bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023–12–17
58 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Red Flags in Primary Mitochondrial Diseases: What Should We Recognize?
  2. The mitochondrial ATP synthase is a negative regulator of the mitochondrial permeability transition pore.
  3. Human frataxin, the Friedreich ataxia deficient protein, interacts with mitochondrial respiratory chain.
  4. The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases.
  5. Involvement of Mitochondria in Parkinson's Disease.
  6. Mitochondrial temperature homeostasis resists external metabolic stresses.
  7. GRAF1 integrates PINK1-Parkin signaling and actin dynamics to mediate cardiac mitochondrial homeostasis.
  8. Methylmalonic aciduria as a biochemical marker for mitochondrial DNA depletion syndrome in patients with developmental delay and movement disorders: a case series.
  9. Prevalence and Clinical Characteristics of Mitochondrial DNA Mutations in Korean Patients With Sensorineural Hearing Loss.
  10. A hub for regulation of mitochondrial metabolism: Fatty acid and lipoic acid biosynthesis.
  11. CMT2A-linked MFN2 mutation, T206I promotes mitochondrial hyperfusion and predisposes cells towards mitophagy.
  12. Genetic, metabolic and clinical delineation of an MRPS23-associated mitochondrial disorder.
  13. Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase.
  14. Plate-Based Assays for the Characterization of Mitochondrial and Cellular Phenotypes.
  15. New insights on mitochondrial heteroplasmy observed in ovarian diseases.
  16. Method for depletion of mitochondria DNA in human bronchial epithelial cells.
  17. POLG1 variants can at most cause MNGIE-like but not classic MNGIE phenotype.
  18. LKB1/AMPK treats myocardial disease by boosting mitochondrial function.
  19. Downregulation of mitochondrial metabolism is a driver for fast skeletal muscle loss during mouse aging.
  20. "ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane".
  21. Novel COX11 Mutations Associated with Mitochondrial Disorder: Functional Characterization in Patient Fibroblasts and Saccharomyces cerevisiae.
  22. Is space the final frontier for mitochondrial study?
  23. Expression and Purification of Recombinant Human Mitochondrial RNA Polymerase (POLRMT) and the Initiation Factors TFAM and TFB2M.
  24. Heme biosynthesis regulates BCAA catabolism and thermogenesis in brown adipose tissue.
  25. A neuroprosthesis for Parkinson's disease.
  26. Mitochondrial Cation Signalling in the Control of Inflammatory Processes.
  27. Sugar-free synapses run on mitochondrial Sirtuin 3.
  28. The lipid flippase ATP10B enables cellular lipid uptake under stress conditions.
  29. A vesicular Warburg effect: Aerobic glycolysis occurs on axonal vesicles for local NAD+ recycling and transport.
  30. The interplay between sex, time of day, fasting status, and their impact on cardiac mitochondrial structure, function, and dynamics.
  31. A mitochondrial inside-out iron-calcium signal reveals drug targets for Parkinson's disease.
  32. Correction to 'ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression'.
  33. Targeted genetic therapies for inherited disorders that affect both cardiac and skeletal muscle.
  34. The critical roles of STING in mitochondrial homeostasis.
  35. Database screening as a strategy to identify endogenous candidate metabolites to probe and assess mitochondrial drug toxicity.
  36. The assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination.
  37. Mitochondrial morphology in the mouse adrenal cortex: Influence of chronic psychosocial stress.
  38. MITOCHONDRIAL MECHANISMS IN IMMUNITY AND INFLAMMATORY CONDITIONS: BEYOND ENERGY MANAGEMENT.
  39. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain.
  40. Structure and Elasticity of Mitochondrial Membranes: A Molecular Dynamics Simulation Study.
  41. Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders.
  42. Spatial metabolic patterns.
  43. Association between plasma L-carnitine levels and mitochondrial DNA copy number.
  44. Mitochondrial Dysfunction in Skeletal Muscle of Rotenone-Induced Rat Model of Parkinson's Disease: SC-Nanophytosomes as Therapeutic Approach.
  45. Additive Impact of Soy Protein Dietary Intake and Exercise on Visceral Fat Mass Reduction and Mitochondrial Complex I Activation in Skeletal Muscle.
  46. Imaging HOCl Generation during the Mitochondria Peripheral Fission with a Tailor-Made Fluorescent Probe.
  47. The interplay between neuroinflammatory pathways and Parkinson's disease.
  48. Mitochondrially Targeted Gene Therapy Rescues Visual Loss in a Mouse Model of Leber's Hereditary Optic Neuropathy.
  49. Intraneuronal β-amyloid impaired mitochondrial proteostasis through the impact on LONP1.
  50. Will variants of uncertain significance still exist in 2030?
  51. Protein import into mitochondria - a new path through the membranes.
  52. Copper homeostasis and cuproptosis in mitochondria.
  53. Modeling aging and retinal degeneration with mitochondrial DNA mutation burden.
  54. Biallelic pathogenic variants of PARS2 cause developmental and epileptic encephalopathy with spike-and-wave activation in sleep.
  55. AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
  56. Are your organs ageing well? The blood holds clues.
  57. Cellular atlases of the entire mouse brain.
  58. Parkinson's VPS35[D620N] mutation induces LRRK2-mediated lysosomal association of RILPL1 and TMEM55B.
  1. Int J Mol Sci. 2023 Nov 25. pii: 16746. [Epub ahead of print]24(23):
    Red Flags in Primary Mitochondrial Diseases: What Should We Recognize?
    Federica Conti, Serena Di Martino, Filippo Drago, Claudio Bucolo, Vincenzo Micale, Vincenzo Montano, Gabriele Siciliano, Michelangelo Mancuso, Piervito Lopriore.
      Primary mitochondrial diseases (PMDs) are complex group of metabolic disorders caused by genetically determined impairment of the mitochondrial oxidative phosphorylation (OXPHOS). The unique features of mitochondrial genetics and the pivotal role of mitochondria in cell biology explain the phenotypical heterogeneity of primary mitochondrial diseases and the resulting diagnostic challenges that follow. Some peculiar features ("red flags") may indicate a primary mitochondrial disease, helping the physician to orient in this diagnostic maze. In this narrative review, we aimed to outline the features of the most common mitochondrial red flags offering a general overview on the topic that could help physicians to untangle mitochondrial medicine complexity.
    Keywords:  mitochondria; primary mitochondrial diseases; rare diseases; red flags
    DOI:  https://doi.org/10.3390/ijms242316746
  2. Proc Natl Acad Sci U S A. 2023 Dec 19. 120(51): e2303713120
    The mitochondrial ATP synthase is a negative regulator of the mitochondrial permeability transition pore.
    Ryan Pekson, Felix G Liang, Joshua L Axelrod, Jaehoon Lee, Dongze Qin, Andre J H Wittig, Victor M Paulino, Min Zheng, Pablo M Peixoto, Richard N Kitsis.
      The mitochondrial permeability transition pore (mPTP) is a channel in the inner mitochondrial membrane whose sustained opening in response to elevated mitochondrial matrix Ca2+ concentrations triggers necrotic cell death. The molecular identity of mPTP is unknown. One proposed candidate is the mitochondrial ATP synthase, whose canonical function is to generate most ATP in multicellular organisms. Here, we present mitochondrial, cellular, and in vivo evidence that, rather than serving as mPTP, the mitochondrial ATP synthase inhibits this pore. Our studies confirm previous work showing persistence of mPTP in HAP1 cell lines lacking an assembled mitochondrial ATP synthase. Unexpectedly, however, we observe that Ca2+-induced pore opening is markedly sensitized by loss of the mitochondrial ATP synthase. Further, mPTP opening in cells lacking the mitochondrial ATP synthase is desensitized by pharmacological inhibition and genetic depletion of the mitochondrial cis-trans prolyl isomerase cyclophilin D as in wild-type cells, indicating that cyclophilin D can modulate mPTP through substrates other than subunits in the assembled mitochondrial ATP synthase. Mitoplast patch clamping studies showed that mPTP channel conductance was unaffected by loss of the mitochondrial ATP synthase but still blocked by cyclophilin D inhibition. Cardiac mitochondria from mice whose heart muscle cells we engineered deficient in the mitochondrial ATP synthase also demonstrate sensitization of Ca2+-induced mPTP opening and desensitization by cyclophilin D inhibition. Further, these mice exhibit strikingly larger myocardial infarctions when challenged with ischemia/reperfusion in vivo. We conclude that the mitochondrial ATP synthase does not function as mPTP and instead negatively regulates this pore.
    Keywords:  mitochondrial ATP synthase; mitochondrial permeability transition pore; necrosis
    DOI:  https://doi.org/10.1073/pnas.2303713120
  3. Cell Death Dis. 2023 Dec 08. 14(12): 805
    Human frataxin, the Friedreich ataxia deficient protein, interacts with mitochondrial respiratory chain.
    Doni Davide, Cavion Federica, Bortolus Marco, Baschiera Elisa, Muccioli Silvia, Tombesi Giulia, d'Ettorre Federica, Daniele Ottaviani, Marchesan Elena, Leanza Luigi, Greggio Elisa, Ziviani Elena, Russo Antonella, Bellin Milena, Sartori Geppo, Carbonera Donatella, Salviati Leonardo, Costantini Paola.
      Friedreich ataxia (FRDA) is a rare, inherited neurodegenerative disease caused by an expanded GAA repeat in the first intron of the FXN gene, leading to transcriptional silencing and reduced expression of frataxin. Frataxin participates in the mitochondrial assembly of FeS clusters, redox cofactors of the respiratory complexes I, II and III. To date it is still unclear how frataxin deficiency culminates in the decrease of bioenergetics efficiency in FRDA patients' cells. We previously demonstrated that in healthy cells frataxin is closely attached to the mitochondrial cristae, which contain both the FeS cluster assembly machinery and the respiratory chain complexes, whereas in FRDA patients' cells with impaired respiration the residual frataxin is largely displaced in the matrix. To gain novel insights into the function of frataxin in the mitochondrial pathophysiology, and in the upstream metabolic defects leading to FRDA disease onset and progression, here we explored the potential interaction of frataxin with the FeS cluster-containing respiratory complexes I, II and III. Using healthy cells and different FRDA cellular models we found that frataxin interacts with these three respiratory complexes. Furthermore, by EPR spectroscopy, we observed that in mitochondria from FRDA patients' cells the decreased level of frataxin specifically affects the FeS cluster content of complex I. Remarkably, we also found that the frataxin-like protein Nqo15 from T. thermophilus complex I ameliorates the mitochondrial respiratory phenotype when expressed in FRDA patient's cells. Our data point to a structural and functional interaction of frataxin with complex I and open a perspective to explore therapeutic rationales for FRDA targeted to this respiratory complex.
    DOI:  https://doi.org/10.1038/s41419-023-06320-y
  4. Mol Neurobiol. 2023 Dec 12.
    The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases.
    Ying Song, Wenjun Wang, Beibei Wang, Qiwen Shi.
      Mitochondrial transcription factor A (TFAM) is a mitochondrial protein encoded by nuclear genes and transported from the cytoplasm to the mitochondria. TFAM is essential for the maintenance, expression, and delivery of mitochondrial DNA (mtDNA) and can regulate the replication and transcription of mtDNA. TFAM is associated with the formation of mtDNA nucleomimetic structures, mtDNA repair, and mtDNA stability. However, the mechanism by which TFAM protects mtDNA is still being studied. This review provides a summary of the protective mechanism of TFAM on mtDNA including the discrete regulatory effects of TFAM acetylation and phosphorylation on mtDNA, the regulation of Ca2+ levels by TFAM to activate transcription in mitochondria, and the increased binding of TFAM to mtDNA damage hot spots. This review also discusses the association between TFAM and some neurodegenerative diseases.
    Keywords:  Mitochondria; Mitochondrial DNA; Mitochondrial transcription factor A; Neurodegenerative diseases
    DOI:  https://doi.org/10.1007/s12035-023-03841-7
  5. Int J Mol Sci. 2023 Dec 01. pii: 17027. [Epub ahead of print]24(23):
    Involvement of Mitochondria in Parkinson's Disease.
    Chi-Jing Choong, Hideki Mochizuki.
      Mitochondrial dysregulation, such as mitochondrial complex I deficiency, increased oxidative stress, perturbation of mitochondrial dynamics and mitophagy, has long been implicated in the pathogenesis of PD. Initiating from the observation that mitochondrial toxins cause PD-like symptoms and mitochondrial DNA mutations are associated with increased risk of PD, many mutated genes linked to familial forms of PD, including PRKN, PINK1, DJ-1 and SNCA, have also been found to affect the mitochondrial features. Recent research has uncovered a much more complex involvement of mitochondria in PD. Disruption of mitochondrial quality control coupled with abnormal secretion of mitochondrial contents to dispose damaged organelles may play a role in the pathogenesis of PD. Furthermore, due to its bacterial ancestry, circulating mitochondrial DNAs can function as damage-associated molecular patterns eliciting inflammatory response. In this review, we summarize and discuss the connection between mitochondrial dysfunction and PD, highlighting the molecular triggers of the disease process, the intra- and extracellular roles of mitochondria in PD as well as the therapeutic potential of mitochondrial transplantation.
    Keywords:  PINK1; Parkin; Parkinson’s disease; extracellular mitochondria; mitochondria; mitochondria transplantation
    DOI:  https://doi.org/10.3390/ijms242317027
  6. Elife. 2023 Dec 11. pii: RP89232. [Epub ahead of print]12
    Mitochondrial temperature homeostasis resists external metabolic stresses.
    Mügen Terzioglu, Kristo Veeroja, Toni Montonen, Teemu O Ihalainen, Tiina S Salminen, Paule Bénit, Pierre Rustin, Young-Tae Chang, Takeharu Nagai, Howard T Jacobs.
      Based on studies with a fluorescent reporter dye, Mito Thermo Yellow (MTY), and the genetically encoded gTEMP ratiometric fluorescent temperature indicator targeted to mitochondria, the temperature of active mitochondria in four mammalian and one insect cell line was estimated to be up to 15°C above that of the external environment to which the cells were exposed. High mitochondrial temperature was maintained in the face of a variety of metabolic stresses, including substrate starvation or modification, decreased ATP demand due to inhibition of cytosolic protein synthesis, inhibition of the mitochondrial adenine nucleotide transporter and, if an auxiliary pathway for electron transfer was available via the alternative oxidase, even respiratory poisons acting downstream of oxidative phosphorylation (OXPHOS) complex I. We propose that the high temperature of active mitochondria is an inescapable consequence of the biochemistry of OXPHOS and is homeostatically maintained as a primary feature of mitochondrial metabolism.
    Keywords:  D. melanogaster; OXPHOS; biochemistry; bioenergetics; cell biology; chemical biology; human; mitochondria; mouse; organelle; temperature; thermogenesis
    DOI:  https://doi.org/10.7554/eLife.89232
  7. Nat Commun. 2023 Dec 11. 14(1): 8187
    GRAF1 integrates PINK1-Parkin signaling and actin dynamics to mediate cardiac mitochondrial homeostasis.
    Qiang Zhu, Matthew E Combs, Juan Liu, Xue Bai, Wenbo B Wang, Laura E Herring, Jiandong Liu, Jason W Locasale, Dawn E Bowles, Ryan T Gross, Michelle Mendiola Pla, Christopher P Mack, Joan M Taylor.
      The serine/threonine kinase, PINK1, and the E3 ubiquitin ligase, Parkin, are known to facilitate LC3-dependent autophagosomal encasement and lysosomal clearance of dysfunctional mitochondria, and defects in this process contribute to a variety of cardiometabolic and neurological diseases. Although recent evidence indicates that dynamic actin remodeling plays an important role in PINK1/Parkin-mediated mitochondrial autophagy (mitophagy), the underlying signaling mechanisms remain unknown. Here, we identify the RhoGAP GRAF1 (Arhgap26) as a PINK1 substrate that regulates mitophagy. GRAF1 promotes the release of damaged mitochondria from F-actin anchors, regulates mitochondrial-associated Arp2/3-mediated actin remodeling and facilitates Parkin-LC3 interactions to enhance mitochondria capture by autophagosomes. Graf1 phosphorylation on PINK1-dependent sites is dysregulated in human heart failure, and cardiomyocyte-restricted Graf1 depletion in mice blunts mitochondrial clearance and attenuates compensatory metabolic adaptations to stress. Overall, we identify GRAF1 as an enzyme that coordinates cytoskeletal and metabolic remodeling to promote cardioprotection.
    DOI:  https://doi.org/10.1038/s41467-023-43889-6
  8. Front Neurol. 2023 ;14 1265115
    Methylmalonic aciduria as a biochemical marker for mitochondrial DNA depletion syndrome in patients with developmental delay and movement disorders: a case series.
    Montaha Almudhry, Arushi Gahlot Saini, Mohammed A Al-Omari, Yashu Sharma, Maryam Nabavi Nouri, C Anthony Rupar, Chitra Prasad, Andrea C Yu, Savita Verma Attri, Asuri Narayan Prasad.
       Background: Mitochondrial DNA (mtDNA) depletion syndromes (MDDS) are genetically and clinically variable disorders resulting from a reduction in mtDNA content in the cells, tissues, and organ systems, leading to symptoms related to energy deficits. Deficiency of the mitochondrial succinyl-CoA ligase/synthetase enzyme secondary to pathogenic variations in the SUCLG1 and SUCLA2 genes is a subtype of MDDS that presents with neurological manifestations and a specific biochemical profile.
    Methods: This cross-sectional series describes five patients with MDDS secondary to pathogenic variations in the SUCLG1 and SUCLA2 genes from two tertiary care centers in Canada and India. Clinical data concerning the course, investigations, and outcome were gathered through chart reviews.
    Results: All subjects presented in early infancy with neurological manifestations, including movement disorder, psychomotor regression, developmental delay, hearing loss, behavioral issues, or a combination thereof. Elevated methylmalonic acid metabolites, an abnormal acylcarnitine profile, and lactic acidemia were noted in the biochemical profile of each patient (n = 5/5, 100%). Molecular genetic testing disclosed the presence of pathogenic homozygous mutations in four subjects and compound heterozygosity in one subject.
    Conclusion: MDDS associated with SUCLG1 and SUCLA2 genes can be detected biochemically by the presence of methylmalonic aciduria besides the elevation of lactate, C3, C4DC, and C5-OH acylcarnitine. Conducting metabolic workups including MMA and acylcarnitine profiles in patients with heterogeneity of clinical symptoms associated with the presence of this biochemical marker may potentially reduce the time to diagnosis and management.
    Keywords:  SUCLA2; SUCLG1; dystonia; methylmalonic acid; mitochondrial DNA depletion syndrome; mitochondrial disorder; movement disorder
    DOI:  https://doi.org/10.3389/fneur.2023.1265115
  9. J Korean Med Sci. 2023 Dec 11. 38(48): e355
    Prevalence and Clinical Characteristics of Mitochondrial DNA Mutations in Korean Patients With Sensorineural Hearing Loss.
    Sun Young Joo, Seung Hyun Jang, Jung Ah Kim, Se Jin Kim, Bonggi Kim, Hye-Youn Kim, Jae Young Choi, Heon Yung Gee, Jinsei Jung.
       BACKGROUND: Mutations in mitochondrial DNA (mtDNA) are associated with several genetic disorders, including sensorineural hearing loss. However, the prevalence of mtDNA mutations in a large cohort of Korean patients with hearing loss has not yet been investigated. Thus, this study aimed to investigate the frequency of mtDNA mutations in a cohort of with pre- or post-lingual hearing loss of varying severity.
    METHODS: A total of 711 Korean families involving 1,099 individuals were evaluated. Six mitochondrial variants associated with deafness (MTRNR1 m.1555A>G, MTTL1 m.3243A>G, MTCO1 m.7444G>A and m.7445A>G, and MTTS1 m.7471dupC and m.7511T>C) were screened using restriction fragment length polymorphism. The prevalence of the six variants was also analyzed in a large control dataset using whole-genome sequencing data from 4,534 Korean individuals with unknown hearing phenotype.
    RESULTS: Overall, 12 of the 711 (1.7%) patients with hearing loss had mtDNA variants, with 10 patients from independent families positive for the MTRNR1 m.1555A>G mutation and 2 patients positive for the MTCO1 m.7444G>A mutation. The clinical characteristics of patients with the mtDNA variants were characterized by post-lingual progressive hearing loss due to the m.1555A>G variant (9 of 472; 1.9%). In addition, 18/4,534 (0.4%) of the Korean population have mitochondrial variants associated with hearing loss, predominantly the m.1555A>G variant.
    CONCLUSION: A significant proportion of Korean patients with hearing loss is affected by the mtDNA variants, with the m.1555A>G variant being the most prevalent. These results clarify the genetic basis of hearing loss in the Korean population and emphasize the need for genetic testing for mtDNA variants.
    Keywords:  Mitochondrial DNA; Restriction Fragment Length Polymorphism; Sensorineural Hearing Loss
    DOI:  https://doi.org/10.3346/jkms.2023.38.e355
  10. IUBMB Life. 2023 Dec 13.
    A hub for regulation of mitochondrial metabolism: Fatty acid and lipoic acid biosynthesis.
    Carol L Dieckmann.
      Having evolved from a prokaryotic origin, mitochondria retain pathways required for the catabolism of energy-rich molecules and for the biosynthesis of molecules that aid catabolism and/or participate in other cellular processes essential for life of the cell. Reviewed here are details of the mitochondrial fatty acid biosynthetic pathway (FAS II) and its role in building both the octanoic acid precursor for lipoic acid biosynthesis (LAS) and longer-chain fatty acids functioning in chaperoning the assembly of mitochondrial multisubunit complexes. Also covered are the details of mitochondrial lipoic acid biosynthesis, which is distinct from that of prokaryotes, and the attachment of lipoic acid to subunits of pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and glycine cleavage system complexes. Special emphasis has been placed on presenting what is currently known about the interconnected paths and loops linking the FAS II-LAS pathway and two other mitochondrial realms, the organellar translation machinery and Fe-S cluster biosynthesis and function.
    Keywords:  Saccharomyces; fatty acid biosynthesis; lipoic acid biosynthesis; mitochondrial biogenesis
    DOI:  https://doi.org/10.1002/iub.2802
  11. Mitochondrion. 2023 Dec 11. pii: S1567-7249(23)00105-8. [Epub ahead of print] 101825
    CMT2A-linked MFN2 mutation, T206I promotes mitochondrial hyperfusion and predisposes cells towards mitophagy.
    Rajdeep Das, Sebabrata Maity, Palamou Das, Izaz Monir Kamal, Saikat Chakrabarti, Oishee Chakrabarti.
      Mutations in Mitofusin2 (MFN2) associated with the pathology of the debilitating neuropathy Charcot-Marie-Tooth type 2A (CMT2A) are known to alter mitochondrial morphology. Previously, such mutations have been shown to elicit two diametrically opposite phenotypes - while some mutations have been causally linked to enhanced mitochondrial fragmentation, others have been shown to induce hyperfusion. Our study identifies one such MFN2 mutant, T206I that causes mitochondrial hyperfusion. Cells expressing this MFN2 mutant have elongated and interconnected mitochondria. T206I-MFN2 mutation in the GTPase domain increases MFN2 stability and renders cells susceptible to stress. We show that cells expressing T206I-MFN2 have a higher predisposition towards mitophagy under conditions of serum starvation. We also detect increased DRP1 recruitment onto the outer mitochondrial membrane, though the total DRP1 protein level remains unchanged. Here we have characterized a lesser studied CMT2A-linked MFN2 mutant to show that its presence affects mitochondrial morphology and homeostasis.
    DOI:  https://doi.org/10.1016/j.mito.2023.101825
  12. Sci Rep. 2023 Dec 12. 13(1): 22005
    Genetic, metabolic and clinical delineation of an MRPS23-associated mitochondrial disorder.
    Chupong Ittiwut, Rungnapa Ittiwut, Chulaluck Kuptanon, Tetsuro Matsuhashi, Masaru Shimura, Yohei Sugiyama, Takanori Onuki, Akira Ohtake, Kei Murayama, Nithiwat Vatanavicharn, Waralee Dejputtawat, Nitchanund Tantisirivit, Phawin Kor-Anantakul, Wuttichart Kamolvisit, Kanya Suphapeetiporn, Vorasuk Shotelersuk.
      MRPS23 is a nuclear gene encoding a mitochondrial ribosomal protein. A patient with a mitochondrial disorder was found to carry a variant in MRPS23. More cases are necessary to establish MRPS23 as a mitochondrial disease gene. Of 5134 exomes performed in our center, we identified five independent patients who had similar clinical manifestations and were homozygous for the same germline variant c.119C>T; p.P40L in MRPS23. Detailed clinical findings, mitochondrial enzyme activity assays from cultured skin fibroblasts, PCR-Sanger-sequencing, and variant age estimation were performed. Their available family members were also studied. Eight members homozygous for the MRPS23 p.P40L were identified. All were from Hmong hilltribe. Seven presented with alteration of consciousness and recurrent vomiting, while the eighth who was a younger brother of a proband was found pre-symptomatically. Patients showed delayed growth and development, hearing impairment, hypoglycemia, lactic acidosis, and liver dysfunction. In vitro assays of cultured fibroblasts showed combined respiratory chain complex deficiency with low activities of complexes I and IV. PCR-Sanger-sequencing confirmed the variant, which was estimated to have occurred 1550 years ago. These results establish the MRPS23-associated mitochondrial disorder inherited in an autosomal recessive pattern and provide insight into its clinical and metabolic features.
    DOI:  https://doi.org/10.1038/s41598-023-49161-7
  13. Nat Commun. 2023 Dec 08. 14(1): 8115
    Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase.
    Helene Jahn, Ladislav Bartoš, Grace I Dearden, Jeremy S Dittman, Joost C M Holthuis, Robert Vácha, Anant K Menon.
      Mitochondria are double-membrane-bounded organelles that depend critically on phospholipids supplied by the endoplasmic reticulum. These lipids must cross the outer membrane to support mitochondrial function, but how they do this is unclear. We identify the Voltage Dependent Anion Channel (VDAC), an abundant outer membrane protein, as a scramblase-type lipid transporter that catalyzes lipid entry. On reconstitution into membrane vesicles, dimers of human VDAC1 and VDAC2 catalyze rapid transbilayer translocation of phospholipids by a mechanism that is unrelated to their channel activity. Coarse-grained molecular dynamics simulations of VDAC1 reveal that lipid scrambling occurs at a specific dimer interface where polar residues induce large water defects and bilayer thinning. The rate of phospholipid import into yeast mitochondria is an order of magnitude lower in the absence of VDAC homologs, indicating that VDACs provide the main pathway for lipid entry. Thus, VDAC isoforms, members of a superfamily of beta barrel proteins, moonlight as a class of phospholipid scramblases - distinct from alpha-helical scramblase proteins - that act to import lipids into mitochondria.
    DOI:  https://doi.org/10.1038/s41467-023-43570-y
  14. Methods Mol Biol. 2024 ;2746 1-20
    Plate-Based Assays for the Characterization of Mitochondrial and Cellular Phenotypes.
    Benjamin Henry Arnold, Oana Sanislav, Paul Robert Fisher, Sarah Jane Annesley.
      The mitochondria are essential to eukaryotic life, acting as key drivers of energy generation while also being involved in the regulation of many cellular processes including apoptosis, cell proliferation, calcium homeostasis, and metabolism. Mitochondrial diseases which disrupt these processes lead to a diverse range of pathologies and lack consistency in symptom presentation. In disease, mitochondrial activity and energy homeostasis can be adapted to cellular requirements, and studies using Dictyostelium and human lymphoblastoid cell lines have shown that such changes can be facilitated by the key cellular and energy regulators, TORC1 and AMPK. Fluorescence-based assays are increasingly utilized to measure mitochondrial and cell signalling function in mitochondrial disease research. Here, we describe a streamlined method for the simultaneous measurement of mitochondrial mass, membrane potential, and reactive oxygen species production using MitoTracker Green™ FM, MitoTracker Red™ CMXRos, and DCFH-DA probes. This protocol has been adapted for both Dictyostelium and human lymphoblastoid cell lines. We also describe a method for assessing TORC1 and AMPK activity simultaneously in lymphoblastoid cells. These techniques allow for the characterization of mitochondrial defects in a rapid and easy to implement manner.
    Keywords:  AMPK; Dictyostelium; Lymphoblast; Membrane potential; Mitochondrial mass; ROS; TORC1
    DOI:  https://doi.org/10.1007/978-1-0716-3585-8_1
  15. J Adv Res. 2023 Dec 05. pii: S2090-1232(23)00372-7. [Epub ahead of print]
    New insights on mitochondrial heteroplasmy observed in ovarian diseases.
    Yong Zhou, Yang Jin, Tianyu Wu, Yinfeng Wang, Yuanhang Dong, Pei Chen, Changchang Hu, Ningping Pan, Chaoshuang Ye, Li Shen, Mengyan Lin, Tao Fang, Ruijin Wu.
       BACKGROUND: The reportedly high mutation rate of mitochondrial DNA (mtDNA) may be attributed to the absence of histone protection and complete repair mechanisms. Mitochondrial heteroplasmy refers to the coexistence of wild-type and mutant mtDNA. Most healthy individuals carry a low point mutation load (<1%) in their mtDNA, typically without any discernible phenotypic effects. However, as it exceeds a certain threshold, it may cause the onset of various diseases. Since the ovary is a highly energy-intensive organ, it relies heavily on mitochondrial function. Mitochondrial heteroplasmy can potentially contribute to a variety of significant ovarian disorders.
    AIM: of Review: In this review, we have elucidated the close relationship between mtDNA heteroplasmy and ovarian diseases, and summarized novel avenues and strategies for the potential treatment of these ovarian diseases. Key Scientific Concepts of Review: Mitochondrial heteroplasmy can potentially contribute to a variety of significant ovarian disorders, including polycystic ovary syndrome, premature ovarian insufficiency, and endometriosis. Current strategies related to mitochondrial heteroplasmy are untargeted and have low bioavailability. Nanoparticle delivery systems loaded with mitochondrial modulators, mitochondrial replacement/transplantation therapy, and mitochondria-targeted gene editing therapy may offer promising paths towards potentially more effective treatments for these diseases, despite ongoing challenges.
    Keywords:  Endometriosis; Mitochondria-targeted therapy; Mitochondrial heteroplasmy; Polycystic ovary syndrome; Premature ovarian insufficiency
    DOI:  https://doi.org/10.1016/j.jare.2023.11.033
  16. MethodsX. 2024 Jun;12 102497
    Method for depletion of mitochondria DNA in human bronchial epithelial cells.
    Michael V Novotny, Weiling Xu, Anny Mulya, Allison J Janocha, Serpil C Erzurum.
      Mitochondria are increasingly recognized to play a role in the airway inflammation of asthma. Model systems to study the role of mitochondrial gene expression in bronchial epithelium are lacking. Here, we create custom bronchial epithelial cell lines that are depleted of mitochondrial DNA. One week of ethidium bromide (EtBr) treatment led to ∼95 % reduction of mtDNA copy number (mtDNA-CN) in cells, which was further reduced by addition of 25 µM 2',3'-dideoxycytidin (ddC). Treatment for up to three weeks with EtBr and ddC led to near complete loss of mtDNA. The basal oxygen consumption rate (OCR) of mtDNA-depleted BET-1A and BEAS-2B cells dropped to near zero. Glycolysis measured by extracellular acidification rate (ECAR) increased ∼two-fold in cells when mtDNA was eliminated. BET-1A ρ0 and BEAS-2B ρ0 cells were cultured for two months, frozen and thawed, cultured for two more months, and maintained near zero mtDNA-CN. Mitochondrial DNA-depleted BET-1A ρ0 and BEAS-2B ρ0 cell lines are viable, lack the capacity for aerobic respiration, and increase glycolysis.•BET-1A and BEAS-2B cells were treated with ethidium bromide (EtBr) with or without 2',3'-dideoxycytidine (ddC) to create cells lacking mitochondrial DNA (mtDNA).•Cells' mtDNA copy number relative to nuclear DNA (nDNA) were verified by quantitative polymerase chain reaction (qPCR).•Cells were also assessed for oxidative phosphorylation by measures of oxygen consumption using the Seahorse analyzer.
    Keywords:  BEAS-2B; Bronchial epithelial cells BET-1A; Depletion of Mitochondria DNA; Mitochondrial DNA; ρ0 cells
    DOI:  https://doi.org/10.1016/j.mex.2023.102497
  17. Clin Neurol Neurosurg. 2023 Nov 28. pii: S0303-8467(23)00485-7. [Epub ahead of print]236 108069
    POLG1 variants can at most cause MNGIE-like but not classic MNGIE phenotype.
    Josef Finsterer.
      
    Keywords:  MNGIE; Mitochondrial; MtDNA depletion; POLG1; Vomiting
    DOI:  https://doi.org/10.1016/j.clineuro.2023.108069
  18. Int J Cardiol. 2023 Dec 06. pii: S0167-5273(23)01780-1. [Epub ahead of print] 131645
    LKB1/AMPK treats myocardial disease by boosting mitochondrial function.
    Zhihuan Luo, Luyuan Yao.
      
    Keywords:  AMPK; Cardiomyopathy; LKB1; Mitochondrial dysfunction
    DOI:  https://doi.org/10.1016/j.ijcard.2023.131645
  19. Commun Biol. 2023 Dec 08. 6(1): 1240
    Downregulation of mitochondrial metabolism is a driver for fast skeletal muscle loss during mouse aging.
    Raquel Fernando, Anastasia V Shindyapina, Mario Ost, Didac Santesmasses, Yan Hu, Alexander Tyshkovskiy, Sun Hee Yim, Jürgen Weiss, Vadim N Gladyshev, Tilman Grune, José Pedro Castro.
      Skeletal muscle aging is characterized by the loss of muscle mass, strength and function, mainly attributed to the atrophy of glycolytic fibers. Underlying mechanisms driving the skeletal muscle functional impairment are yet to be elucidated. To unbiasedly uncover its molecular mechanisms, we recurred to gene expression and metabolite profiling in a glycolytic muscle, Extensor digitorum longus (EDL), from young and aged C57BL/6JRj mice. Employing multi-omics approaches we found that the main age-related changes are connected to mitochondria, exhibiting a downregulation in mitochondrial processes. Consistent is the altered mitochondrial morphology. We further compared our mouse EDL aging signature with human data from the GTEx database, reinforcing the idea that our model may recapitulate muscle loss in humans. We are able to show that age-related mitochondrial downregulation is likely to be detrimental, as gene expression signatures from commonly used lifespan extending interventions displayed the opposite direction compared to our EDL aging signature.
    DOI:  https://doi.org/10.1038/s42003-023-05595-3
  20. Free Radic Biol Med. 2023 Dec 11. pii: S0891-5849(23)01151-6. [Epub ahead of print]
    "ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane".
    Paula Gaudó, Elena de Tomás-Mateo, Nuria Garrido-Pérez, Alfredo Santana, Eduardo Ruiz-Pesini, Julio Montoya, Pilar Bayona-Bafaluy.
      Mitochondrial ATAD3A is an ATPase Associated with diverse cellular Activities (AAA) domain containing enzyme, involved in the structural organization of the inner mitochondrial membrane and of increasing importance in childhood disease. In humans, two ATAD3A paralogs arose by gene duplication during evolution: ATAD3B and ATAD3C. Here we investigate the cellular activities of the ATAD3C paralog that has been considered a pseudogene. We detected unique ATAD3C peptides in HEK 293T cells, with expression similar to that in human tissues, and showed that it is an integral membrane protein that exposes its carboxy-terminus to the intermembrane space. Overexpression of ATAD3C, but not of ATAD3A, in fibroblasts caused a decrease in cell proliferation and oxygen consumption rate, and an increase of cellular ROS. This was due to the incorporation of ATAD3C monomers in ATAD3A complex in the mitochondrial membrane reducing its size. Consistent with a negative regulation of ATAD3A function in mitochondrial membrane organization, ATAD3C expression led to increased accumulation of respiratory chain dimeric CIII in the inner membrane, to the detriment to that assembled in respiratory supercomplexes. Our results demonstrate a negative dominant role of the ATAD3C paralog with implications for mitochondrial OXPHOS function and suggest that its expression regulates ATAD3A in the cell.
    Keywords:  ATAD3A; ATAD3B; ATAD3C; Mitochondria; OXPHOS; Respiratory complexes; Respiratory supercomplexes
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.12.006
  21. Int J Mol Sci. 2023 Nov 23. pii: 16636. [Epub ahead of print]24(23):
    Novel COX11 Mutations Associated with Mitochondrial Disorder: Functional Characterization in Patient Fibroblasts and Saccharomyces cerevisiae.
    Chenelle A Caron-Godon, Stefania Della Vecchia, Alessandro Romano, Stefano Doccini, Flavio Dal Canto, Rosa Pasquariello, Anna Rubegni, Roberta Battini, Filippo Maria Santorelli, D Moira Glerum, Claudia Nesti.
      Genetic defects in the nuclear encoded subunits and assembly factors of cytochrome c oxidase (mitochondrial complex IV) are very rare and are associated with a wide variety of phenotypes. Biallelic pathogenic variants in the COX11 protein were previously identified in two unrelated children with infantile-onset mitochondrial encephalopathies. Through comprehensive clinical, genetic and functional analyses, here we report on a new patient harboring novel heterozygous variants in COX11, presenting with Leigh-like features, and provide additional experimental evidence for a direct correlation between COX11 protein expression and sensitivity to oxidative stress. To sort out the contribution of the single mutations to the phenotype, we employed a multi-faceted approach using Saccharomyces cerevisiae as a genetically manipulable system, and in silico structure-based analysis of human COX11. Our results reveal differential effects of the two novel COX11 mutations on yeast growth, respiration, and cellular redox status, as well as their potential impact on human protein stability and function. Strikingly, the functional deficits observed in patient fibroblasts are recapitulated in yeast models, validating the conservation of COX11's role in mitochondrial integrity across evolutionarily distant organisms. This study not only expands the mutational landscape of COX11-associated mitochondrial disorders but also underscores the continued translational relevance of yeast models in dissecting complex molecular pathways.
    Keywords:  COX11 mutation; COX11 protein structure; mitochondrial diseases; yeast model
    DOI:  https://doi.org/10.3390/ijms242316636
  22. Biotechniques. 2023 Dec 12.
    Is space the final frontier for mitochondrial study?
    Kit Neikirk, Dominique C Stephens, Heather K Beasley, Andrea G Marshall, Jennifer A Gaddy, Steven M Damo, Antentor Hinton.
      Tweetable abstract This perspective considers several avenues for future research on mitochondrial dynamics, stress, and DNA in outer space.
    Keywords:  metabolism; mitochondria; mitochondrial structure; space travel
    DOI:  https://doi.org/10.2144/btn-2023-0071
  23. Bio Protoc. 2023 Dec 05. 13(23): e4892
    Expression and Purification of Recombinant Human Mitochondrial RNA Polymerase (POLRMT) and the Initiation Factors TFAM and TFB2M.
    An H Hsieh, Sean D Reardon, Jubilee H Munozvilla-Cabellon, Jiayu Shen, Smita S Patel, Tatiana V Mishanina.
      Human mitochondrial DNA (mtDNA) encodes several components of oxidative phosphorylation responsible for the bulk of cellular energy production. The mtDNA is transcribed by a dedicated human mitochondrial RNA polymerase (POLRMT) that is structurally distinct from its nuclear counterparts, instead closely resembling the single-subunit viral RNA polymerases (e.g., T7 RNA polymerase). The initiation of transcription by POLRMT is aided by two initiation factors: transcription factor A, mitochondrial (TFAM), and transcription factor B2, mitochondrial (TFB2M). Although many details of human mitochondrial transcription initiation have been elucidated with in vitro biochemical and structural studies, much remains to be addressed relating to the mechanism and regulation of transcription. Studies of such mechanisms require reliable, high-yield, and high-purity methods for protein production, and this protocol provides the level of detail and troubleshooting tips that are necessary for a novice to generate meaningful amounts of proteins for experimental work. The current protocol describes how to purify recombinant POLRMT, TFAM, and TFB2M from Escherichia coli using techniques such as affinity column chromatography (Ni2+ and heparin), how to remove the solubility tags with TEV protease and recover untagged proteins of interest, and how to overcome commonly encountered challenges in obtaining high yield of each protein. Key features • This protocol builds upon purification methods developed by Patel lab (Ramachandran et al., 2017) and others with greater detail than previously published works. • The protocol requires several days to complete as various steps are designed to be performed overnight. • The recombinantly purified proteins have been successfully used for in vitro transcription experiments, allowing for finer control of experimental components in a minimalistic system.
    Keywords:  Bacterial protein expression; Heparin; Maltose binding protein (MBP) fusion protein purification; Ni-NTA; POLRMT; Protein purification; TEV protease; TFAM; TFB2M
    DOI:  https://doi.org/10.21769/BioProtoc.4892
  24. bioRxiv. 2023 Nov 28. pii: 2023.11.28.568893. [Epub ahead of print]
    Heme biosynthesis regulates BCAA catabolism and thermogenesis in brown adipose tissue.
    Dylan J Duerre, Julia K Hansen, Steven John, Annie Jen, Noah Carrillo, Hoang Bui, Yutong Bao, Matias Fabregat, Katherine Overmeyer, Evgenia Shishkova, Mark P Keller, Richard A Anderson, Vincent L Cryns, Alan D Attie, Joshua J Coon, Jing Fan, Andrea Galmozzi.
      With age, people tend to accumulate body fat and reduce energy expenditure 1 . Brown (BAT) and beige adipose tissue dissipate heat and increase energy expenditure via the activity of the uncoupling protein UCP1 and other thermogenic futile cycles 2,3 . The activity of brown and beige depots inversely correlates with BMI and age 4-11 , suggesting that promoting thermogenesis may be an effective approach for combating age-related metabolic disease 12-15 . Heme is an enzyme cofactor and signaling molecule that we recently showed to regulate BAT function 16 . Here, we show that heme biosynthesis is the primary contributor to intracellular heme levels in brown adipocytes. Inhibition of heme biosynthesis leads to mitochondrial dysfunction and reduction in UCP1. Although supplementing heme can restore mitochondrial function in heme-synthesis-deficient cells, the downregulation of UCP1 persists due to the accumulation of the heme precursors, particularly propionyl-CoA, which is a product of branched-chain amino acids (BCAA) catabolism. Cold exposure promotes BCAA uptake in BAT, and defects in BCAA catabolism in this tissue hinder thermogenesis 17 . However, BCAAs' contribution to the TCA cycle in BAT and WAT never exceeds 2% of total TCA flux 18 . Our work offers a way to integrate current literature by describing heme biosynthesis as an important metabolic sink for BCAAs.
    DOI:  https://doi.org/10.1101/2023.11.28.568893
  25. Nat Biotechnol. 2023 Dec;41(12): 1689
    A neuroprosthesis for Parkinson's disease.
    Anahita Bishop.
      
    DOI:  https://doi.org/10.1038/s41587-023-02067-1
  26. Int J Mol Sci. 2023 Nov 24. pii: 16724. [Epub ahead of print]24(23):
    Mitochondrial Cation Signalling in the Control of Inflammatory Processes.
    Pampa Pain, Francesca Spinelli, Gaia Gherardi.
      Mitochondria are the bioenergetic organelles responsible for the maintenance of cellular homeostasis and have also been found to be associated with inflammation. They are necessary to induce and maintain innate and adaptive immune cell responses, acting as signalling platforms and mediators in effector responses. These organelles are also known to play a pivotal role in cation homeostasis as well, which regulates the inflammatory responses through the modulation of these cation channels. In particular, this review focuses on mitochondrial Ca2+ and K+ fluxes in the regulation of inflammatory response. Nevertheless, this review aims to understand the interplay of these inflammation inducers and pathophysiological conditions. In detail, we discuss some examples of chronic inflammation such as lung, bowel, and metabolic inflammatory diseases caused by a persistent activation of the innate immune response due to a dysregulation of mitochondrial cation homeostasis.
    Keywords:  inflammation; mitochondrial Ca2+ uptake; mitochondrial K+ flux
    DOI:  https://doi.org/10.3390/ijms242316724
  27. J Cell Biol. 2024 Jan 01. pii: e202312035. [Epub ahead of print]223(1):
    Sugar-free synapses run on mitochondrial Sirtuin 3.
    Alexander P Walsh, David J Simon.
      Metabolic plasticity of neurons ensures their activity continues when glucose is limited. Walsh and Simon discuss new work by Ashrafi and colleagues (https://doi.org/10.1083/jcb.202305048) that finds Sirtuin 3 directs local metabolic adaptation at synapses during sustained glucose deprivation.
    DOI:  https://doi.org/10.1083/jcb.202312035
  28. Biochim Biophys Acta Mol Cell Res. 2023 Dec 10. pii: S0167-4889(23)00225-2. [Epub ahead of print] 119652
    The lipid flippase ATP10B enables cellular lipid uptake under stress conditions.
    Rosanne Wouters, Igor Beletchi, Chris Van den Haute, Veerle Baekelandt, Shaun Martin, Jan Eggermont, Peter Vangheluwe.
      Pathogenic ATP10B variants have been described in patients with Parkinson's disease and dementia with Lewy body disease, and we previously established ATP10B as a late endo-/lysosomal lipid flippase transporting both phosphatidylcholine (PC) and glucosylceramide (GluCer) from the lysosomal exoplasmic to cytoplasmic membrane leaflet. Since several other lipid flippases regulate cellular lipid uptake, we here examined whether also ATP10B impacts cellular lipid uptake. Transient co-expression of ATP10B with its obligatory subunit CDC50A stimulated the uptake of fluorescently (NBD-) labeled PC in HeLa cells. This uptake is dependent on the transport function of ATP10B, is impaired by disease-associated variants and appears specific for NBD-PC. Uptake of non-ATP10B substrates, such as NBD-sphingomyelin or NBD-phosphatidylethanolamine is not increased. Remarkably, in stable cell lines co-expressing ATP10B/CDC50A we only observed increased NBD-PC uptake following treatment with rotenone, a mitochondrial complex I inhibitor that induces transport-dependent ATP10B phenotypes. Conversely, Im95m and WM-115 cells with endogenous ATP10B expression, present a decreased NBD-PC uptake following ATP10B knockdown, an effect that is exacerbated under rotenone stress. Our data show that the endo-/lysosomal lipid flippase ATP10B contributes to cellular PC uptake under specific cell stress conditions.
    Keywords:  Endo-/lysosomes; Glucosylceramide; Lipid transport; Parkinson's disease; Phosphatidylcholine
    DOI:  https://doi.org/10.1016/j.bbamcr.2023.119652
  29. Traffic. 2023 Dec 12.
    A vesicular Warburg effect: Aerobic glycolysis occurs on axonal vesicles for local NAD+ recycling and transport.
    Maximilian Mc Cluskey, Hervé Dubouchaud, Anne-Sophie Nicot, Frédéric Saudou.
      In neurons, fast axonal transport (FAT) of vesicles occurs over long distances and requires constant and local energy supply for molecular motors in the form of adenosine triphosphate (ATP). FAT is independent of mitochondrial metabolism. Indeed, the glycolytic machinery is present on vesicles and locally produces ATP, as well as nicotinamide adenine dinucleotide bonded with hydrogen (NADH) and pyruvate, using glucose as a substrate. It remains unclear whether pyruvate is transferred to mitochondria from the vesicles as well as how NADH is recycled into NAD+ on vesicles for continuous glycolysis activity. The optimization of a glycolytic activity test for subcellular compartments allowed the evaluation of the kinetics of vesicular glycolysis in the brain. This revealed that glycolysis is more efficient on vesicles than in the cytosol. We also found that lactate dehydrogenase (LDH) enzymatic activity is required for effective vesicular ATP production. Indeed, inhibition of LDH or the forced degradation of pyruvate inhibited ATP production from axonal vesicles. We found LDHA rather than the B isoform to be enriched on axonal vesicles suggesting a preferential transformation of pyruvate to lactate and a concomitant recycling of NADH into NAD+ on vesicles. Finally, we found that LDHA inhibition dramatically reduces the FAT of both dense-core vesicles and synaptic vesicle precursors in a reconstituted cortico-striatal circuit on-a-chip. Together, this shows that aerobic glycolysis is required to supply energy for vesicular transport in neurons, similar to the Warburg effect.
    Keywords:  Warburg effect; aerobic glycolysis; axonal transport; brain-derived neurotrophic factor; cortico-striatal network; dense-core vesicles; lactate dehydrogenase; metabolism; microfluidic device; nicotinamide adenine dinucleotide; synaptic vesicle precursors
    DOI:  https://doi.org/10.1111/tra.12926
  30. Sci Rep. 2023 Dec 07. 13(1): 21638
    The interplay between sex, time of day, fasting status, and their impact on cardiac mitochondrial structure, function, and dynamics.
    Mariame S Kane, Gloria A Benavides, Edie Osuma, Michelle S Johnson, Helen E Collins, Yecheng He, David Westbrook, Silvio H Litovsky, Kasturi Mitra, John C Chatham, Victor Darley-Usmar, Martin E Young, Jianhua Zhang.
      Mitochondria morphology and function, and their quality control by mitophagy, are essential for heart function. We investigated whether these are influenced by time of the day (TOD), sex, and fed or fasting status, using transmission electron microscopy (EM), mitochondrial electron transport chain (ETC) activity, and mito-QC reporter mice. We observed peak mitochondrial number at ZT8 in the fed state, which was dependent on the intrinsic cardiac circadian clock, as hearts from cardiomyocyte-specific BMAL1 knockout (CBK) mice exhibit different TOD responses. In contrast to mitochondrial number, mitochondrial ETC activities do not fluctuate across TOD, but decrease immediately and significantly in response to fasting. Concurrent with the loss of ETC activities, ETC proteins were decreased with fasting, simultaneous with significant increases of mitophagy, mitochondrial antioxidant protein SOD2, and the fission protein DRP1. Fasting-induced mitophagy was lost in CBK mice, indicating a direct role of BMAL1 in regulating mitophagy. This is the first of its kind report to demonstrate the interactions between sex, fasting, and TOD on cardiac mitochondrial structure, function and mitophagy. These studies provide a foundation for future investigations of mitochondrial functional perturbation in aging and heart diseases.
    DOI:  https://doi.org/10.1038/s41598-023-49018-z
  31. Cell Rep. 2023 Dec 06. pii: S2211-1247(23)01556-5. [Epub ahead of print]42(12): 113544
    A mitochondrial inside-out iron-calcium signal reveals drug targets for Parkinson's disease.
    Vinita Bharat, Aarooran S Durairaj, Roeland Vanhauwaert, Li Li, Colin M Muir, Sujyoti Chandra, Chulhwan S Kwak, Yann Le Guen, Pawan Nandakishore, Chung-Han Hsieh, Stefano E Rensi, Russ B Altman, Michael D Greicius, Liang Feng, Xinnan Wang.
      Dysregulated iron or Ca2+ homeostasis has been reported in Parkinson's disease (PD) models. Here, we discover a connection between these two metals at the mitochondria. Elevation of iron levels causes inward mitochondrial Ca2+ overflow, through an interaction of Fe2+ with mitochondrial calcium uniporter (MCU). In PD neurons, iron accumulation-triggered Ca2+ influx across the mitochondrial surface leads to spatially confined Ca2+ elevation at the outer mitochondrial membrane, which is subsequently sensed by Miro1, a Ca2+-binding protein. A Miro1 blood test distinguishes PD patients from controls and responds to drug treatment. Miro1-based drug screens in PD cells discover Food and Drug Administration-approved T-type Ca2+-channel blockers. Human genetic analysis reveals enrichment of rare variants in T-type Ca2+-channel subtypes associated with PD status. Our results identify a molecular mechanism in PD pathophysiology and drug targets and candidates coupled with a convenient stratification method.
    Keywords:  CP: Neuroscience
    DOI:  https://doi.org/10.1016/j.celrep.2023.113544
  32. Nucleic Acids Res. 2023 Dec 12. pii: gkad1169. [Epub ahead of print]
    Correction to 'ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression'.
      
    DOI:  https://doi.org/10.1093/nar/gkad1169
  33. Exp Physiol. 2023 Dec 14.
    Targeted genetic therapies for inherited disorders that affect both cardiac and skeletal muscle.
    Yiangos Psaras, Christopher N Toepfer.
      Skeletal myopathies and ataxias with secondary cardiac involvement are complex, progressive and debilitating conditions. As life expectancy increases across these conditions, cardiac involvement often becomes more prominent. This highlights the need for targeted therapies that address these evolving cardiac pathologies. Musculopathies by and large lack cures that directly target the genetic basis of the diseases; however, as our understanding of the genetic causes of these conditions has evolved, it has become tractable to develop targeted therapies using biologics, to design precision approaches to target the primary genetic causes of these varied diseases. Using the examples of Duchenne muscular dystrophy, Friedreich ataxia and Pompe disease, we discuss how the genetic causes of such diseases derail diverse homeostatic, energetic and signalling pathways, which span multiple cellular systems in varied tissues across the body. We outline existing therapeutics and treatments in the context of emerging novel genetic approaches. We discuss the hurdles that the field must overcome to deliver targeted therapies across the many tissue types affected in primary myopathies. NEW FINDINGS: What is the topic of this review? Overlapping disease pathomechanisms and therapeutic opportunities in neuromuscular, skeletal and cardiac muscle diseases in the context of novel genetic therapies. What advances does it highlight? This review outlines the diverse genetic changes that drive pathomechanism across a set of neuromuscular conditions and highlight the emerging targeted biological therapies that are being developed to treat these conditions, with additional discussion of the hurdles to actualising genetically targeted precision medicine.
    Keywords:  Duchenne muscular dystrophy; Friedreich's ataxia; Pompe disease; gene therapy; skeletal and cardiac muscle disease; therapeutics
    DOI:  https://doi.org/10.1113/EP090436
  34. Biochem Pharmacol. 2023 Dec 10. pii: S0006-2952(23)00531-2. [Epub ahead of print] 115938
    The critical roles of STING in mitochondrial homeostasis.
    Shishi Zou, Bo Wang, Ke Yi, Dandan Su, Yukai Chen, Ning Li, Qing Geng.
      The stimulator of interferon genes (STING) is a crucial signaling hub in the immune system's antiviral and antimicrobial defense by detecting exogenous and endogenous DNA. The multifaceted functions of STING have been uncovered gradually during past decades, including homeostasis maintenance and overfull immunity or inflammation induction. However, the subcellular regulation of STING and mitochondria is poorly understood. The main functions of STING are outlined in this review. Moreover, we discuss how mitochondria and STING interact through multiple mechanisms, including the release of mitochondrial DNA (mtDNA), modulation of mitochondria-associated membrane (MAM) and mitochondrial dynamics, alterations in mitochondrial metabolism, regulation of reactive oxygen species (ROS) production, and mitochondria-related cell death. Finally, we discuss how STING is crucial to disease development, providing a novel perspective on its role in cellular physiology and pathology.
    Keywords:  Cell death; Innate immunity; Mitochondrial dynamics; Mitochondrial metabolism; MtDNA; STING
    DOI:  https://doi.org/10.1016/j.bcp.2023.115938
  35. Sci Rep. 2023 Dec 12. 13(1): 22013
    Database screening as a strategy to identify endogenous candidate metabolites to probe and assess mitochondrial drug toxicity.
    Mery Vet George De la Rosa, Dipali Patel, Marc R McCann, Kathleen A Stringer, Gus R Rosania.
      Adverse drug reactions (ADRs) are considered an inherent risk of medication use, and some ADRs have been associated with off-target drug interactions with mitochondria. Metabolites that reflect mitochondrial function may help identify patients at risk of mitochondrial toxicity. We employed a database strategy to identify candidate mitochondrial metabolites that could be clinically useful to identify individuals at increased risk of mitochondrial-related ADRs. This led to L-carnitine being identified as the candidate mitochondrial metabolite. L-carnitine, its acetylated metabolite, acetylcarnitine and other acylcarnitines are mitochondrial biomarkers used to detect inborn errors of metabolism. We hypothesized that changes in L-carnitine disposition, induced by a "challenge test" of intravenous L-carnitine, could identify mitochondrial-related ADRs by provoking variation in L-carnitine and/or acetylcarnitine blood levels. To test this hypothesis, we induced mitochondrial drug toxicity with clofazimine (CFZ) in a mouse model. Following CFZ treatment, mice received an L-carnitine "challenge test". CFZ-induced changes in weight were consistent with previous work and reflect CFZ-induced catabolism. L-carnitine induced differences in whole blood acetylcarnitine concentrations in a manner that was dependent on CFZ treatment. This supports the usefulness of a database strategy for the discovery of candidate metabolite biomarkers of drug toxicity and substantiates the potential of the L-carnitine "challenge test" as a "probe" to identify drug-related toxicological manifestations.
    DOI:  https://doi.org/10.1038/s41598-023-49443-0
  36. Nat Commun. 2023 Dec 12. 14(1): 8248
    The assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination.
    Lindsay McGregor, Samira Acajjaoui, Ambroise Desfosses, Melissa Saïdi, Maria Bacia-Verloop, Jennifer J Schwarz, Pauline Juyoux, Jill von Velsen, Matthew W Bowler, Andrew A McCarthy, Eaazhisai Kandiah, Irina Gutsche, Montserrat Soler-Lopez.
      The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer's disease (AD) pathogenesis. However, how MCIA facilitates CI assembly, and how it is linked with AD pathogenesis, is poorly understood. Here we report the structural basis of the complex formation between the MCIA subunits ECSIT and ACAD9. ECSIT binding induces a major conformational change in the FAD-binding loop of ACAD9, releasing the FAD cofactor and converting ACAD9 from a fatty acid β-oxidation (FAO) enzyme to a CI assembly factor. We provide evidence that ECSIT phosphorylation downregulates its association with ACAD9 and is reduced in neuronal cells upon exposure to amyloid-β (Aβ) oligomers. These findings advance our understanding of the MCIA complex assembly and suggest a possible role for ECSIT in the reprogramming of bioenergetic pathways linked to Aβ toxicity, a hallmark of AD.
    DOI:  https://doi.org/10.1038/s41467-023-43865-0
  37. Psychoneuroendocrinology. 2023 Nov 24. pii: S0306-4530(23)00661-3. [Epub ahead of print]160 106683
    Mitochondrial morphology in the mouse adrenal cortex: Influence of chronic psychosocial stress.
    Tamara Vega-Vásquez, Dominik Langgartner, Jennifer Y Wang, Stefan O Reber, Martin Picard, Carla Basualto-Alarcón.
      Mitochondria within the adrenal cortex play a key role in synthesizing steroid hormones. The adrenal cortex is organized in three functionally specialized zones (glomerulosa, fasciculata, and reticularis) that produce different classes of steroid hormones in response to various stimuli, including psychosocial stress. Given that the functions and morphology of mitochondria are dynamically related and respond to stress, we applied transmission electron microscopy (TEM) to examine potential differences in mitochondrial morphology under basal and chronic psychosocial stress conditions. We used the chronic subordinate colony housing (CSC) paradigm, a murine model of chronic psychosocial stress. Our findings quantitatively define how mitochondrial morphology differs among each of the three adrenal cortex zones under basal conditions, and show that chronic psychosocial stress mainly affected mitochondria in the zona glomerulosa, shifting their morphology towards the more typical glucocorticoid-producing zona fasciculata mitochondrial phenotype. Analysis of adrenocortical lipid droplets that provide cholesterol for steroidogenesis showed that chronic psychosocial stress altered lipid droplet diameter, without affecting droplet number or inter-organellar mitochondria-lipid droplet interactions. Together, our findings support the hypothesis that each adrenal cortex layer is characterized by morphologically distinct mitochondria and that this adrenal zone-specific mitochondrial morphology is sensitive to environmental stimuli, including chronic psychosocial stressors. Further research is needed to define the role of these stress-induced changes in mitochondrial morphology, particularly in the zona glomerulosa, on stress resilience and related behaviors.
    Keywords:  Adrenal cortex; Chronic psychosocial stress; Electron microscopy; Lipid droplet; Mitochondria; Peridroplet mitochondria
    DOI:  https://doi.org/10.1016/j.psyneuen.2023.106683
  38. Antioxid Redox Signal. 2023 Dec 07.
    MITOCHONDRIAL MECHANISMS IN IMMUNITY AND INFLAMMATORY CONDITIONS: BEYOND ENERGY MANAGEMENT.
    Silvia Alvarez, Virginia Vanasco, Juan Santiago Adán Areán, Natalia D Magnani, Pablo Andres Evelson.
       SIGNIFICANCE: The growing importance of mitochondria in the immune response and inflammation is multifaceted. Unraveling the different mechanisms by which mitochondria have a relevant role in the inflammatory response beyond the energy management of the process, is necessary for improving our understanding of the host immune defense and the pathogenesis of various inflammatory diseases and syndromes.
    CRITICAL ISSUES: Mitochondria are relevant in the immune response at different levels, including releasing activation molecules, changing its structure and function to accompany the immune response, and serving as a structural base for activating intermediates as NLRP3 inflammasome. In this scientific journey of dissecting mitochondrial mechanisms, new questions and interesting aspects arise, such as the involvement of mitochondrial-derived vesicles in the immune response with the putative role of preventing uncontrolled situations.
    RECENT ADVANCES: Researchers are continuously rethinking the role of mitochondria in acute and chronic inflammation and related disorders. As such, mitochondria have important roles as centrally positioned signaling hubs in regulating inflammatory and immune responses. In this review, we present the current understanding of mitochondrial mechanisms involved, beyond the largely known mitochondrial dysfunction, in the onset and development of inflammatory situations.
    FUTURE DIRECTIONS: Mitochondria emerge as an interesting and multifaceted platform for studying and developing pharmaceutical and therapeutic approaches. There are many ongoing studies aimed to describe the effects of specific mitochondrial targeted molecules and treatments to ameliorate consequences of exacerbated inflammatory components of pathologies and syndromes, resulting in an open area of increasing research interest.
    DOI:  https://doi.org/10.1089/ars.2023.0367
  39. Nature. 2023 Dec;624(7991): 366-377
    Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain.
    Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa G Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, Antonio Pinto-Duarte, Jasper Lee, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zhanghao Wu, Ion Stoica, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Chongyuan Luo, Jesse R Dixon, Hongkui Zeng, Bing Ren, M Margarita Behrens, Joseph R Ecker.
      Cytosine DNA methylation is essential in brain development and is implicated in various neurological disorders. Understanding DNA methylation diversity across the entire brain in a spatial context is fundamental for a complete molecular atlas of brain cell types and their gene regulatory landscapes. Here we used single-nucleus methylome sequencing (snmC-seq3) and multi-omic sequencing (snm3C-seq)1 technologies to generate 301,626 methylomes and 176,003 chromatin conformation-methylome joint profiles from 117 dissected regions throughout the adult mouse brain. Using iterative clustering and integrating with companion whole-brain transcriptome and chromatin accessibility datasets, we constructed a methylation-based cell taxonomy with 4,673 cell groups and 274 cross-modality-annotated subclasses. We identified 2.6 million differentially methylated regions across the genome that represent potential gene regulation elements. Notably, we observed spatial cytosine methylation patterns on both genes and regulatory elements in cell types within and across brain regions. Brain-wide spatial transcriptomics data validated the association of spatial epigenetic diversity with transcription and improved the anatomical mapping of our epigenetic datasets. Furthermore, chromatin conformation diversities occurred in important neuronal genes and were highly associated with DNA methylation and transcription changes. Brain-wide cell-type comparisons enabled the construction of regulatory networks that incorporate transcription factors, regulatory elements and their potential downstream gene targets. Finally, intragenic DNA methylation and chromatin conformation patterns predicted alternative gene isoform expression observed in a whole-brain SMART-seq2 dataset. Our study establishes a brain-wide, single-cell DNA methylome and 3D multi-omic atlas and provides a valuable resource for comprehending the cellular-spatial and regulatory genome diversity of the mouse brain.
    DOI:  https://doi.org/10.1038/s41586-023-06805-y
  40. J Phys Chem B. 2023 Dec 12.
    Structure and Elasticity of Mitochondrial Membranes: A Molecular Dynamics Simulation Study.
    Thi Ly Mai, Philippe Derreumaux, Phuong H Nguyen.
      Mitochondria are known as the powerhouse of the cell because they produce energy in the form of adenosine triphosphate. They also have other crucial functions such as regulating apoptosis, calcium homeostasis, and reactive oxygen species production. To perform these diverse functions, mitochondria adopt specific structures and frequently undergo dynamic shape changes, indicating that their mechanical properties play an essential role in their functions. To gain a detailed understanding at the molecular level of the structure and mechanical properties of mitochondria, we carry out atomistic molecular dynamics simulations for three inner mitochondrial membranes and three outer mitochondrial membrane models. These models take into account variations in cardiolipin and cholesterol concentrations as well as the symmetry/asymmetry between the two leaflets. Our simulations allow us to calculate various structural quantities and the bending, twisting, and tilting elastic moduli of the membrane models. Our results indicate that the structures of the inner and outer mitochondrial membranes are quite similar and do not depend much on the variation in lipid compositions. However, the bending modulus of the membranes increases with increasing concentrations of cardiolipin or cholesterol but decreases with a membrane asymmetry. Notably, we found that the dipole potential of the membrane increases with an increasing cardiolipin concentration. Finally, possible roles of cardiolipin in regulating ion and proton currents and maintaining the cristate are discussed in some details.
    DOI:  https://doi.org/10.1021/acs.jpcb.3c05112
  41. medRxiv. 2023 Nov 28. pii: 2023.11.27.23299062. [Epub ahead of print]
    Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders.
    Rose Orenbuch, Aaron W Kollasch, Hansen D Spinner, Courtney A Shearer, Thomas A Hopf, Dinko Franceschi, Mafalda Dias, Jonathan Frazer, Debora S Marks.
      Identifying causal mutations accelerates genetic disease diagnosis, and therapeutic development. Missense variants present a bottleneck in genetic diagnoses as their effects are less straightforward than truncations or nonsense mutations. While computational prediction methods are increasingly successful at prediction for variants in known disease genes, they do not generalize well to other genes as the scores are not calibrated across the proteome. To address this, we developed a deep generative model, popEVE, that combines evolutionary information with population sequence data and achieves state-of-the-art performance at ranking variants by severity to distinguish patients with severe developmental disorders from potentially healthy individuals. popEVE identifies 442 genes in a cohort of developmental disorder cases, including evidence of 119 novel genetic disorders without the need for gene-level enrichment and without overestimating the prevalence of pathogenic variants in the population. By placing variants on a unified scale, our model offers a comprehensive perspective on the distribution of fitness effects across the entire proteome and the broader human population. popEVE provides compelling evidence for genetic diagnoses even in exceptionally rare single-patient disorders where conventional techniques relying on repeated observations may not be applicable. Interactive web viewer and downloads available at pop.evemodel.org .
    DOI:  https://doi.org/10.1101/2023.11.27.23299062
  42. Nat Rev Cancer. 2023 Dec 11.
    Spatial metabolic patterns.
    Anna Dart.
      
    DOI:  https://doi.org/10.1038/s41568-023-00654-7
  43. BMC Mol Cell Biol. 2023 Dec 11. 24(1): 35
    Association between plasma L-carnitine levels and mitochondrial DNA copy number.
    Mingyue Li, Keming Yang, Immaculata De Vivo, A Heather Eliassen, Abrar A Qureshi, Hongmei Nan, Jiali Han.
      Mitochondria are key cytoplasmic organelles in eukaryotic cells that generate adenosine triphosphate (ATP) through the electron transport chain and oxidative phosphorylation. Mitochondrial DNA (mtDNA) copy number (mtDNAcn) is considered a biomarker for both mitochondrial quantity and function as well as cellular oxidative stress level. Previous epidemiologic findings revealed that weight gain, higher body mass index (BMI), smoking, and high insulinemic potential of lifestyle were associated with lower leukocyte mtDNAcn. Carnitines are a group of compounds that play a critical role in energy production. We quantified the associations of plasma L-carnitine levels with leukocyte mtDNAcn. We then examined the association between mtDNAcn and L-carnitine (HMDB0000062) in 538 U.S. men without cancers, diabetes, or cardiovascular disease at blood collection from the Health Professionals Follow-Up Study (HPFS). We found a significant inverse association between L-carnitine and mtDNAcn (ρ = -0.1, P = 0.02). This implies that the carnitine metabolic pathway may be associated with mitochondrial function and oxidative stress.
    Keywords:  Body mass index; Cross-sectional study; L-carnitine; Metabolites; Mitochondria; Mitochondrial DNA copy number
    DOI:  https://doi.org/10.1186/s12860-023-00496-z
  44. Int J Mol Sci. 2023 Nov 27. pii: 16787. [Epub ahead of print]24(23):
    Mitochondrial Dysfunction in Skeletal Muscle of Rotenone-Induced Rat Model of Parkinson's Disease: SC-Nanophytosomes as Therapeutic Approach.
    Daniela Mendes, Francisco Peixoto, Maria Manuel Oliveira, Paula Branquinho Andrade, Romeu António Videira.
      The development of new therapeutic options for Parkinson's disease (PD) requires formulations able to mitigate both brain degeneration and motor dysfunctions. SC-Nanophytosomes, an oral mitochondria-targeted formulation developed with Codium tomentosum membrane polar lipids and elderberry anthocyanin-enriched extract, promote significant brain benefits on a rotenone-induced rat model of PD. In the present work, the effects of SC-Nanophytosome treatment on the skeletal muscle tissues are disclosed. It is unveiled that the rotenone-induced PD rat model exhibits motor disabilities and skeletal muscle tissues with deficient activity of mitochondrial complexes I and II along with small changes in antioxidant enzyme activity and skeletal muscle lipidome. SC-Nanophytosome treatment mitigates the impairment of complexes I and II activity, improving the mitochondrial respiratory chain performance at levels that surpass the control. Therefore, SC-Nanophytosome competence to overcome the PD-related motor disabilities should be also associated with its positive outcomes on skeletal muscle mitochondria. Providing a cellular environment with more reduced redox potential, SC-Nanophytosome treatment improves the skeletal muscle tissue's ability to deal with oxidative stress stimuli. The PD-related small changes on skeletal muscle lipidome were also counteracted by SC-Nanophytosome treatment. Thus, the present results reinforces the concept of SC-Nanophytosomes as a mitochondria-targeted therapy to address the neurodegeneration challenge.
    Keywords:  Parkinson’s disease; algae polar lipids; elderberry anthocyanins; mitochondrial dysfunction; nanomedicine; skeletal muscle
    DOI:  https://doi.org/10.3390/ijms242316787
  45. Am J Physiol Endocrinol Metab. 2023 Dec 13.
    Additive Impact of Soy Protein Dietary Intake and Exercise on Visceral Fat Mass Reduction and Mitochondrial Complex I Activation in Skeletal Muscle.
    Kohei Kido, Shinya Watanabe, Masaki Kusano, Ai Ito, Kazuya Sakai, Miki Kosugi, Yayoi Gotoh, Toshio Suzuki, Kentaro Kawanaka, Yasuki Higaki.
      Soy protein has shown remarkable effectiveness in reducing fat mass compared with other protein sources, and exercise has the potential to further enhance this fat loss effect. Previous studies have demonstrated that soy protein intake leads to decreased fatty acid synthesis, which contributes to its fat-loss properties. However, the exact mechanism by which these lipids are consumed remains unclear. To investigate this, we conducted a comprehensive study using C57/BL6 male mice, comparing the effects of soy and casein proteins with and without exercise (Casein-Sed, Casein-Ex, Soy-Sed, and Soy-Ex groups) under high- and low-protein conditions (14% or 40% protein). Our findings revealed that combining soy protein intake with exercise significantly reduced epididymal white adipose tissue (eWAT) weight, particularly in the high-protein diet group. Further analysis revealed that exercise increased the expression of lipid oxidation-regulatory proteins, including mitochondrial oxidative phosphorylation protein (OXPHOS) complexes, in the plantaris muscle regardless of the protein source. Although soy protein intake did not directly affect muscle mitochondrial protein expression, the activity of OXPHOS complex I was additively enhanced by exercise and soy protein under the 40% protein condition. Notably, complex I activity inversely correlated with eWAT weight in the soy protein diet group. These results highlight the potential link between improved complex I activity induced by soy protein and fat mass reduction, which emphasizes the promising benefits of combining soy protein with exercise in promoting fat loss.
    Keywords:  Exercise; OXPHOS complex enzyme activity; Skeletal muscle; Soy protein; Visceral fat mass
    DOI:  https://doi.org/10.1152/ajpendo.00196.2023
  46. Anal Chem. 2023 Dec 12.
    Imaging HOCl Generation during the Mitochondria Peripheral Fission with a Tailor-Made Fluorescent Probe.
    Haolin Zhang, Ya Liu, Xiaofan Zhang, Huimin Ma, Wen Shi, Xiaohua Li.
      Mitochondrial fission is a highly regulated process that can affect metabolism, proliferation, and apoptosis. Division at the periphery enables damaged material to be shed into smaller mitochondria destined for mitophagy, which is found preceded by increased Ca2+ and reactive oxygen species, as well as reduced membrane potential and pH. However, the variation of hypochlorous acid (HOCl) during the peripheral fission has not been well studied, and the existing fluorescent probes are unsuitable for detecting mitochondrial HOCl because of the 0.8-fold decreased pH during this process. Herein, we design a novel CCS (changeable π-conjugation system)-based probe (ON-mito) with a dibenzo[1,4]oxazepine core, which can selectively react with HOCl at pH 6.4, generating an oxazine-containing product that emits at 660 nm. The capability of ON-mito for imaging the HOCl generation in HeLa cells during mitophagy is demonstrated under weakly acidic condition. Further, with ON-mito, we find for the first time a burst increase of the mitochondrial HOCl in COS-7 cells during peripheral fission, which may serve as an important indicator of this process. Probe ON-mito may be useful for studying mitochondrial damage under diverse conditions.
    DOI:  https://doi.org/10.1021/acs.analchem.3c04215
  47. Exp Neurol. 2023 Dec 05. pii: S0014-4886(23)00329-1. [Epub ahead of print]372 114644
    The interplay between neuroinflammatory pathways and Parkinson's disease.
    Pinar Eser, Ersoy Kocabicak, Ahmet Bekar, Yasin Temel.
      Parkinson's disease, a progressive neurodegenerative disorder predominantly affecting elderly, is marked by the gradual degeneration of the nigrostriatal dopaminergic pathway, culminating in neuronal loss within the substantia nigra pars compacta (SNpc) and dopamine depletion. At the molecular level, neuronal loss in the SNpc has been attributed to factors including neuroinflammation, impaired protein homeostasis, as well as mitochondrial dysfunction and the resulting oxidative stress. This review focuses on the interplay between neuroinflammatory pathways and Parkinson's disease, drawing insights from current literature.
    Keywords:  Mitochondria dysfunction; Neuroinflammation; Parkinson's disease
    DOI:  https://doi.org/10.1016/j.expneurol.2023.114644
  48. Int J Mol Sci. 2023 Dec 02. pii: 17068. [Epub ahead of print]24(23):
    Mitochondrially Targeted Gene Therapy Rescues Visual Loss in a Mouse Model of Leber's Hereditary Optic Neuropathy.
    Tsung-Han Chou, Zixuan Hao, Diego Alba, Angelina Lazo, Gabriele Gallo Afflitto, Jeremy D Eastwood, Vittorio Porciatti, John Guy, Hong Yu.
      Leber's hereditary optic neuropathy (LHON) is a common mitochondrial genetic disease, causing irreversible blindness in young individuals. Current treatments are inadequate, and there is no definitive cure. This study evaluates the effectiveness of delivering wildtype human NADH ubiquinone oxidoreductase subunit 4 (hND4) gene using mito-targeted AAV(MTSAAV) to rescue LHOH mice. We observed a declining pattern in electroretinograms amplitudes as mice aged across all groups (p < 0.001), with significant differences among groups (p = 0.023; Control vs. LHON, p = 0.008; Control vs. Rescue, p = 0.228). Inner retinal thickness and intraocular pressure did not change significantly with age or groups. Compared to LHON mice, those rescued with wildtype hND4 exhibited improved retinal visual acuity (0.29 ± 0.1 cy/deg vs. 0.15 ± 0.1 cy/deg) and increased functional hyperemia response (effect of flicker, p < 0.001, effect of Group, p = 0.004; Interaction Flicker × Group, p < 0.001). Postmortem analysis shows a marked reduction in retinal ganglion cell density in the LHON group compared to the other groups (Effect of Group, p < 0.001, Control vs. LHON, p < 0.001, Control vs. Rescue, p = 0.106). These results suggest that MTSAAV-delivered wildtype hND4 gene rescues, at least in part, visual impairment in an LHON mouse model and has the therapeutic potential to treat this disease.
    Keywords:  LHON; MTSAAV; gene therapy; human ND4
    DOI:  https://doi.org/10.3390/ijms242317068
  49. Proc Natl Acad Sci U S A. 2023 Dec 19. 120(51): e2316823120
    Intraneuronal β-amyloid impaired mitochondrial proteostasis through the impact on LONP1.
    Wenzhang Wang, Xiaopin Ma, Sabina Bhatta, Changjuan Shao, Fanpeng Zhao, Hisashi Fujioka, Sandy Torres, Fengqin Wu, Xiongwei Zhu.
      Mitochondrial dysfunction plays a critical role in the pathogenesis of Alzheimer's disease (AD). Mitochondrial proteostasis regulated by chaperones and proteases in each compartment of mitochondria is critical for mitochondrial function, and it is suspected that mitochondrial proteostasis deficits may be involved in mitochondrial dysfunction in AD. In this study, we identified LONP1, an ATP-dependent protease in the matrix, as a top Aβ42 interacting mitochondrial protein through an unbiased screening and found significantly decreased LONP1 expression and extensive mitochondrial proteostasis deficits in AD experimental models both in vitro and in vivo, as well as in the brain of AD patients. Impaired METTL3-m6A signaling contributed at least in part to Aβ42-induced LONP1 reduction. Moreover, Aβ42 interaction with LONP1 impaired the assembly and protease activity of LONP1 both in vitro and in vivo. Importantly, LONP1 knockdown caused mitochondrial proteostasis deficits and dysfunction in neurons, while restored expression of LONP1 in neurons expressing intracellular Aβ and in the brain of CRND8 APP transgenic mice rescued Aβ-induced mitochondrial deficits and cognitive deficits. These results demonstrated a critical role of LONP1 in disturbed mitochondrial proteostasis and mitochondrial dysfunction in AD and revealed a mechanism underlying intracellular Aβ42-induced mitochondrial toxicity through its impact on LONP1 and mitochondrial proteostasis.
    Keywords:  Alzheimer’s disease; Aβ42; LONP1; mitochondrial dysfunction; protein aggregate
    DOI:  https://doi.org/10.1073/pnas.2316823120
  50. Am J Hum Genet. 2023 Dec 02. pii: S0002-9297(23)00400-7. [Epub ahead of print]
    Will variants of uncertain significance still exist in 2030?
    Douglas M Fowler, Heidi L Rehm.
      In 2020, the National Human Genome Research Institute (NHGRI) made ten "bold predictions," including that "the clinical relevance of all encountered genomic variants will be readily predictable, rendering the diagnostic designation 'variant of uncertain significance (VUS)' obsolete." We discuss the prospects for this prediction, arguing that many, if not most, VUS in coding regions will be resolved by 2030. We outline a confluence of recent changes making this possible, especially advances in the standards for variant classification that better leverage diverse types of evidence, improvements in computational variant effect predictor performance, scalable multiplexed assays of variant effect capable of saturating the genome, and data-sharing efforts that will maximize the information gained from each new individual sequenced and variant interpreted. We suggest that clinicians and researchers can realize a future where VUSs have largely been eliminated, in line with the NHGRI's bold prediction. The length of time taken to reach this future, and thus whether we are able to achieve the goal of largely eliminating VUSs by 2030, is largely a consequence of the choices made now and in the next few years. We believe that investing in eliminating VUSs is worthwhile, since their predominance remains one of the biggest challenges to precision genomic medicine.
    DOI:  https://doi.org/10.1016/j.ajhg.2023.11.005
  51. Nat Struct Mol Biol. 2023 Dec;30(12): 1831-1833
    Protein import into mitochondria - a new path through the membranes.
    Michal Wasilewski, Piotr Draczkowski, Agnieszka Chacinska.
      
    DOI:  https://doi.org/10.1038/s41594-023-01170-w
  52. Life Sci. 2023 Dec 01. pii: S0024-3205(23)00858-5. [Epub ahead of print]334 122223
    Copper homeostasis and cuproptosis in mitochondria.
    Ziying Tian, Su Jiang, Jieyu Zhou, Wenling Zhang.
      Mitochondria serve as sites for energy production and are essential for regulating various forms of cell death induced by metal metabolism, targeted anticancer drugs, radiotherapy and immunotherapy. Cuproptosis is an autonomous form of cell death that depends on copper (Cu) and mitochondrial metabolism. Although the recent discovery of cuproptosis highlights the significance of Cu and mitochondria, there is still a lack of biological evidence and experimental verification for the underlying mechanism. We provide an overview of how Cu and cuproptosis affect mitochondrial morphology and function. Through comparison with ferroptosis, similarities and differences in mitochondrial metabolism between cuproptosis and ferroptosis have been identified. These findings provide implications for further exploration of cuproptotic mechanisms. Furthermore, we explore the correlation between cuproptosis and immunotherapy or radiosensitivity. Ultimately, we emphasize the therapeutic potential of targeting cuproptosis as a novel approach for disease treatment.
    Keywords:  Copper homeostasis; Cuproptosis; Immunotherapy; Mitochondria; Radiosensitivity
    DOI:  https://doi.org/10.1016/j.lfs.2023.122223
  53. bioRxiv. 2023 Dec 01. pii: 2023.11.30.569464. [Epub ahead of print]
    Modeling aging and retinal degeneration with mitochondrial DNA mutation burden.
    John Sturgis, Rupesh Singh, Quinn Caron, Ivy S Samuels, Thomas Micheal Shiju, Aditi Mukkara, Paul Freedman, Vera L Bonilha.
      Somatic mitochondrial DNA (mtDNA) mutation accumulation has been observed in individuals with retinal degenerative disorders. To study the effects of aging and mtDNA mutation accumulation in the retina, a Polymerase gamma (POLG) deficiency model, the POLG D257A mutator mice (PolgD257A), was used. POLG is an enzyme responsible for regulating mtDNA replication and repair. Retinas of young and older mice with this mutation were analyzed in vivo and ex vivo to provide new insights into the contribution of age-related mitochondrial dysfunction due to mtDNA damage. Optical coherence tomography (OCT) image analysis revealed a decrease in retinal and photoreceptor thickness starting at 6 months of age in mice with the POLG D257A mutation compared to wild-type (WT) mice. Electroretinography (ERG) testing showed a significant decrease in all recorded responses at 6 months of age. Sections labeled with markers of different types of retinal cells, including cones, rods, and bipolar cells, exhibited decreased labeling starting at 6 months. However, electron microscopy analysis revealed differences in retinal pigment epithelium (RPE) mitochondria morphology beginning at 3 months. Interestingly, there was no increase in oxidative stress observed in the retina or RPE of POLGD257A mice. Additionally, POLGD257A RPE exhibited an accelerated rate of autofluorescence cytoplasmic granule formation and accumulation. Mitochondrial markers displayed decreased abundance in protein lysates obtained from retina and RPE samples. These findings suggest that the accumulation of mitochondrial DNA mutations leads to impaired mitochondrial function and accelerated aging, resulting in retinal degeneration.
    DOI:  https://doi.org/10.1101/2023.11.30.569464
  54. Mol Genet Genomic Med. 2023 Dec 13. e2311
    Biallelic pathogenic variants of PARS2 cause developmental and epileptic encephalopathy with spike-and-wave activation in sleep.
    Laura Licchetta, Lucia Di Giorgi, Margherita Santucci, Lisa Taruffi, Carlotta Stipa, Raffaella Minardi, Valerio Carelli, Francesca Bisulli.
       BACKGROUND: Biallelic pathogenic variants in the mitochondrial prolyl-tRNA synthetase 2 gene (PARS2, OMIM * 612036) have been associated with Developmental and Epileptic Encephalopathy-75 (DEE-75, MIM #618437). This condition is typically characterized by early-onset refractory infantile spasms with hypsarrhythmia, intellectual disability, microcephaly, cerebral atrophy with hypomyelination, lactic acidemia, and cardiomyopathy. Most affected individuals do not survive beyond the age of 10 years.
    METHODS: We describe a patient with early-onset DEE, consistently showing an EEG pattern of Spike-and-Wave Activation in Sleep (SWAS) since childhood. The patient underwent extensive clinical, metabolic and genetic investigations, including whole exome sequencing (WES).
    RESULTS: WES analysis identified compound heterozygous variants in PARS2 that have been already reported as pathogenic. A literature review of PARS2-associated DEE, focusing mainly on the electroclinical phenotype, did not reveal the association of SWAS with pathogenic variants in PARS2. Notably, unlike previously reported cases with the same genotype, this patient had longer survival without cardiac involvement or lactic acidosis, suggesting potential genetic modifiers contributing to disease variability.
    CONCLUSION: These findings widen the genetic heterogeneity of DEE-SWAS, including PARS2 as a causative gene in this syndromic entity, and highlight the importance of prolonged sleep EEG recording for the recognition of SWAS as a possible electroclinical evolution of PARS2-related DEE.
    Keywords:   PARS2 ; continuous spikes and waves during slow sleep (CSWS); developmental and epileptic encephalopathy (DEE); spike-and-wave activation in sleep (SWAS)
    DOI:  https://doi.org/10.1002/mgg3.2311
  55. bioRxiv. 2023 Dec 01. pii: 2023.11.29.569103. [Epub ahead of print]
    AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
    Jung Kim, Ammar S Naqvi, Ryan J Corbett, Rebecca S Kaufman, Zalman Vaksman, Miguel A Brown, Daniel P Miller, Saksham Phul, Zhuangzhuang Geng, Phillip B Storm, Adam C Resnick, Douglas R Stewart, Jo Lynne Rokita, Sharon J Diskin.
       Summary: With the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics - Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5/BP6). This tool facilitates large-scale, clinically-focused classification of germline sequence variants in a research setting.
    Availability and Implementation: AutoGVP is an open-source dockerized workflow implemented in R and freely available on GitHub at https://github.com/diskin-lab-chop/AutoGVP .
    DOI:  https://doi.org/10.1101/2023.11.29.569103
  56. Nature. 2023 Dec;624(7991): 237-238
    Are your organs ageing well? The blood holds clues.
    Max Kozlov.
      
    Keywords:  Ageing; Diseases; Medical research; Proteomics
    DOI:  https://doi.org/10.1038/d41586-023-03821-w
  57. Nature. 2023 Dec;624(7991): 253-255
    Cellular atlases of the entire mouse brain.
    Maria Antonietta Tosches, Heather J Lee.
      
    Keywords:  Brain; Epigenetics; Neuroscience; Transcriptomics
    DOI:  https://doi.org/10.1038/d41586-023-03781-1
  58. Sci Adv. 2023 Dec 15. 9(50): eadj1205
    Parkinson's VPS35[D620N] mutation induces LRRK2-mediated lysosomal association of RILPL1 and TMEM55B.
    Prosenjit Pal, Matthew Taylor, Pui Yiu Lam, Francesca Tonelli, Chloe A Hecht, Pawel Lis, Raja S Nirujogi, Toan K Phung, Wondwossen M Yeshaw, Ebsy Jaimon, Rotimi Fasimoye, Emily A Dickie, Melanie Wightman, Thomas Macartney, Suzanne R Pfeffer, Dario R Alessi.
      We demonstrate that the Parkinson's VPS35[D620N] mutation alters the expression of ~220 lysosomal proteins and stimulates recruitment and phosphorylation of Rab proteins at the lysosome. This recruits the phospho-Rab effector protein RILPL1 to the lysosome where it binds to the lysosomal integral membrane protein TMEM55B. We identify highly conserved regions of RILPL1 and TMEM55B that interact and design mutations that block binding. In mouse fibroblasts, brain, and lung, we demonstrate that the VPS35[D620N] mutation reduces RILPL1 levels, in a manner reversed by LRRK2 inhibition and proteasome inhibitors. Knockout of RILPL1 enhances phosphorylation of Rab substrates, and knockout of TMEM55B increases RILPL1 levels. The lysosomotropic agent LLOMe also induced LRRK2 kinase-mediated association of RILPL1 to the lysosome, but to a lower extent than the D620N mutation. Our study uncovers a pathway through which dysfunctional lysosomes resulting from the VPS35[D620N] mutation recruit and activate LRRK2 on the lysosomal surface, driving assembly of the RILPL1-TMEM55B complex.
    DOI:  https://doi.org/10.1126/sciadv.adj1205
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