Among the non-syndromic mitochondrial disorders, PCOS has been described in association with insulin resistance. Several other studies suggest that mtDNA point mutations or mtDNA deletions can be associated with PCOS without manifesting in organs other than the ovaries. Evidence from animal studies suggests that function, morphology, and biogenesis of mitochondria in ovarian tissue are generally impaired in PCOS patients. In conclusion, there is increasing evidence that mtDNA variants play a pathophysiological role in the development of PCOS. Further studies are needed to establish the causal link between mtDNA variants and PCOS.

Keywords:  Endocrine; Polycystic ovary syndrome; Respiratory chain; mtDNA

DOI:  https://doi.org/10.1007/s43032-022-01100-z
Int J Mol Sci. 2022 Sep 27. pii: 11391. [Epub ahead of print]23(19):

Mitochondrial DNA Repair in Neurodegenerative Diseases and Ageing.

Veronica Bazzani, Mara Equisoain Redin, Joshua McHale, Lorena Perrone, Carlo Vascotto.

  Mitochondria are the only organelles, along with the nucleus, that have their own DNA. Mitochondrial DNA (mtDNA) is a double-stranded circular molecule of ~16.5 kbp that can exist in multiple copies within the organelle. Both strands are translated and encode for 22 tRNAs, 2 rRNAs, and 13 proteins. mtDNA molecules are anchored to the inner mitochondrial membrane and, in association with proteins, form a structure called nucleoid, which exerts a structural and protective function. Indeed, mitochondria have evolved mechanisms necessary to protect their DNA from chemical and physical lesions such as DNA repair pathways similar to those present in the nucleus. However, there are mitochondria-specific mechanisms such as rapid mtDNA turnover, fission, fusion, and mitophagy. Nevertheless, mtDNA mutations may be abundant in somatic tissue due mainly to the proximity of the mtDNA to the oxidative phosphorylation (OXPHOS) system and, consequently, to the reactive oxygen species (ROS) formed during ATP production. In this review, we summarise the most common types of mtDNA lesions and mitochondria repair mechanisms. The second part of the review focuses on the physiological role of mtDNA damage in ageing and the effect of mtDNA mutations in neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Considering the central role of mitochondria in maintaining cellular homeostasis, the analysis of mitochondrial function is a central point for developing personalised medicine.

Keywords:  Alzheimer’s disease; DNA damage; DNA repair pathways; Parkinson’s disease; mitochondria; neurodegenerative diseases

DOI:  https://doi.org/10.3390/ijms231911391
Nat Commun. 2022 Oct 13. 13(1): 6058

Mitochondrial network configuration influences sarcomere and myosin filament structure in striated muscles.

Prasanna Katti, Alexander S Hall, Hailey A Parry, Peter T Ajayi, Yuho Kim, T Bradley Willingham, Christopher K E Bleck, Han Wen, Brian Glancy.

Sustained muscle contraction occurs through interactions between actin and myosin filaments within sarcomeres and requires a constant supply of adenosine triphosphate (ATP) from nearby mitochondria. However, it remains unclear how different physical configurations between sarcomeres and mitochondria alter the energetic support for contractile function. Here, we show that sarcomere cross-sectional area (CSA) varies along its length in a cell type-dependent manner where the reduction in Z-disk CSA relative to the sarcomere center is closely coordinated with mitochondrial network configuration in flies, mice, and humans. Further, we find myosin filaments near the sarcomere periphery are curved relative to interior filaments with greater curvature for filaments near mitochondria compared to sarcoplasmic reticulum. Finally, we demonstrate variable myosin filament lattice spacing between filament ends and filament centers in a cell type-dependent manner. These data suggest both sarcomere structure and myofilament interactions are influenced by the location and orientation of mitochondria within muscle cells.

DOI: https://doi.org/10.1038/s41467-022-33678-y
FEBS Lett. 2022 Oct 11.

Rapid fractionation of mitochondria from mouse liver and heart reveals in vivo metabolite compartmentation.

Fay M Allen, Ana S H Costa, Anja V Gruszczyk, Georgina R Bates, Hiran A Prag, Efterpi Nikitopoulou, Carlo Viscomi, Christian Frezza, Andrew M James, Michael P Murphy.

  The compartmentation and distribution of metabolites between mitochondria and the rest of the cell is a key parameter of cell signalling and pathology. Here, we have developed a rapid fractionation procedure that enables us to take mouse heart and liver from in vivo and within ~ 30 seconds stabilise the distribution of metabolites between mitochondria and the cytosol by rapid cooling, homogenisation and dilution. This is followed by centrifugation of mitochondria through an oil layer to separate mitochondrial and cytosolic fractions for subsequent metabolic analysis. Using this procedure revealed the in vivo compartmentation of mitochondrial metabolites and will enable assessment of the distribution of metabolites between the cytosol and mitochondria during a range of situations in vivo.

Keywords:  compartmentation; in vivo; ischemia; metabolites; mitochondria; rapid fractionation

DOI:  https://doi.org/10.1002/1873-3468.14511
Int J Mol Sci. 2022 Sep 20. pii: 11002. [Epub ahead of print]23(19):

Pathological Features in Paediatric Patients with TK2 Deficiency.

Cristina Jou, Andres Nascimento, Anna Codina, Julio Montoya, Ester López-Gallardo, Sonia Emperador, Eduardo Ruiz-Pesini, Raquel Montero, Daniel Natera-de Benito, Carlos I Ortez, Jesus Marquez, Maria V Zelaya, Alfonso Gutierrez-Mata, Carmen Badosa, Laura Carrera-García, Jesica Expósito-Escudero, Monica Roldán, Yolanda Camara, Ramon Marti, Isidre Ferrer, Cecilia Jimenez-Mallebrera, Rafael Artuch.

  Thymidine kinase (TK2) deficiency causes mitochondrial DNA depletion syndrome. We aimed to report the clinical, biochemical, genetic, histopathological, and ultrastructural features of a cohort of paediatric patients with TK2 deficiency. Mitochondrial DNA was isolated from muscle biopsies to assess depletions and deletions. The TK2 genes were sequenced using Sanger sequencing from genomic DNA. All muscle biopsies presented ragged red fibres (RRFs), and the prevalence was greater in younger ages, along with an increase in succinate dehydrogenase (SDH) activity and cytochrome c oxidase (COX)-negative fibres. An endomysial inflammatory infiltrate was observed in younger patients and was accompanied by an overexpression of major histocompatibility complex type I (MHC I). The immunofluorescence study for complex I and IV showed a greater number of fibres than those that were visualized by COX staining. In the ultrastructural analysis, we found three major types of mitochondrial alterations, consisting of concentrically arranged lamellar cristae, electrodense granules, and intramitochondrial vacuoles. The pathological features in the muscle showed substantial differences in the youngest patients when compared with those that had a later onset of the disease. Additional ultrastructural features are described in the muscle biopsy, such as sarcomeric de-structuration in the youngest patients with a more severe phenotype.

Keywords:  TK2 deficiency; mitochondrial myopathies; muscle biopsy; paediatric patients; ragged red fibres; ultrastructural studies

DOI:  https://doi.org/10.3390/ijms231911002
Sci Rep. 2022 Oct 12. 12(1): 17074

Universal dynamics of mitochondrial networks: a finite-size scaling analysis.

Nahuel Zamponi, Emiliano Zamponi, Sergio A Cannas, Dante R Chialvo.

Evidence from models and experiments suggests that the networked structure observed in mitochondria emerges at the critical point of a phase transition controlled by fission and fusion rates. If mitochondria are poised at criticality, the relevant network quantities should scale with the system's size. However, whether or not the expected finite-size effects take place has not been demonstrated yet. Here, we first provide a theoretical framework to interpret the scaling behavior of mitochondrial network quantities by analyzing two conceptually different models of mitochondrial dynamics. Then, we perform a finite-size scaling analysis of real mitochondrial networks extracted from microscopy images and obtain scaling exponents comparable with critical exponents from models and theory. Overall, we provide a universal description of the structural phase transition in mammalian mitochondria.

DOI: https://doi.org/10.1038/s41598-022-14946-9
FEBS Open Bio. 2022 Oct 10.

Knockdown of TMEM160 leads to an increase in reactive oxygen species generation and the induction of the mitochondrial unfolded protein response.

Kosei Yamashita, Misa Haraguchi, Masato Yano.

  Transmembrane protein 160 (TMEM160) was recently reported to be localized to the mitochondrial inner membrane, but mitochondrial function was noted to be unaffected by loss of TMEM160. In contrast to these previously published findings, we report here that the absence of TMEM160 influences intracellular responses. After confirming that TMEM160 is localized in the inner mitochondrial membrane, we knocked down TMEM160 in human cultured cells and analyzed the changes in cellular responses. TMEM160 depletion led to an upregulation of the mitochondrial chaperone HSPD1, suggesting that depletion induced the mitochondrial unfolded protein response (UPRmt ). Indeed, the expression of key transcription factors that induce the UPRmt (ATF4, ATF5, and DDIT3) was increased following TMEM160 depletion. Expression of the mitochondrial protein import-receptors TOMM22 and TOMM20 was also enhanced. In addition, we observed a significant increase in reactive oxygen species (ROS) generation following TMEM160 depletion. Glutathione S-transferases, which detoxify the products of oxidative stress, were also upregulated in TMEM160-depleted cells. Immunoblot analysis was performed to detect proteins modified by 4-hydroxynonenal (which is released after the peroxidation of lipids by ROS): the expression patterns of 4-hydroxynonenal-modified proteins were altered after TMEM160 depletion, suggesting that depletion enhanced degadation of these proteins. HSPD1, TOMM22, ATF4, ATF5, and DDIT3 remained upregulated after ROS was scavenged by N-acetylcysteine, suggesting that once the UPRmt is induced by TMEM160 depletion, it is not suppresed by the subsequent detoxification of ROS. These findings suggest that TMEM160 may suppress ROS generation and stabilize mitochondrial protein(s).

Keywords:  TMEM160; mitochondria; mitochondrial unfolded protein response; oxidative stress; reactive oxygen species

DOI:  https://doi.org/10.1002/2211-5463.13496
FEBS J. 2022 Oct 14.

Early loss of endogenous NAD+ following rotenone treatment leads to mitochondrial dysfunction and Sarm1 induction that is ameliorated by PARP inhibition.

Ankita Sarkar, Sourav Dutta, Malinki Sur, Semanti Chakraborty, Puja Dey, Piyali Mukherjee.

  Sarm1 is an evolutionary conserved innate immune adaptor protein that has emerged as a primary regulator of programmed axonal degeneration over the past decade. In vitro structural insights have revealed that although Sarm1 induces energy depletion by breaking down NAD+ , it is also allosterically inhibited by NAD+ . However, how NAD+ levels modulate the activation of intracellular Sarm1 has not been elucidated so far. This study focuses on understanding the events leading to Sarm1 activation in both neuronal and non-neuronal cells using the mitochondrial complex I inhibitor rotenone. Here we report the regulation of rotenone-induced cell death by loss of NAD+ that may act as a "biological trigger" of Sarm1 activation. Our study revealed that early loss of endogenous NAD+ levels arising due to PARP1 hyperactivation preceded Sarm1 induction following rotenone treatment. Interestingly, replenishing NAD+ levels by the PARP inhibitor, PJ34 restored mitochondrial complex I activity and also prevented subsequent Sarm1 activation in rotenone treated cells. These cellular data were further validated in Drosophila melanogaster where a significant reduction in rotenone mediated loss of locomotor abilities and reduced dSarm expression was observed in the flies following PARP inhibition. Taken together, these observations not only uncover a novel regulation of Sarm1 induction by endogenous NAD+ levels but also point towards an important understanding on how PARP inhibitors could be repurposed in the treatment of mitochondrial complex I deficiency disorders.

Keywords:  Autophagy; Mitochondria; NAD+; PARP inhibitor; PJ34; Rotenone; Sarm1

DOI:  https://doi.org/10.1111/febs.16652
FEBS J. 2022 Oct 11.

Senescent cells in the brain and where to find them.

Noa Rachmian, Valery Krizhanovsky.

  Cellular senescence is a process in which cells change their characteristic phenotype in response to stress and enter a state of prolonged cell cycle arrest accompanied by a distinct secretory phenotype. Cellular senescence has both beneficial and detrimental outcomes. With age, senescent cells progressively accumulate in tissues and might be the bridge connecting ageing to many age-related pathologies. In recent years, evidence emerged supporting the accumulation of brain senescent cells during neurological disorders and ageing. Here, we will discuss the different brain cell populations that exhibit a senescent phenotype. Subsequently, we will explore several senolytic strategies which have been developed to eliminate senescent cells. Finally, we will examine their potential to directly eliminate these senescent brain cells.

Keywords:  Ageing; Blood-brain barrier; Cellular Senescence; Neurodegeneration; Senolytics

DOI:  https://doi.org/10.1111/febs.16649
EMBO J. 2022 Oct 10. e111115

BNIP3L/NIX regulates both mitophagy and pexophagy.

Léa P Wilhelm, Juan Zapata-Muñoz, Beatriz Villarejo-Zori, Stephanie Pellegrin, Catarina Martins Freire, Ashley M Toye, Patricia Boya, Ian G Ganley.

  Mitochondria and peroxisomes are closely related metabolic organelles, both in terms of origin and in terms of function. Mitochondria and peroxisomes can also be turned over by autophagy, in processes termed mitophagy and pexophagy, respectively. However, despite their close relationship, it is not known if both organelles are turned over under similar conditions, and if so, how this might be coordinated molecularly. Here, we find that multiple selective autophagy pathways are activated upon iron chelation and show that mitophagy and pexophagy occur in a BNIP3L/NIX-dependent manner. We reveal that the outer mitochondrial membrane-anchored NIX protein, previously described as a mitophagy receptor, also independently localises to peroxisomes and drives pexophagy. We show this process happens in vivo, with mouse tissue that lacks NIX having a higher peroxisomal content. We further show that pexophagy is stimulated under the same physiological conditions that activate mitophagy, including cardiomyocyte and erythrocyte differentiation. Taken together, our work uncovers a dual role for NIX, not only in mitophagy but also in pexophagy, thus illustrating the interconnection between selective autophagy pathways.

Keywords:  autophagy; mitochondria; mitophagy; peroxisomes; pexophagy

DOI:  https://doi.org/10.15252/embj.2022111115
Cells. 2022 Oct 01. pii: 3099. [Epub ahead of print]11(19):

Effects of Noonan Syndrome-Germline Mutations on Mitochondria and Energy Metabolism.

Donald Bajia, Emanuela Bottani, Katarzyna Derwich.

  Noonan syndrome (NS) and related Noonan syndrome with multiple lentigines (NSML) contribute to the pathogenesis of human diseases in the RASopathy family. This family of genetic disorders constitute one of the largest groups of developmental disorders with variable penetrance and severity, associated with distinctive congenital disabilities, including facial features, cardiopathies, growth and skeletal abnormalities, developmental delay/mental retardation, and tumor predisposition. NS was first clinically described decades ago, and several genes have since been identified, providing a molecular foundation to understand their physiopathology and identify targets for therapeutic strategies. These genes encode proteins that participate in, or regulate, RAS/MAPK signalling. The RAS pathway regulates cellular metabolism by controlling mitochondrial homeostasis, dynamics, and energy production; however, little is known about the role of mitochondrial metabolism in NS and NSML. This manuscript comprehensively reviews the most frequently mutated genes responsible for NS and NSML, covering their role in the current knowledge of cellular signalling pathways, and focuses on the pathophysiological outcomes on mitochondria and energy metabolism.

Keywords:  OXPHOS; RASopathies; energy metabolism; mitochondria

DOI:  https://doi.org/10.3390/cells11193099
Nat Commun. 2022 Oct 11. 13(1): 5989

An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.

Ondřej Gahura, Alexander Mühleip, Carolina Hierro-Yap, Brian Panicucci, Minal Jain, David Hollaus, Martina Slapničková, Alena Zíková, Alexey Amunts.

Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

DOI: https://doi.org/10.1038/s41467-022-33588-z
FEBS Lett. 2022 Oct 10.

Mitochondrial network expansion and dynamic redistribution during islet morphogenesis in zebrafish larvae.

Julia Freudenblum, Dirk Meyer, Robin A Kimmel.

  Mitochondria, organelles critical for energy production, modify their shape and location in response to developmental state and metabolic demands. Mitochondria are altered in diabetes, but the mechanistic basis is poorly defined, due to difficulties in assessing mitochondria within an intact organism. Here, we use in vivo imaging in transparent zebrafish larvae to demonstrate filamentous, interconnected mitochondrial networks within islet cells. Mitochondrial movements highly resemble what has been reported for human islet cells in vitro, showing conservation in behavior across species and cellular context. During islet development, mitochondrial content increases with emergence of cell motility, and mitochondria disperse within fine protrusions. Overall, this work presents quantitative analysis of mitochondria within their native environment and provides insights into mitochondrial behavior during organogenesis.

Keywords:  Mitochondria; image analysis; in vivo imaging; islet; pancreas; zebrafish

DOI:  https://doi.org/10.1002/1873-3468.14508
J Neurol Neurosurg Psychiatry. 2022 Oct 11. pii: jnnp-2022-329320. [Epub ahead of print]

Adults with spinal muscular atrophy: a large-scale natural history study shows gender effect on disease.

Lorenzo Maggi, Luca Bello, Silvia Bonanno, Alessandra Govoni, Claudia Caponnetto, Luigia Passamano, Marina Grandis, Francesca Trojsi, Federica Cerri, Alice Gardani, Manfredi Ferraro, Giulio Gadaleta, Vittoria Zangaro, Luca Caumo, Mariantonietta Maioli, Raffaella Tanel, Elena Saccani, Megi Meneri, Veria Vacchiano, Giulia Ricci, Gianni Sorarù, Eustachio D'Errico, Sara Bortolani, Giovanni Pavesi, Cinzia Gellera, Riccardo Zanin, Stefania Corti, Mauro Silvestrini, Luisa Politano, Angelo Schenone, Stefano Carlo Previtali, Angela Berardinelli, Mara Turri, Lorenzo Verriello, Michela Coccia, Renato Mantegazza, Rocco Liguori, Massimiliano Filosto, Gianni Marrosu, Francesco Danilo Tiziano, Gabriele Siciliano, Isabella Laura Simone, Tiziana Mongini, Giacomo Comi, Elena Pegoraro.

  BACKGROUND: Natural history of spinal muscular atrophy (SMA) in adult age has not been fully elucidated yet, including factors predicting disease progression and response to treatments. Aim of this retrospective, cross-sectional study, is to investigate motor function across different ages, disease patterns and gender in adult SMA untreated patients.METHODS: Inclusion criteria were as follows: (1) clinical and molecular diagnosis of SMA2, SMA3 or SMA4 and (2) clinical assessments performed in adult age (>18 years).
RESULTS: We included 64 (38.8%) females and 101 (61.2%) males (p=0.0025), among which 21 (12.7%) SMA2, 141 (85.5%) SMA3 and 3 (1.8%) SMA4. Ratio of sitters/walkers within the SMA3 subgroup was significantly (p=0.016) higher in males (46/38) than in females (19/38). Median age at onset was significantly (p=0.0071) earlier in females (3 years; range 0-16) than in males (4 years; range 0.3-28), especially in patients carrying 4 SMN2 copies. Median Hammersmith Functional Rating Scale Expanded scores were significantly (p=0.0040) lower in males (16, range 0-64) than in females (40, range 0-62); median revised upper limb module scores were not significantly (p=0.059) different between males (24, 0-38) and females (33, range 0-38), although a trend towards worse performance in males was observed. In SMA3 patients carrying three or four SMN2 copies, an effect of female sex in prolonging ambulation was statistically significant (p=0.034).
CONCLUSIONS: Our data showed a relevant gender effect on SMA motor function with higher disease severity in males especially in the young adult age and in SMA3 patients.

Keywords:  MOTOR NEURON DISEASE; NEUROMUSCULAR; SPINAL MUSCULAR ATRO

DOI:  https://doi.org/10.1136/jnnp-2022-329320
Mol Genet Metab. 2022 Oct 05. pii: S1096-7192(22)00408-5. [Epub ahead of print]137(3): 283-291

PKAN pathogenesis and treatment.

Susan J Hayflick, Suh Young Jeong, Ody C M Sibon.

  Studies aimed at supporting different treatment approaches for pantothenate kinase-associated neurodegeneration (PKAN) have revealed the complexity of coenzyme A (CoA) metabolism and the limits of our current knowledge about disease pathogenesis. Here we offer a foundation for critically evaluating the myriad approaches, argue for the importance of unbiased disease models, and highlight some of the outstanding questions that are central to our understanding and treating PKAN.

Keywords:  Brain iron; Coenzyme A; Mitochondrial acyl carrier protein; PKAN; Pantothenate kinase; Phosphopantetheinylation

DOI:  https://doi.org/10.1016/j.ymgme.2022.09.011
Nat Commun. 2022 Oct 10. 13(1): 5947

Cross-species evolution of a highly potent AAV variant for therapeutic gene transfer and genome editing.

Trevor J Gonzalez, Katherine E Simon, Leo O Blondel, Marco M Fanous, Angela L Roger, Maribel Santiago Maysonet, Garth W Devlin, Timothy J Smith, Daniel K Oh, L Patrick Havlik, Ruth M Castellanos Rivera, Jorge A Piedrahita, Mai K ElMallah, Charles A Gersbach, Aravind Asokan.

Recombinant adeno-associated viral (AAV) vectors are a promising gene delivery platform, but ongoing clinical trials continue to highlight a relatively narrow therapeutic window. Effective clinical translation is confounded, at least in part, by differences in AAV biology across animal species. Here, we tackle this challenge by sequentially evolving AAV capsid libraries in mice, pigs and macaques. We discover a highly potent, cross-species compatible variant (AAV.cc47) that shows improved attributes benchmarked against AAV serotype 9 as evidenced by robust reporter and therapeutic gene expression, Cre recombination and CRISPR genome editing in normal and diseased mouse models. Enhanced transduction efficiency of AAV.cc47 vectors is further corroborated in macaques and pigs, providing a strong rationale for potential clinical translation into human gene therapies. We envision that ccAAV vectors may not only improve predictive modeling in preclinical studies, but also clinical translatability by broadening the therapeutic window of AAV based gene therapies.

DOI: https://doi.org/10.1038/s41467-022-33745-4
Bio Protoc. 2022 Sep 05. pii: e4500. [Epub ahead of print]12(17):

Generation of iMyoblasts from Human Induced Pluripotent Stem Cells.

Dongsheng Guo, Katelyn Daman, Danielle Fernandes Durso, Jing Yan, Charles P Emerson.

  Skeletal muscle stem cells differentiated from human-induced pluripotent stem cells (hiPSCs) serve as a uniquely promising model system for investigating human myogenesis and disease pathogenesis, and for the development of gene editing and regenerative stem cell therapies. Here, we present an effective and reproducible transgene-free protocol for derivation of human skeletal muscle stem cells, iMyoblasts, from hiPSCs. Our two-step protocol consists of 1) small molecule-based differentiation of hiPSCs into myocytes, and 2) stimulation of differentiated myocytes with growth factor-rich medium to activate the proliferation of undifferentiated reserve cells, for expansion and cell line establishment. iMyoblasts are PAX3 + /MyoD1 + myogenic stem cells with dual potential to undergo muscle differentiation and to self-renew as a regenerative cell population for muscle regeneration both ex vivo and in vivo . The simplicity and robustness of iMyoblast generation and expansion have enabled their application to model the molecular pathogenesis of Facioscapulohumeral Muscular Dystrophy and Limb-Girdle Muscular Dystrophies, to both ex vivo and in vivo muscle xenografts, and to respond efficiently to gene editing, enabling the co-development of gene correction and stem cell regenerative therapeutic technologies for the treatment of muscular dystrophies and muscle injury. Graphical abstract.

Keywords:   Differentiation ; Human induced pluripotent stem cells (hiPSCs) ; Muscular dystrophy ; Myogenesis ; Reserve cell ; iMyoblast

DOI:  https://doi.org/10.21769/BioProtoc.4500