bims-mitmed 2022-02-20 papers

bims-mitmed

Biomed News

on Mitochondrial medicine

Issue of 2022‒02‒20
27 papers selected by
Dario Brunetti
Fondazione IRCCS Istituto Neurologico

A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit.
Clinical Heterogeneity in MT-ATP6 Pathogenic Variants: Same Genotype-Different Onset.
LONP-1 and ATFS-1 sustain deleterious heteroplasmy by promoting mtDNA replication in dysfunctional mitochondria.
Mitochondrial Processing Peptidases-Structure, Function and the Role in Human Diseases.
Mitochondrial Dynamics and Mitochondria-Lysosome Contacts in Neurogenetic Diseases.
Whole-exome sequencing confirms implication of VPS13D as a potential cause of progressive spastic ataxia.
Mitochondrial fusion regulates proliferation and differentiation in the type II neuroblast lineage in Drosophila.
Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L.
The ins and outs of the flavin mononucleotide cofactor of respiratory complex I.
Implications of mitochondrial fusion and fission in skeletal muscle mass and health.
Mitochondrial dysfunction and oxidative stress contribute to cognitive and motor impairment in FOXP1 syndrome.
Assessing Mitochondrial DNA Release into the Cytosol and Subsequent Activation of Innate Immune-related Pathways in Mammalian Cells.
Disuse-associated loss of the protease LONP1 in muscle impairs mitochondrial function and causes reduced skeletal muscle mass and strength.
Quantification of mitophagy using mKeima-mito in cultured human primary retinal pigment epithelial cells.
Metabolic determination of cell fate through selective inheritance of mitochondria.
Legionella takes aim at mitochondria.
Enhanced Expression of TRAP1 Protects Mitochondrial Function in Motor Neurons under Conditions of Oxidative Stress.
Lifetime risk of autosomal recessive neurodegeneration with brain iron accumulation (NBIA) disorders calculated from genetic databases.
Mitochondrial Quality Control: A Pathophysiological Mechanism and Therapeutic Target for Stroke.
Mitochondrial efficiency directs cell fate.
De Novo and Dominantly Inherited SPTAN1 Mutations Cause Spastic Paraplegia and Cerebellar Ataxia.
Inhibition of mitochondrial LonP1 protease by allosteric blockade of ATP -binding and -hydrolysis via CDDO and its derivatives.
The strange case of Drp1 in autophagy: Jekyll and Hyde?
Mitochondrial-Targeted Therapy for Doxorubicin-Induced Cardiotoxicity.
Metabolomics-Based Frailty Biomarkers in Older Chinese Adults.
Muscle mitochondrial remodeling by intermittent glucocorticoid drugs requires an intact circadian clock and muscle PGC1α.
Mitochondrial oxidative stress contributes to the pathological aggregation and accumulation of tau oligomers in Alzheimer's disease.

Nat Commun. 2022 Feb 17. 13(1): 929

A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit.

Pedro Rebelo-Guiomar, Simone Pellegrino, Kyle C Dent, Aldema Sas-Chen, Leonor Miller-Fleming, Caterina Garone, Lindsey Van Haute, Jack F Rogan, Adam Dinan, Andrew E Firth, Byron Andrews, Alexander J Whitworth, Schraga Schwartz, Alan J Warren, Michal Minczuk.

Many cellular processes, including ribosome biogenesis, are regulated through post-transcriptional RNA modifications. Here, a genome-wide analysis of the human mitochondrial transcriptome shows that 2'-O-methylation is limited to residues of the mitoribosomal large subunit (mtLSU) 16S mt-rRNA, introduced by MRM1, MRM2 and MRM3, with the modifications installed by the latter two proteins being interdependent. MRM2 controls mitochondrial respiration by regulating mitoribosome biogenesis. In its absence, mtLSU particles (visualized by cryo-EM at the resolution of 2.6 Å) present disordered RNA domains, partial occupancy of bL36m and bound MALSU1:L0R8F8:mtACP anti-association module, allowing five mtLSU biogenesis intermediates with different intersubunit interface configurations to be placed along the assembly pathway. However, mitoribosome biogenesis does not depend on the methyltransferase activity of MRM2. Disruption of the MRM2 Drosophila melanogaster orthologue leads to mitochondria-related developmental arrest. This work identifies a key checkpoint during mtLSU assembly, essential to maintain mitochondrial homeostasis.

DOI: https://doi.org/10.1038/s41467-022-28503-5
Cells. 2022 Jan 30. pii: 489. [Epub ahead of print]11(3):

Clinical Heterogeneity in MT-ATP6 Pathogenic Variants: Same Genotype-Different Onset.

Sara Capiau, Joél Smet, Boel De Paepe, Yilmaz Yildiz, Mutluay Arslan, Olivier Stevens, Maxime Verschoore, Hedwig Stepman, Sara Seneca, Arnaud Vanlander.

  Human mitochondrial disease exhibits large variation of clinical phenotypes, even in patients with the same causative gene defect. We illustrate this heterogeneity by confronting clinical and biochemical data of two patients with the uncommon pathogenic homoplasmic NC_012920.1(MT-ATP6):m.9035T>C variant in MT-ATP6. Patient 1 presented as a toddler with severe motor and speech delay and spastic ataxia without extra-neurologic involvement. Patient 2 presented in adolescence with ataxia and ophthalmoplegia without cognitive or motor impairment. Respiratory chain complex activities were normal in cultured skin fibroblasts from both patients when calculated as ratios over citrate synthase activity. Native gels found presence of subcomplexes of complex V in fibroblast and/or skeletal muscle. Bioenergetic measurements in fibroblasts from both patients detected reduced spare respiratory capacities and altered extracellular acidification rates, revealing a switch from mitochondrial respiration to glycolysis to uphold ATP production. Thus, in contrast to the differing disease presentation, biochemical evidence of mitochondrial deficiency turned out quite similar. We conclude that biochemical analysis remains a valuable tool to confirm the genetic diagnosis of mitochondrial disease, especially in patients with new gene variants or atypical clinical presentation.

Keywords:  ATP-synthase; MT-ATP6; NC_012920.1(MT-ATP6):m.9035T>C; complex V deficiency; genotype-phenotype correlation; mitochondrial disorder; p.L170P

DOI:  https://doi.org/10.3390/cells11030489
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 Jan 24. pii: 1297. [Epub ahead of print]23(3):

Mitochondrial Processing Peptidases-Structure, Function and the Role in Human Diseases.

Nina Kunová, Henrieta Havalová, Gabriela Ondrovičová, Barbora Stojkovičová, Jacob A Bauer, Vladena Bauerová-Hlinková, Vladimir Pevala, Eva Kutejová.

  Mitochondrial proteins are encoded by both nuclear and mitochondrial DNA. While some of the essential subunits of the oxidative phosphorylation (OXPHOS) complexes responsible for cellular ATP production are synthesized directly in the mitochondria, most mitochondrial proteins are first translated in the cytosol and then imported into the organelle using a sophisticated transport system. These proteins are directed mainly by targeting presequences at their N-termini. These presequences need to be cleaved to allow the proper folding and assembly of the pre-proteins into functional protein complexes. In the mitochondria, the presequences are removed by several processing peptidases, including the mitochondrial processing peptidase (MPP), the inner membrane processing peptidase (IMP), the inter-membrane processing peptidase (MIP), and the mitochondrial rhomboid protease (Pcp1/PARL). Their proper functioning is essential for mitochondrial homeostasis as the disruption of any of them is lethal in yeast and severely impacts the lifespan and survival in humans. In this review, we focus on characterizing the structure, function, and substrate specificities of mitochondrial processing peptidases, as well as the connection of their malfunctions to severe human diseases.

Keywords:  IMP; MIP; MPP; mitochondrial disease; mitochondrial processing peptidases; mitochondrial rhomboid protease

DOI:  https://doi.org/10.3390/ijms23031297
Front Neurosci. 2022 ;16 784880

Mitochondrial Dynamics and Mitochondria-Lysosome Contacts in Neurogenetic Diseases.

Jordi Pijuan, Lara Cantarero, Daniel Natera-de Benito, Arola Altimir, Anna Altisent-Huguet, Yaiza Díaz-Osorio, Laura Carrera-García, Jessica Expósito-Escudero, Carlos Ortez, Andrés Nascimento, Janet Hoenicka, Francesc Palau.

  Mitochondrial network is constantly in a dynamic and regulated balance of fusion and fission processes, which is known as mitochondrial dynamics. Mitochondria make physical contacts with almost every other membrane in the cell thus impacting cellular functions. Mutations in mitochondrial dynamics genes are known to cause neurogenetic diseases. To better understand the consequences on the cellular phenotype and pathophysiology of neurogenetic diseases associated with defective mitochondrial dynamics, we have compared the fibroblasts phenotypes of (i) patients carrying pathogenic variants in genes involved in mitochondrial dynamics such as DRP1 (also known as DNM1L), GDAP1, OPA1, and MFN2, and (ii) patients carrying mutated genes that their dysfunction affects mitochondria or induces a mitochondrial phenotype, but that are not directly involved in mitochondrial dynamic network, such as FXN (encoding frataxin, located in the mitochondrial matrix), MED13 (hyperfission phenotype), and CHKB (enlarged mitochondria phenotype). We identified mitochondrial network alterations in all patients' fibroblasts except for CHKB Q198*/Q198*. Functionally, all fibroblasts showed mitochondrial oxidative stress, without membrane potential abnormalities. The lysosomal area and distribution were abnormal in GDAP1 W67L/W67L, DRP1 K75E/+, OPA1 F570L/+, and FXN R165C/GAA fibroblasts. These lysosomal alterations correlated with mitochondria-lysosome membrane contact sites (MCSs) defects in GDAP1 W67L/W67L exclusively. The study of mitochondrial contacts in all samples further revealed a significant decrease in MFN2 R104W/+ fibroblasts. GDAP1 and MFN2 are outer mitochondrial membrane (OMM) proteins and both are related to Charcot-Marie Tooth neuropathy. Here we identified their constitutive interaction as well as MFN2 interaction with LAMP-1. Therefore MFN2 is a new mitochondria-lysosome MCSs protein. Interestingly, GDAP1 W67L/W67L and MFN2 R104W/+ fibroblasts carry pathogenic changes that occur in their catalytic domains thus suggesting a functional role of GDAP1 and MFN2 in mitochondria-lysosome MCSs. Finally, we observed starvation-induced autophagy alterations in DRP1 K75E/+, GDAP1 W67L/W67L, OPA1 F570L/+, MFN2 R104W/+, and CHKB Q198*/Q198* fibroblasts. These genes are related to mitochondrial membrane structure or lipid composition, which would associate the OMM with starvation-induced autophagy. In conclusion, the study of mitochondrial dynamics and mitochondria-lysosome axis in a group of patients with different neurogenetic diseases has deciphered common and unique cellular phenotypes of degrading and non-degrading pathways that shed light on pathophysiological events, new biomarkers and pharmacological targets for these disorders.

Keywords:  lysosome; membrane contact sites (MCSs); mitochondria; mitochondrial dynamics; neurogenetic diseases

DOI:  https://doi.org/10.3389/fnins.2022.784880
BMC Neurol. 2022 Feb 12. 22(1): 53

Whole-exome sequencing confirms implication of VPS13D as a potential cause of progressive spastic ataxia.

Christelle M Durand, Chloé Angelini, Vincent Michaud, Claire Delleci, Isabelle Coupry, Cyril Goizet, Aurelien Trimouille.

  BACKGROUND: VPS13D is a large ubiquitin-binding protein playing an essential role in mitophagy by regulating mitochondrial fission. Recently, VPS13D biallelic pathogenic variants have been reported in patients displaying variable neurological phenotypes, with an autosomic recessive inheritance. The objectives of the study were to determine the genetic etiology of a patient with early onset sporadic progressive spastic ataxia, and to investigate the pathogenicity of VPS13D variants through functional studies on patient's skin fibroblasts.CASE PRESENTATION: We report the case of a 51-year-old patient with spastic ataxia, with an acute onset of the disease at age 7. Walking difficulties slowly worsened over time, with the use of a wheelchair since age 26. We have used trio-based whole-exome sequencing (WES) to identify genes associated with spastic ataxia. The impact of the identified variants on mitochondrial function was assessed in patient's fibroblasts by imaging mitochondrial network and measuring level of individual OXPHOS complex subunits. Compound heterozygous variants were identified in VPS13D: c.946C > T, p.Arg316* and c.12416C > T, p.(Ala4139Val). Primary fibroblasts obtained from this patient revealed an altered mitochondrial morphology, and a decrease in levels of proteins from complex I, III and IV.
CONCLUSIONS: Our findings confirmed implication of VPS13D in spastic ataxia and provided further support for mitochondrial defects in patient's skin fibroblasts with VPS13D variants. This report of long-term follow up showed a slowly progressive course of the spastic paraplegia with cerebellar features. Furthermore, the performed functional studies could be used as biomarker helping diagnosis of VPS13D-related neurological disorders when molecular results are uneasy to interpret.

Keywords:  Mitochondrial network; Spastic ataxia; VPS13D; Whole exome sequencing

DOI:  https://doi.org/10.1186/s12883-022-02553-0
PLoS Genet. 2022 Feb 14. 18(2): e1010055

Mitochondrial fusion regulates proliferation and differentiation in the type II neuroblast lineage in Drosophila.

Dnyanesh Dubal, Prachiti Moghe, Rahul Kumar Verma, Bhavin Uttekar, Richa Rikhy.

Optimal mitochondrial function determined by mitochondrial dynamics, morphology and activity is coupled to stem cell differentiation and organism development. However, the mechanisms of interaction of signaling pathways with mitochondrial morphology and activity are not completely understood. We assessed the role of mitochondrial fusion and fission in the differentiation of neural stem cells called neuroblasts (NB) in the Drosophila brain. Depleting mitochondrial inner membrane fusion protein Opa1 and mitochondrial outer membrane protein Marf in the Drosophila type II NB lineage led to mitochondrial fragmentation and loss of activity. Opa1 and Marf depletion did not affect the numbers of type II NBs but led to a decrease in differentiated progeny. Opa1 depletion decreased the mature intermediate precursor cells (INPs), ganglion mother cells (GMCs) and neurons by the decreased proliferation of the type II NBs and mature INPs. Marf depletion led to a decrease in neurons by a depletion of proliferation of GMCs. On the contrary, loss of mitochondrial fission protein Drp1 led to mitochondrial clustering but did not show defects in differentiation. Depletion of Drp1 along with Opa1 or Marf also led to mitochondrial clustering and suppressed the loss of mitochondrial activity and defects in proliferation and differentiation in the type II NB lineage. Opa1 depletion led to decreased Notch signaling in the type II NB lineage. Further, Notch signaling depletion via the canonical pathway showed mitochondrial fragmentation and loss of differentiation similar to Opa1 depletion. An increase in Notch signaling showed mitochondrial clustering similar to Drp1 mutants. Further, Drp1 mutant overexpression combined with Notch depletion showed mitochondrial fusion and drove differentiation in the lineage, suggesting that fused mitochondria can influence differentiation in the type II NB lineage. Our results implicate crosstalk between proliferation, Notch signaling, mitochondrial activity and fusion as an essential step in differentiation in the type II NB lineage.

DOI: https://doi.org/10.1371/journal.pgen.1010055
Cell Rep. 2022 02 15. pii: S2211-1247(22)00091-2. [Epub ahead of print]38(7): 110370

Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L.

Gulzar A Wani, Hans-Georg Sprenger, Kristiano Ndoci, Srikanth Chandragiri, Richard James Acton, Désirée Schatton, Sandra M V Kochan, Vignesh Sakthivelu, Milica Jevtic, Jens M Seeger, Stefan Müller, Patrick Giavalisco, Elena I Rugarli, Elisa Motori, Thomas Langer, Matteo Bergami.

  The transition between quiescence and activation in neural stem and progenitor cells (NSPCs) is coupled with reversible changes in energy metabolism with key implications for lifelong NSPC self-renewal and neurogenesis. How this metabolic plasticity is ensured between NSPC activity states is unclear. We find that a state-specific rewiring of the mitochondrial proteome by the i-AAA peptidase YME1L is required to preserve NSPC self-renewal. YME1L controls the abundance of numerous mitochondrial substrates in quiescent NSPCs, and its deletion activates a differentiation program characterized by broad metabolic changes causing the irreversible shift away from a fatty-acid-oxidation-dependent state. Conditional Yme1l deletion in adult NSPCs in vivo results in defective self-renewal and premature differentiation, ultimately leading to NSPC pool depletion. Our results disclose an important role for YME1L in coordinating the switch between metabolic states of NSPCs and suggest that NSPC fate is regulated by compartmentalized changes in protein network dynamics.

Keywords:  OMA1; YME1L; adult neurogenesis; metabolic rewiring; mitochondria; mitochondrial dynamics; mitochondrial proteome; neural stem cells; proliferation; self-renewal

DOI:  https://doi.org/10.1016/j.celrep.2022.110370
IUBMB Life. 2022 Feb 14.

The ins and outs of the flavin mononucleotide cofactor of respiratory complex I.

Andrea Curtabbi, José Antonio Enríquez.

  The flavin mononucleotide (FMN) cofactor of respiratory complex I occupies a key position in the electron transport chain. Here, the electrons coming from NADH start the sequence of oxidoreduction reactions, which drives the generation of the proton-motive force necessary for ATP synthesis. The overall architecture and the general catalytic proprieties of the FMN site are mostly well established. However, several aspects regarding the complex I flavin cofactor are still unknown. For example, the flavin binding to the N-module, the NADH-oxidizing portion of complex I, lacks a molecular description. The dissociation of FMN from the enzyme is beginning to emerge as an important regulatory mechanism of complex I activity and ROS production. Finally, how mitochondria import and metabolize FMN is still uncertain. This review summarizes the current knowledge on complex I flavin cofactor and discusses the open questions for future research.

Keywords:  FMN; N-module; ROS; complex I; mitochondria; respiratory chain; riboflavin

DOI:  https://doi.org/10.1002/iub.2600
Semin Cell Dev Biol. 2022 Feb 12. pii: S1084-9521(22)00050-7. [Epub ahead of print]

Implications of mitochondrial fusion and fission in skeletal muscle mass and health.

Vanina Romanello, Marco Sandri.

  The continuous dynamic reshaping of mitochondria by fusion and fission events is critical to keep mitochondrial quality and function under control in response to changes in energy and stress. Maintaining a functional, highly interconnected mitochondrial reticulum ensures rapid energy production and distribution. Moreover, mitochondrial networks act as dynamic signaling hub to adapt to the metabolic demands imposed by contraction, energy expenditure, and general metabolism. However, excessive mitochondrial fusion or fission results in the disruption of the skeletal muscle mitochondrial network integrity and activates a retrograde response from mitochondria to the nucleus, leading to muscle atrophy, weakness and influencing whole-body homeostasis. These actions are mediated via the secretion of mitochondrial-stress myokines such as FGF21 and GDF15. Here we will summarize recent discoveries in the role of mitochondrial fusion and fission in the control of muscle mass and in regulating physiological homeostasis and disease progression.

Keywords:  Atrophy; DRP1; FGF21; Fission; Fusion; GDF15; Mitochondria; Myokines; OPA1; Skeletal muscle

DOI:  https://doi.org/10.1016/j.semcdb.2022.02.011
Proc Natl Acad Sci U S A. 2022 Feb 22. pii: e2112852119. [Epub ahead of print]119(8):

Mitochondrial dysfunction and oxidative stress contribute to cognitive and motor impairment in FOXP1 syndrome.

Jing Wang, Henning Fröhlich, Felipe Bodaleo Torres, Rangel Leal Silva, Gernot Poschet, Amit Agarwal, Gudrun A Rappold.

  FOXP1 syndrome caused by haploinsufficiency of the forkhead box protein P1 (FOXP1) gene is a neurodevelopmental disorder that manifests motor dysfunction, intellectual disability, autism, and language impairment. In this study, we used a Foxp1 +/- mouse model to address whether cognitive and motor deficits in FOXP1 syndrome are associated with mitochondrial dysfunction and oxidative stress. Here, we show that genes with a role in mitochondrial biogenesis and dynamics (e.g., Foxo1, Pgc-1α, Tfam, Opa1, and Drp1) were dysregulated in the striatum of Foxp1 +/- mice at different postnatal stages. Furthermore, these animals exhibit a reduced mitochondrial membrane potential and complex I activity, as well as decreased expression of the antioxidants superoxide dismutase 2 (Sod2) and glutathione (GSH), resulting in increased oxidative stress and lipid peroxidation. These features can explain the reduced neurite branching, learning and memory, endurance, and motor coordination that we observed in these animals. Taken together, we provide strong evidence of mitochondrial dysfunction in Foxp1 +/- mice, suggesting that insufficient energy supply and excessive oxidative stress underlie the cognitive and motor impairment in FOXP1 deficiency.

Keywords:  ASD; FOXP1 syndrome; ROS; cognitive and motor impairment; mitochondrial defect

DOI:  https://doi.org/10.1073/pnas.2112852119
Curr Protoc. 2022 Feb;2(2): e372

Assessing Mitochondrial DNA Release into the Cytosol and Subsequent Activation of Innate Immune-related Pathways in Mammalian Cells.

Joshua D Bryant, Yuanjiu Lei, Jordyn J VanPortfliet, Ashley D Winters, A Phillip West.

  Mitochondria have emerged as key drivers of mammalian innate immune responses, functioning as signaling hubs to trigger inflammation and orchestrating metabolic switches required for phagocyte activation. Mitochondria also contain damage-associated molecular patterns (DAMPs), molecules that share similarity with pathogen-associated molecular patterns (PAMPs) and can engage innate immune sensors to drive inflammation. The aberrant release of mitochondrial DAMPs during cellular stress and injury is an increasingly recognized trigger of inflammatory responses in human diseases. Mitochondrial DNA (mtDNA) is a particularly potent DAMP that engages multiple innate immune sensors, although mounting evidence suggests that cytosolic mtDNA is primarily detected via the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. cGAS and STING are widely expressed in mammalian cells and serve as key regulators of type I interferon and cytokine expression in both infectious and inflammatory diseases. Despite growing roles for the mtDNA-cGAS-STING axis in human disease, assays to quantify mtDNA release into the cytosol and approaches to link mtDNA to cGAS-STING signaling are not standardized, which increases the possibility for experimental artifacts and misinterpretation of data. Here, we present a series of protocols for assaying the release of mtDNA into the cytosol and subsequent activation of innate immune signaling in mammalian cells. We highlight genetic and pharmacological approaches to induce and inhibit mtDNA release from mitochondria. We also describe immunofluorescence microscopy and cellular fractionation assays to visualize morphological changes in mtDNA and quantify mtDNA accumulation in the cytosol. Finally, we include protocols to examine mtDNA-dependent cGAS-STING activation by RT-qPCR and western blotting. These methods can be performed with standard laboratory equipment and are highly adaptable to a wide range of mammalian cell types. They will permit researchers working across the spectrum of biological and biomedical sciences to accurately and reproducibly measure cytosolic mtDNA release and resulting innate immune responses. © 2022 Wiley Periodicals LLC. Basic Protocol 1: siRNA-mediated knockdown of TFAM to induce mtDNA instability, cytosolic release, and activation of the cGAS-STING pathway Alternate Protocol: Pharmacological induction of mtDNA release and cGAS-STING activation using ABT-737 and Q-VD-OPH Basic Protocol 2: Isolation and quantitation of DNA from cytosolic, mitochondrial, and nuclear fractions Basic Protocol 3: Pharmacological inhibition of mtDNA replication and release.

Keywords:  STING; cGAS; innate immunity; mitochondria; mitochondrial DNA

DOI:  https://doi.org/10.1002/cpz1.372
Nat Commun. 2022 Feb 16. 13(1): 894

Disuse-associated loss of the protease LONP1 in muscle impairs mitochondrial function and causes reduced skeletal muscle mass and strength.

Zhisheng Xu, Tingting Fu, Qiqi Guo, Danxia Zhou, Wanping Sun, Zheng Zhou, Xinyi Chen, Jingzi Zhang, Lin Liu, Liwei Xiao, Yujing Yin, Yuhuan Jia, Erkai Pang, Yuncong Chen, Xin Pan, Lei Fang, Min-Sheng Zhu, Wenyong Fei, Bin Lu, Zhenji Gan.

Mitochondrial proteolysis is an evolutionarily conserved quality-control mechanism to maintain proper mitochondrial integrity and function. However, the physiological relevance of stress-induced impaired mitochondrial protein quality remains unclear. Here, we demonstrate that LONP1, a major mitochondrial protease resides in the matrix, plays a role in controlling mitochondrial function as well as skeletal muscle mass and strength in response to muscle disuse. In humans and mice, disuse-related muscle loss is associated with decreased mitochondrial LONP1 protein. Skeletal muscle-specific ablation of LONP1 in mice resulted in impaired mitochondrial protein turnover, leading to mitochondrial dysfunction. This caused reduced muscle fiber size and strength. Mechanistically, aberrant accumulation of mitochondrial-retained protein in muscle upon loss of LONP1 induces the activation of autophagy-lysosome degradation program of muscle loss. Overexpressing a mitochondrial-retained mutant ornithine transcarbamylase (ΔOTC), a known protein degraded by LONP1, in skeletal muscle induces mitochondrial dysfunction, autophagy activation, and cause muscle loss and weakness. Thus, these findings reveal a role of LONP1-dependent mitochondrial protein quality-control in safeguarding mitochondrial function and preserving skeletal muscle mass and strength, and unravel a link between mitochondrial protein quality and muscle mass maintenance during muscle disuse.

DOI: https://doi.org/10.1038/s41467-022-28557-5
Exp Eye Res. 2022 Feb 12. pii: S0014-4835(22)00062-8. [Epub ahead of print] 108981

Quantification of mitophagy using mKeima-mito in cultured human primary retinal pigment epithelial cells.

Cody R Fisher, Mara C Ebeling, Deborah A Ferrington.

The retinal pigment epithelium is a pigmented monolayer of cells that help maintain a healthy retina. Loss of this essential cell layer is implicated in a number of visual disorders, including age-related macular degeneration (AMD). Utilizing primary RPE cultures to investigate disease is an important step in understanding disease mechanisms. However, the use of primary RPE cultures presents a number of challenges, including the limited number of cells available and the presence of auto-fluorescent pigment that interferes with quantifying fluorescent probes. Additionally, primary RPE are difficult to transfect with exogenous nucleic acids traditionally used for fluorescent imaging. To overcome these challenges, we used an adeno-associated viral (AAV) vector to express a pH sensitive fluorescent protein, mKeima, fused to the mitochondrial targeting sequence of cytochrome oxidase subunit 8A (mKeima-mito). mKeima-mito allows for quantification of mitochondrial autophagy (mitophagy) in live cell time lapse imaging experiments. We also developed an image analysis pipeline to selectively quantify mKeima-mito while removing the signal of auto-fluorescent pigment from the dataset by utilizing information from the mKeima fluorescent channels. These techniques are demonstrated in primary RPE cultures expressing mKeima-mito treated with 2-[2-[4-(trifluoromethoxy)phenyl]hydrazinylidene]-propanedinitrile (FCCP), an uncoupler that depolarizes the mitochondrial membrane and leads to mitochondrial fragmentation and mitophagy. The techniques outlined provide a roadmap for investigating disease mechanisms or the effect of treatments utilizing fluorescent probes in an important cell culture model.

DOI: https://doi.org/10.1016/j.exer.2022.108981
Nat Cell Biol. 2022 Feb;24(2): 148-154

Metabolic determination of cell fate through selective inheritance of mitochondria.

Julia Döhla, Emilia Kuuluvainen, Nadja Gebert, Ana Amaral, Johanna I Englund, Swetha Gopalakrishnan, Svetlana Konovalova, Anni I Nieminen, Ella S Salminen, Rubén Torregrosa Muñumer, Kati Ahlqvist, Yang Yang, Hien Bui, Timo Otonkoski, Reijo Käkelä, Ville Hietakangas, Henna Tyynismaa, Alessandro Ori, Pekka Katajisto.

Metabolic characteristics of adult stem cells are distinct from their differentiated progeny, and cellular metabolism is emerging as a potential driver of cell fate conversions1-4. How these metabolic features are established remains unclear. Here we identified inherited metabolism imposed by functionally distinct mitochondrial age-classes as a fate determinant in asymmetric division of epithelial stem-like cells. While chronologically old mitochondria support oxidative respiration, the electron transport chain of new organelles is proteomically immature and they respire less. After cell division, selectively segregated mitochondrial age-classes elicit a metabolic bias in progeny cells, with oxidative energy metabolism promoting differentiation in cells that inherit old mitochondria. Cells that inherit newly synthesized mitochondria with low levels of Rieske iron-sulfur polypeptide 1 have a higher pentose phosphate pathway activity, which promotes de novo purine biosynthesis and redox balance, and is required to maintain stemness during early fate determination after division. Our results demonstrate that fate decisions are susceptible to intrinsic metabolic bias imposed by selectively inherited mitochondria.

DOI: https://doi.org/10.1038/s41556-021-00837-0
Sci Signal. 2022 Feb 15. 15(721): eabo5437

Legionella takes aim at mitochondria.

Annalisa M VanHook.

A Legionella virulence factor blocks mitochondrial ADP/ATP exchange in infected cells.

DOI: https://doi.org/10.1126/scisignal.abo5437
Int J Mol Sci. 2022 Feb 04. pii: 1789. [Epub ahead of print]23(3):

Enhanced Expression of TRAP1 Protects Mitochondrial Function in Motor Neurons under Conditions of Oxidative Stress.

Benjamin E Clarke, Bernadett Kalmar, Linda Greensmith.

  TNF-receptor associated protein (TRAP1) is a cytoprotective mitochondrial-specific member of the Hsp90 heat shock protein family of protein chaperones that has been shown to antagonise mitochondrial apoptosis and oxidative stress, regulate the mitochondrial permeability transition pore and control protein folding in mitochondria. Here we show that overexpression of TRAP1 protects motor neurons from mitochondrial dysfunction and death induced by exposure to oxidative stress conditions modelling amyotrophic lateral sclerosis (ALS). ALS is a fatal neurodegenerative disease in which motor neurons degenerate, leading to muscle weakness and atrophy and death, typically within 3 years of diagnosis. In primary murine motor neurons, shRNA-mediated knockdown of TRAP1 expression results in mitochondrial dysfunction but does not further exacerbate damage induced by oxidative stress alone. Together, these results show that TRAP1 may be a potential therapeutic target for neurodegenerative diseases such as ALS, where mitochondrial dysfunction has been shown to be an early marker of pathogenesis.

Keywords:  TRAP1; mitochondria; motor neuron; oxidative stress

DOI:  https://doi.org/10.3390/ijms23031789
EBioMedicine. 2022 Feb 15. pii: S2352-3964(22)00053-6. [Epub ahead of print]77 103869

Lifetime risk of autosomal recessive neurodegeneration with brain iron accumulation (NBIA) disorders calculated from genetic databases.

Hana Kolarova, Jing Tan, Tim M Strom, Thomas Meitinger, Matias Wagner, Thomas Klopstock.

  BACKGROUND: Neurodegeneration with brain iron accumulation (NBIA) are a group of clinically and genetically heterogeneous diseases characterized by iron overload in basal ganglia and progressive neurodegeneration. Little is known about the epidemiology of NBIA disorders. In the absence of large-scale population-based studies, obtaining reliable epidemiological data requires innovative approaches.METHODS: All pathogenic variants were collected from the 13 genes associated with autosomal recessive NBIA (PLA2G6, PANK2, COASY, ATP13A2, CP, AP4M1, FA2H, CRAT, SCP2, C19orf12, DCAF17, GTPBP2, REPS1). The allele frequencies of these disease-causing variants were assessed in exome/genome collections: the Genome Aggregation Database (gnomAD) and our in-house database. Lifetime risks were calculated from the sum of allele frequencies in the respective genes under assumption of Hardy-Weinberg equilibrium.
FINDINGS: The combined estimated lifetime risk of all 13 investigated NBIA disorders is 0.88 (95% confidence interval 0.70-1.10) per 100,000 based on the global gnomAD dataset (n = 282,912 alleles), 0.92 (0.65-1.29) per 100,000 in the European gnomAD dataset (n = 129,206), and 0.90 (0.48-1.62) per 100,000 in our in-house database (n = 44,324). Individually, the highest lifetime risks (>0.15 per 100,000) are found for disorders caused by variants in PLA2G6, PANK2 and COASY.
INTERPRETATION: This population-genetic estimation on lifetime risks of recessive NBIA disorders reveals frequencies far exceeding previous population-based numbers. Importantly, our approach represents lifetime risks from conception, thus including prenatal deaths. Understanding the true lifetime risk of NBIA disorders is important in estimating disease burden, allocating resources and targeting specific interventions.

Keywords:  Autosomal recessive NBIA disorders; CoPAN; Lifetime risk; Neurodegeneration; PKAN; PLAN

DOI:  https://doi.org/10.1016/j.ebiom.2022.103869
Front Mol Neurosci. 2021 ;14 786099

Mitochondrial Quality Control: A Pathophysiological Mechanism and Therapeutic Target for Stroke.

Miaoxian Yang, Yu He, Shuixiang Deng, Lei Xiao, Mi Tian, Yuewen Xin, Chaocheng Lu, Feng Zhao, Ye Gong.

  Stroke is a devastating disease with high mortality and disability rates. Previous research has established that mitochondria, as major regulators, are both influenced by stroke, and further regulated the development of poststroke injury. Mitochondria are involved in several biological processes such as energy generation, calcium homeostasis, immune response, apoptosis regulation, and reactive oxygen species (ROS) generation. Meanwhile, mitochondria can evolve into various quality control systems, including mitochondrial dynamics (fission and fusion) and mitophagy, to maintain the homeostasis of the mitochondrial network. Various activities of mitochondrial fission and fusion are associated with mitochondrial integrity and neurological injury after stroke. Additionally, proper mitophagy seems to be neuroprotective for its effect on eliminating the damaged mitochondria, while excessive mitophagy disturbs energy generation and mitochondria-associated signal pathways. The balance between mitochondrial dynamics and mitophagy is more crucial than the absolute level of each process. A neurovascular unit (NVU) is a multidimensional system by which cells release multiple mediators and regulate diverse signaling pathways across the whole neurovascular network in a way with a high dynamic interaction. The turbulence of mitochondrial quality control (MQC) could lead to NVU dysfunctions, including neuron death, neuroglial activation, blood-brain barrier (BBB) disruption, and neuroinflammation. However, the exact changes and effects of MQC on the NVU after stroke have yet to be fully illustrated. In this review, we will discuss the updated mechanisms of MQC and the pathophysiology of mitochondrial dynamics and mitophagy after stroke. We highlight the regulation of MQC as a potential therapeutic target for both ischemic and hemorrhagic stroke.

Keywords:  fission; fusion; mitochondrial quality control; mitophagy; neurovascular unit; stroke

DOI:  https://doi.org/10.3389/fnmol.2021.786099
Nat Cell Biol. 2022 Feb;24(2): 125-126

Mitochondrial efficiency directs cell fate.

Jessica Brooke Spinelli, Elma Zaganjor.

DOI: https://doi.org/10.1038/s41556-021-00834-3
Mov Disord. 2022 Feb 12.

De Novo and Dominantly Inherited SPTAN1 Mutations Cause Spastic Paraplegia and Cerebellar Ataxia.

PREPARE Consortium

  BACKGROUND: Pathogenic variants in SPTAN1 have been linked to a remarkably broad phenotypical spectrum. Clinical presentations include epileptic syndromes, intellectual disability, and hereditary motor neuropathy.OBJECTIVES: We investigated the role of SPTAN1 variants in rare neurological disorders such as ataxia and spastic paraplegia.
METHODS: We screened 10,000 NGS datasets across two international consortia and one local database, indicative of the level of international collaboration currently required to identify genes causative for rare disease. We performed in silico modeling of the identified SPTAN1 variants.
RESULTS: We describe 22 patients from 14 families with five novel SPTAN1 variants. Of six patients with cerebellar ataxia, four carry a de novo SPTAN1 variant and two show a sporadic inheritance. In this group, one variant (p.Lys2083del) is recurrent in four patients. Two patients have novel de novo missense mutations (p.Arg1098Cys, p.Arg1624Cys) associated with cerebellar ataxia, in one patient accompanied by intellectual disability and epilepsy. We furthermore report a recurrent missense mutation (p.Arg19Trp) in 15 patients with spastic paraplegia from seven families with a dominant inheritance pattern in four and a de novo origin in one case. One further patient carrying a de novo missense mutation (p.Gln2205Pro) has a complex spastic ataxic phenotype. Through protein modeling we show that mutated amino acids are located at crucial interlinking positions, interconnecting the three-helix bundle of a spectrin repeat.
CONCLUSIONS: We show that SPTAN1 is a relevant candidate gene for ataxia and spastic paraplegia. We suggest that for the mutations identified in this study, disruption of the interlinking of spectrin helices could be a key feature of the pathomechanism. © 2022 International Parkinson and Movement Disorder Society.

Keywords:  ataxia; next-generation sequencing; rare diseases; spastic paraplegia; spectrin

DOI:  https://doi.org/10.1002/mds.28959
J Biol Chem. 2022 Feb 10. pii: S0021-9258(22)00159-4. [Epub ahead of print] 101719

Inhibition of mitochondrial LonP1 protease by allosteric blockade of ATP -binding and -hydrolysis via CDDO and its derivatives.

Jae Lee, Ashutosh K Pandey, Sundararajan Venkatesh, Jayapalraja Thilagavathi, Tadashi Honda, Kamal Singh, Carolyn K Suzuki.

  The mitochondrial protein LonP1 is an ATP-dependent protease that mitigates cell stress and calibrates mitochondrial metabolism and energetics. Bi-allelic mutations in the LONP1 gene are known to cause a broad spectrum of diseases, and LonP1 dysregulation is also implicated in cancer and age-related disorders. Despite the importance of LonP1 in health and disease, specific inhibitors of this protease are unknown. Here, we demonstrate that 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (CDDO) and its -methyl and -imidazole derivatives reversibly inhibit LonP1 by a non-competitive mechanism, blocking ATP-hydrolysis and thus proteolysis. By contrast, we found that CDDO-anhydride inhibits the LonP1 ATPase competitively. Docking of CDDO derivatives in the cryo-EM structure of LonP1 shows these compounds bind a hydrophobic pocket adjacent to the ATP-binding site. The binding site of CDDO derivatives was validated by amino acid substitutions that increased LonP1 inhibition, and also by a pathogenic mutation that causes cerebral, ocular, dental, auricular and skeletal (CODAS) syndrome, which ablated inhibition. CDDO failed to inhibit the ATPase activity of the purified 26S proteasome, which like LonP1 belongs to the AAA+ superfamily of ATPases Associated with diverse cellular Activities, suggesting that CDDO shows selectivity within this family of ATPases. Furthermore, we show that non-cytotoxic concentrations of CDDO derivatives in cultured cells inhibited LonP1, but not the 26S proteasome. Taken together, these findings provide insights for future development of LonP1-specific inhibitors with chemotherapeutic potential.

Keywords:  ATP-dependent protease; CDDO; LonP1; allosteric inhibition; mitochondria; mitochondrial metabolism; protein quality control; proteostasis

DOI:  https://doi.org/10.1016/j.jbc.2022.101719
Bioessays. 2022 Feb 15. e2100271

The strange case of Drp1 in autophagy: Jekyll and Hyde?

Yanfang Chen, Emmanuel Culetto, Renaud Legouis.

  There is a debate regarding the function of Drp1, a GTPase involved in mitochondrial fission, during the elimination of mitochondria by autophagy. A number of experiments indicate that Drp1 is needed to eliminate mitochondria during mitophagy, either by reducing the mitochondrial size or by providing a noncanonical mitophagy function. Yet, other convincing experimental results support the conclusion that Drp1 is not necessary. Here, we review the possible functions for Drp1 in mitophagy and autophagy, depending on tissues, organisms and stresses, and discuss these apparent discrepancies. In this regard, it appears that the reduction of mitochondria size is often required for mitophagy but not always in a Drp1-dependent manner. Finally, we speculate on Drp1-independent mitochondrial fission mechanism that may take place during mitophagy and on noncanonical roles, which Drp1 may play such as modulating organelle contact sites dynamic during the autophagosome formation.

Keywords:  Dnm1; Drp1; MERCs; autophagosome; fission; mitochondria; mitophagy

DOI:  https://doi.org/10.1002/bies.202100271
Int J Mol Sci. 2022 Feb 09. pii: 1912. [Epub ahead of print]23(3):

Mitochondrial-Targeted Therapy for Doxorubicin-Induced Cardiotoxicity.

Bin Bin Wu, Kam Tong Leung, Ellen Ngar-Yun Poon.

  Anthracyclines, such as doxorubicin, are effective chemotherapeutic agents for the treatment of cancer, but their clinical use is associated with severe and potentially life-threatening cardiotoxicity. Despite decades of research, treatment options remain limited. The mitochondria is commonly considered to be the main target of doxorubicin and mitochondrial dysfunction is the hallmark of doxorubicin-induced cardiotoxicity. Here, we review the pathogenic mechanisms of doxorubicin-induced cardiotoxicity and present an update on cardioprotective strategies for this disorder. Specifically, we focus on strategies that can protect the mitochondria and cover different therapeutic modalities encompassing small molecules, post-transcriptional regulators, and mitochondrial transfer. We also discuss the shortcomings of existing models of doxorubicin-induced cardiotoxicity and explore advances in the use of human pluripotent stem cell derived cardiomyocytes as a platform to facilitate the identification of novel treatments against this disorder.

Keywords:  anthracyclines; cardiotoxicity; doxorubicin (DOX); hPSC-cardiomyocytes; human pluripotent stem cells (hPSC); mitochondria

DOI:  https://doi.org/10.3390/ijms23031912
Front Med (Lausanne). 2021 ;8 830723

Metabolomics-Based Frailty Biomarkers in Older Chinese Adults.

Yiming Pan, Yun Li, Pan Liu, Yaxin Zhang, Bowen Li, Zuyun Liu, Guanghou Shui, Lina Ma.

  Background/Objectives: Owing to accelerated population aging, health in older adults is becoming increasingly important. Frailty can reflect the health status and disease risks of older adults; however, appropriate biomarkers for early screening of frailty have not been identified. Here, we applied metabolomics to identify frailty biomarkers and potential pathogenic mechanisms of frailty.Methods: Serum metabolic profiles from 25 frail and 49 non-frail (control) older adults were systematically investigated by liquid chromatography-mass spectrometry-based metabolomics.
Results: We identified 349 metabolites of 46 classes, with four increased and seven decreased metabolites in frail older adults. Pearson correlation analysis identified 11 and 21 metabolites that were positively and negatively correlated with grip strength, and 7 and 76 metabolites that were positively and negatively correlated with gait speed, respectively. Pathway analysis identified 10 metabolite sets and 13 pathways significantly associated with one or more frailty phenotype criteria.
Conclusion: These results revealed the metabolite characteristics of serum in frail older adults. Intermediates of carbohydrate metabolism (e.g., isocitrate, malate, fumarate, cis-aconitate, glucuronate, and pyruvate), saturated fatty acids (e.g., palmitic acid), unsaturated fatty acids (e.g., arachidonate and linoleic acid), and certain essential amino acids (e.g., tryptophan) may be candidate biomarkers for the early diagnosis of frailty. Mitochondrial function disorders, saturated fatty acid-mediated lipotoxicity, aberrant unsaturated fatty acid metabolism, and increased tryptophan degradation could be potential mechanisms of frailty.

Keywords:  biomarker; frailty; metabolomics; older adults; physical function

DOI:  https://doi.org/10.3389/fmed.2021.830723
Sci Adv. 2022 Feb 18. 8(7): eabm1189

Muscle mitochondrial remodeling by intermittent glucocorticoid drugs requires an intact circadian clock and muscle PGC1α.

Mattia Quattrocelli, Michelle Wintzinger, Karen Miz, Daniel C Levine, Clara Bien Peek, Joseph Bass, Elizabeth M McNally.

Exogenous glucocorticoids interact with the circadian clock, but little attention is paid to the timing of intake. We recently found that intermittent once-weekly prednisone improved nutrient oxidation in dystrophic muscle. Here, we investigated whether dosage time affected prednisone effects on muscle bioenergetics. In mice treated with once-weekly prednisone, drug dosing in the light-phase promoted nicotinamide adenine dinucleotide (NAD+) levels and mitochondrial function in wild-type muscle, while this response was lost with dark-phase dosing. These effects depended on a normal circadian clock since they were disrupted in muscle from [Brain and muscle Arnt-like protein-1 (Bmal1)]-knockout mice. The light-phase prednisone pulse promoted BMAL1-dependent glucocorticoid receptor recruitment on noncanonical targets, including Nampt and Ppargc1a [peroxisome proliferator-activated receptor-γ coactivator 1α (PGC1α)]. In mice with muscle-restricted inducible PGC1α ablation, bioenergetic stimulation by light-phase prednisone required PGC1α. These results demonstrate that glucocorticoid "chronopharmacology" for muscle bioenergetics requires an intact clock and muscle PGC1α activity.

DOI: https://doi.org/10.1126/sciadv.abm1189
Hum Mol Genet. 2022 Feb 15. pii: ddab363. [Epub ahead of print]

Mitochondrial oxidative stress contributes to the pathological aggregation and accumulation of tau oligomers in Alzheimer's disease.

Fang Du, Qing Yu, Shirley ShiDu Yan.

Tau oligomers, prior to neurofibrillary tangle formation, are toxic species responsible for tau pathology. The present study addresses whether mitochondrial reactive oxygen species (ROS) contribute to tau oligomer accumulation. First, we determined whether elevated oxidative stress correlates with aggregation of tau oligomers in the brain and platelets of human Alzheimer's disease (AD) patient, tauopathy mice, primary cortical neurons from tau mice, and human trans-mitochondrial 'cybrid' (cytoplasmic hybrid) neuronal cells, whose mitochondria are derived from platelets of patients with sporadic AD- or mild cognitive impairment (MCI)-derived mitochondria. Increased formation of tau oligomers correlates with elevated ROS levels in the hippocampi of AD patients and tauopathy mice, AD- and MCI-derived mitochondria, and AD and MCI cybrid cells. Furthermore, scavenging ROS by application of mito-TEMPO, a mitochondria-targeted antioxidant, not only inhibits the generation of mitochondrial ROS and rescues mitochondrial respiratory function, but also robustly suppresses tau oligomers accumulation in MCI and AD cybrids as well as cortical neurons from tau mice. These studies provide substantial evidence that mitochondria-mediated oxidative stress contributes to tau oligomer formation and accumulation.

DOI: https://doi.org/10.1093/hmg/ddab363