bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–07–13
sixty-six papers selected by
Catalina Vasilescu, Helmholz Munich



  1. J Cell Sci. 2025 Jul 01. pii: jcs263701. [Epub ahead of print]138(13):
      Most mitochondrial proteins are imported through the actions of the presequence translocase of the inner membrane, the TIM23 complex, which requires energy in the form of the electrochemical potential of the inner membrane and ATP. Conversions of energy in mitochondria are disturbed in mitochondrial disorders that affect oxidative phosphorylation. Despite the widely accepted dependence of protein import into mitochondria on mitochondrial bioenergetics, effects of mitochondrial disorders on biogenesis of the mitochondrial proteome are poorly characterized. Here, we describe molecular tools that can be used to explore mitochondrial protein import in intact cells, the mitoRUSH assay, and a novel method based on labeling of nascent proteins with an amino acid analog and click chemistry. Using these orthogonal approaches, we discovered that defects in the electron transport chain and manipulating the expression of TIMM23, as well as the TIMM17A or TIMM17B paralogs, in human cells are associated with a decrease in protein import into mitochondria. We postulate that in the absence of a functional electron transfer chain, the mechanisms that support electrochemical potential of the inner membrane and ATP production are insufficient to sustain the import of proteins to mitochondria.
    Keywords:  Bioenergetics; Mitochondria; Mitochondrial diseases; Protein import; TIM23; Translocase; mitoRUSH
    DOI:  https://doi.org/10.1242/jcs.263701
  2. Nucleic Acids Res. 2025 Jul 08. pii: gkaf665. [Epub ahead of print]53(13):
      The first post-transcriptional step in mammalian mitochondrial gene expression, required for the synthesis of the 13 polypeptides encoded in mitochondrial DNA (mtDNA), is endonucleolytic cleavage of the primary polycistronic transcripts. Excision of the mtDNA-encoded transfer RNAs (tRNAs) releases most mature RNAs; however, processing of three noncanonical messenger RNAs (mRNAs) not flanked by tRNAs (CO1, CO3, and CYB) requires FASTKD5. To investigate the molecular mechanism involved, we created knockout human cell lines to use as assay systems. The absence of FASTKD5 produced a severe OXPHOS assembly defect due to the inability to translate two unprocessed noncanonical mRNAs and predicted altered folding patterns specifically at the 5'-end of the CO1 coding sequence. Structural features 13-15 nt upstream of the CO1 and CYB cleavage sites suggest FASTKD5 recognition mechanisms. Remarkably, a map of essential FASTKD5 amino acid residues revealed RNA substrate specificity; however, a key, putative active site residue was required for processing all three noncanonical pre-RNAs. Mutating this site did not significantly alter the binding of any client RNA substrate. A reconstituted in vitro system showed that wild-type, but not mutant, FASTKD5, was able to cleave client substrates correctly. These results establish FASTKD5 as the missing piece of biochemical machinery required to completely process the primary mitochondrial transcript.
    DOI:  https://doi.org/10.1093/nar/gkaf665
  3. J Biol Chem. 2025 Jul 08. pii: S0021-9258(25)02314-2. [Epub ahead of print] 110464
      Leber's hereditary optic neuropathy (LHON) is a paradigm for mitochondrial retinopathy due to mitochondrial DNA (mtDNA) mutations. However, the mechanism underlying LHON-linked mtDNA mutations, especially their impact on mitochondrial and cellular integrity, is not well understood. Recently, the ND1 3733G>C (p.E143Q) mutation was identified in three Chinese pedigrees with suggestively maternal inheritance of LHON. In this study, we investigated the pathogenic mechanism of m.3733G>C mutation using cybrids generated by fusing mtDNA-less ρ0 cells with enucleated cells from a Chinese patient carrying the m.3733G>C mutation and control subject. Molecular dynamics simulations showed that p.E143Q mutation destabilized these interactions between residues E143 and S110/Y114, or between S141 and W290 in the ND1. Its impact of ND1 structure and function was further evidenced by reduced levels of ND1 in mutant cells. The m.3733G>C mutation caused defective assembly and activity of complex I, respiratory deficiency, diminished mitochondrial ATP production, and increased production of mitochondrial ROS in the mutant cybrids carrying the m.3733G>C mutation. These mitochondrial dysfunctions regulated mitochondrial quality control via mitochondrial dynamics and mitophagy. The m.3733G>C mutation-induced dysfunction yielded elevating mitochondrial localization of DRP1, decreasing network connectivity and increasing fission with abnormal morphologies. Furthermore, the m.3733G>C mutation downregulated ubiquitin-dependent mitophagy pathway, evidenced by decreasing the levels of Parkin and Pink, but not ubiquitin-independent mitophagy pathway. The m.3733G>C mutation-induced deficiencies reshaped the cellular homeostasis via impairing autophagy process and promoting intrinsic apoptosis. Our findings provide new insights into pathophysiology of LHON arising from the m.3733G>C mutation-induced mitochondrial dysfunctions and reprograming organellular and cellular homeostasis.
    DOI:  https://doi.org/10.1016/j.jbc.2025.110464
  4. Nucleic Acids Res. 2025 Jul 08. pii: gkaf634. [Epub ahead of print]53(13):
      Mitochondrial gene expression needs to be balanced with cytosolic translation to produce oxidative phosphorylation complexes. In yeast, translational feedback loops involving lowly expressed proteins called translational activators help to achieve this balance. Synthesis of cytochrome b (Cytb or COB), a core subunit of complex III in the respiratory chain, is controlled by three translational activators and the assembly factor Cbp3-Cbp6. However, the molecular interface between the COB translational feedback loop and complex III assembly is yet unknown. Here, using protein-proximity mapping combined with selective mitoribosome profiling, we reveal the components and dynamics of the molecular switch controlling COB translation. Specifically, we demonstrate that Mrx4, a previously uncharacterized ligand of the mitoribosomal polypeptide tunnel exit, interacts with either the assembly factor Cbp3-Cbp6 or with the translational activator Cbs2. These reciprocal interactions determine whether the translational activator complex with bound COB messenger RNA (mRNA) can interact with the mRNA channel exit on the small ribosomal subunit for translation initiation. Organization of the feedback loop at the tunnel exit therefore orchestrates mitochondrial translation with respiratory chain biogenesis.
    DOI:  https://doi.org/10.1093/nar/gkaf634
  5. PLoS Genet. 2025 Jul 07. 21(7): e1011773
      Mitochondria perform essential metabolic functions and respond rapidly to changes in metabolic and stress conditions. As the majority of mitochondrial proteins are nuclear-encoded, intricate post-transcriptional regulation is crucial to enable mitochondria to adapt to changing cellular demands. The eukaryotic Clustered mitochondria protein family has emerged as an important regulator of mitochondrial function during metabolic shifts. Here, we show that the Drosophila melanogaster and Saccharomyces cerevisiae Clu/Clu1 proteins form dynamic, membraneless, mRNA-containing granules adjacent to mitochondria in response to metabolic changes. Yeast Clu1 regulates the translation of a subset of nuclear-encoded mitochondrial proteins by interacting with their mRNAs while these are engaged in translation. We further show that Clu1 regulates translation by interacting with polysomes, independently of whether it is in a diffuse or granular state. Our results demonstrate remarkable functional conservation with other members of the Clustered mitochondria protein family and suggest that Clu/Clu1 granules isolate and concentrate ribosomes engaged in translating their mRNA targets, thus, integrating metabolic signals with the regulation of mitochondrial protein synthesis.
    DOI:  https://doi.org/10.1371/journal.pgen.1011773
  6. Am J Med Genet A. 2025 Jul 09. e64177
      POLG2 encodes an accessory subunit in DNA polymerase gamma that is required for mitochondrial DNA synthesis. Monoallelic pathogenic variants in POLG2 are associated primarily with progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant type 4 (PEOA4, MIM #610131). We report a rare case of severe infantile hepatocerebral syndrome associated with biallelic variants in POLG2. The proband, a 5-week-old female infant, presented with seizures and acute liver failure. Extensive metabolic workup, including untargeted metabolomics analysis and elevated plasma growth differentiation factor 15, was suggestive of mitochondrial dysfunction. Rapid trio genome sequencing identified compound heterozygous variants, a likely pathogenic variant and a variant of uncertain significance in POLG2. This case expands the clinical phenotype associated with POLG2-related mitochondrial disease to include a severe hepatocerebral syndrome manifesting in early childhood. This case underscores the utility of integrated genomic and metabolomic analyses in diagnosing rare and complex mitochondrial disorders. These findings also emphasize the importance of considering POLG2-related mitochondrial disease in the differential diagnosis of infants presenting with liver failure and neurological symptoms and enhance our understanding of the phenotypic spectrum associated with this disorder.
    Keywords:   POLG2 ; liver failure; mitochondrial DNA replication; mitochondrial disorder; untargeted metabolomics analysis
    DOI:  https://doi.org/10.1002/ajmg.a.64177
  7. Mol Genet Metab. 2025 Jun 28. pii: S1096-7192(25)00175-1. [Epub ahead of print]145(4): 109184
      Cardiolipin is a mitochondria-specific phospholipid essential for maintaining mitochondrial membrane architecture, supporting respiratory chain function, and regulating apoptotic signaling. Its biosynthesis and remodeling are mediated by a coordinated set of enzymes, and disruptions in this pathway are increasingly recognized as causes of inherited mitochondrial diseases. This review provides a comprehensive overview of the genetic disorders associated with defects in cardiolipin metabolism, highlighting genetic and molecular characteristics, clinical manifestations, and available models with which to study these diseases. We examine the roles of key genes involved in cardiolipin biosynthesis (PGS1, CRLS1) and remodeling (TAZ, AGK, among others), and describe how pathogenic variants disrupt mitochondrial function. The prototypical disorder, Barth syndrome, is discussed in depth alongside recently identified conditions linked to defects in related enzymes.
    Keywords:  Barth syndrome; Cardiolipin; Lipid biosynthesis; Mitochondrial disease
    DOI:  https://doi.org/10.1016/j.ymgme.2025.109184
  8. Science. 2025 Jul 10. 389(6756): 130-131
      Peroxisome-mitochondria contact sites manage mitochondrial oxidative stress.
    DOI:  https://doi.org/10.1126/science.adz0109
  9. Nat Commun. 2025 Jul 10. 16(1): 6391
      Mitochondria contain their own DNA (mtDNA) and a dedicated gene expression machinery. As the mitochondrial dimensions are close to the diffraction limit of classical light microscopy, the spatial distribution of mitochondrial proteins and in particular of mitochondrial mRNAs remains underexplored. Here, we establish single-molecule fluorescence in situ hybridization (smFISH) combined with STED and MINFLUX super-resolution microscopy (nanoscopy) to visualize individual mitochondrial mRNA molecules and associated proteins. STED nanoscopy reveals the spatial relationships between distinct mRNA species and proteins such as the RNA granule marker GRSF1, demonstrating adaptive changes in mRNA distribution and quantity in challenged mammalian cells and patient-derived cell lines. Notably, STED-smFISH shows the release of mRNAs during apoptosis, while MINFLUX reveals the folding of the mRNAs into variable shapes, as well as their spatial proximity to mitochondrial ribosomes. These protocols are transferable to various cell types and open new avenues for understanding mitochondrial gene regulation in health and disease.
    DOI:  https://doi.org/10.1038/s41467-025-61577-5
  10. Sci Rep. 2025 Jul 08. 15(1): 24369
      A mutation (m.8993T > G) in MT-ATP6 in mitochondrial DNA (mtDNA) causes the neuropathy, ataxia, retinitis pigmentosa (NARP) syndrome by impairing mitochondrial energy production. Extremely low-frequency electromagnetic field (ELF-EMF) suppresses mitochondrial oxidative phosphorylation (OXPHOS) Complex II and induces mitohormetic activation of mitochondrial OXPHOS activities. We examined the effects of ELF-EMF on normal cybrids carrying 100% wild-type mtDNA (2SA cybrids) and NARP cybrids carrying 40% wild-type and 60% mutant mtDNA (NARP3-2 cybrids). We found that ELF-EMF had no effect on the copy number of mtDNA either in 2SA or NARP3-2 cybrids, or the ratio of wild-type-to-mutant mtDNA in NARP3-2 cybrids. Instead, ELF-EMF increased the transcription of mtDNA and the transcription ratio of wild-type-to-mutant mtDNA in NARP3-2 cybrids. In addition, ELF-EMF increased the expression of mitochondrial OXPHOS proteins and the mitochondrial OXPHOS Complex V activity in NARP3-2 cybrids. ELF-EMF upregulated fission-promoting phosphorylation of DRP1, as well as the expression of fusion-promoting MFN1 and MFN2, in NARP3-2 cybrids. ELF-EMF also increased ATP production estimated by oxygen consumption rates (OCR) and by a biochemical assay in NARP3-2 cybrids. Hormetic activation of mitochondria by ELF-EMF is likely to be effective to ameliorate defective mitochondrial energy production in NARP and other mitochondrial diseases.
    Keywords:  And mitohormesis; Extremely low-frequency electromagnetic field (ELF-EMF); Mitochondrial DNA; Mitochondrial biogenesis; Mitophagy; Neuropathy, ataxia, retinitis pigmentosa (NARP) syndrome
    DOI:  https://doi.org/10.1038/s41598-025-10536-7
  11. Bioessays. 2025 Jul 06. e70038
      Mitochondrial membrane potential is highly dependent on coupled as well as uncoupled respiration. While brown adipose tissue (BAT) mediates non-shivering thermogenesis (NST), a highly adaptive bioenergetic process critical for energy metabolism, the relationship of coupled and uncoupled respiration in thermogenic adipocytes remains complicated. Uncoupling protein 1 (UCP1)-mediated proton leak is the primary driver of NST, but recent studies have shown that oxidative phosphorylation may be an underappreciated contributor to UCP1-dependent NST. Here, we highlight the role of ATP synthase for BAT thermogenesis and discuss the implications of fine-tuning adrenergic signaling in brown adipocytes by the protein inhibitory factor 1 (IF1). We conclude by hypothesizing future directions for mitochondrial research, such as investigating the potential role of IF1 for mitochondrial substrate preference, structural dynamics, as well as its role in cell fate decision and differentiation.
    Keywords:  UCP1; adipocytes; bioenergetics; metabolism; mitochondria; obesity; thermogenesis
    DOI:  https://doi.org/10.1002/bies.70038
  12. Science. 2025 Jul 10. 389(6756): 157-162
      Maintenance of mitochondrial redox homeostasis is of fundamental importance to cellular health. Mitochondria harbor a host of intrinsic antioxidant defenses, but the contribution of extrinsic, nonmitochondrial antioxidant mechanisms is less well understood. We found a direct role for peroxisomes in maintaining mitochondrial redox homeostasis through contact-mediated reactive oxygen species (ROS) transfer. We found that ACBD5 and PTPIP51 form a contact between peroxisomes and mitochondria. The percentage of these contacts increased during mitochondrial oxidative stress and helped to maintain mitochondrial health through the transfer of mitochondrial ROS to the peroxisome lumen. Our findings reveal a multiorganelle layer of mitochondrial antioxidant defense-suggesting a direct mechanism by which peroxisomes contribute to mitochondrial health-and broaden the scope of known membrane contact site functions.
    DOI:  https://doi.org/10.1126/science.adn2804
  13. bioRxiv. 2025 Jul 02. pii: 2025.06.18.660357. [Epub ahead of print]
      Mitochondria contribute to compartmentalized metabolism in eukaryotic cells, supporting key enzymatic reactions for cell function and energy homeostasis. However, this compartmentalization necessitates regulated metabolite transport across mitochondrial membranes. Although many transport proteins have been identified, several mitochondrial amino acid transporters remain largely uncharacterized. Using CRISPR-Cas9-mediated candidate transporter knockouts coupled with assessment of metabolite transport via a mitochondrial swelling assay, we identify SFXN1, previously characterized for its role in mitochondrial serine transport, as a protein that mediates mitochondrial transport of a range of other polar neutral amino acids including proline, glycine, threonine, taurine, hypotaurine, β-alanine, and γ-aminobutyric acid (GABA). Furthermore, the SFXN1 paralogues SFXN2 and SFXN3 partially complement loss of SFXN1 to enable glycine transport, while SFXN2 and SFXN5 partially complement loss of SFXN1 to enable GABA transport. Altogether, these data suggest that sideroflexins facilitate the transport of polar neutral amino acids across the inner mitochondrial membrane.
    DOI:  https://doi.org/10.1101/2025.06.18.660357
  14. Nature. 2025 Jul 09.
      Decreased brain levels of coenzyme Q10 (CoQ10), an endogenously synthesized lipophilic antioxidant1,2, underpin encephalopathy in primary CoQ10 deficiencies3,4 and are associated with common neurodegenerative diseases and the ageing process5,6. CoQ10 supplementation does not increase CoQ10 pools in the brain or in other tissues. The recent discovery of the mammalian CoQ10 headgroup synthesis pathway, in which 4-hydroxyphenylpyruvate dioxygenase-like protein (HPDL) makes 4-hydroxymandelate (4-HMA) to synthesize the CoQ10 headgroup precursor 4-hydroxybenzoate (4-HB)7, offers an opportunity to pharmacologically restore CoQ10 synthesis and mechanistically treat CoQ10 deficiencies. To test whether 4-HMA or 4-HB supplementation promotes CoQ10 headgroup synthesis in vivo, here we administered 4-HMA and 4-HB to Hpdl-/- mice, which model an ultra-rare, lethal mitochondrial encephalopathy in humans. Both 4-HMA and 4-HB were incorporated into CoQ9 and CoQ10 in the brains of Hpdl-/- mice. Oral treatment of Hpdl-/- pups with 4-HMA or 4-HB enabled 90-100% of Hpdl-/- mice to live to adulthood. Furthermore, 4-HB treatment stabilized and improved the neurological symptoms of a patient with progressive spasticity due to biallelic HPDL variants. Our work shows that 4-HMA and 4-HB can modify the course of mitochondrial encephalopathy driven by HPDL variants and demonstrates that CoQ10 headgroup intermediates can restore CoQ10 synthesis in vivo.
    DOI:  https://doi.org/10.1038/s41586-025-09246-x
  15. Mov Disord. 2025 Jul 09.
    Global Parkinson's Genetics Program (GP2)
      
    Keywords:  LRRK2; Parkinson's disease; mitochondria; mitochondrial polygenic score; polygenic score
    DOI:  https://doi.org/10.1002/mds.30285
  16. Am J Physiol Cell Physiol. 2025 Jul 11.
      Brown adipose tissue (BAT) plays a central role in mammalian non-shivering thermogenesis, dissipating mitochondrial membrane potentials through the activity of uncoupling protein UCP1 to release heat. Inner membranes of mitochondria are known to be permeable to potassium ions (K+), which enter the matrix either through ATP-sensitive channels (MitoKATP) or leakage across the bilayer driven by inner membrane potentials. Mitochondrial K+ influx is associated with increased osmotic pressure, promoting water influx and increasing matrix volume. Since BAT mitochondria have lower inner membrane potentials due to uncoupling protein 1 (UCP1) activity, we hypothesized this could involve compensatory changes in MitoKATP activity, and thus tested MitoKATP involvement in brown adipocyte activities under basal and stimulated conditions. We find that cold exposure and adrenergic stimulation in mice modulate BAT MitoK levels, the channel portion of MitoKATP. Genetic ablation of the gene that codes for the pore-forming subunit of MitoKATP in human pre-adipocytes decreased cellular respiration and proliferation, compromising differentiation into mature adipocytes. In mouse cell lines, the absence of the protein limited cellular oxygen consumption in the precursor stage, but not in mature adipocytes. Interestingly, inhibition of MitoKATP in mature adipocytes increased adrenergic-stimulated oxygen consumption, indicating that shutdown of this pathway is important for full BAT thermogenesis. Similarly, MitoKATP inhibition increased oxygen consumption in BAT mitochondria isolated from mice treated with beta 3 adrenergic receptor agonist CL316,243. Overall, our results suggest that the activity of MitoKATP regulates differentiation and metabolism of brown adipocytes, impacting on thermogenesis.
    Keywords:  K+ transport; brown adipose tissue; mitochondria; thermogenesis; uncoupling
    DOI:  https://doi.org/10.1152/ajpcell.00070.2025
  17. Neural Regen Res. 2025 Jul 05.
      Phosphatidylethanolamine is a major phospholipid class abundant in the brain, particularly in the inner leaflet of the plasma and mitochondrial membranes. Although it is primarily synthesized from phosphatidylserine via decarboxylation in mitochondria or from ethanolamine via the cytidine diphosphate-ethanolamine pathway in the endoplasmic reticulum, phosphatidylethanolamine that resides in mitochondria is preferentially produced locally and is distinct and separate from the pool of phosphatidylethanolamine made in the endoplasmic reticulum. Mitochondria-derived phosphatidylethanolamine is not only essential for mitochondrial integrity but also is exported to other organelles to fulfill diverse cellular functions. Neurons are highly enriched with phosphatidylethanolamine, and the importance of phosphatidylethanolamine metabolism in neuronal health has recently been recognized following its reported links to Alzheimer's disease, Parkinson's disease, and hereditary spastic paraplegia, among other neurological disorders. Indeed, disturbances in mitochondrial function and phosphatidylethanolamine metabolism and the resulting neuronal dysfunction are the common features of individuals suffering from these diseases, highlighting the great importance of maintaining proper phosphatidylethanolamine homeostasis in neurons. In this review, we summarize the current knowledge of phosphatidylethanolamine metabolism and its role in neuronal function with a special emphasis on the phosphatidylethanolamine biosynthetic pathway in mitochondria. We then review findings on how phosphatidylethanolamine biosynthesis is affected in major neurodegenerative diseases. Finally, we highlight promising future research areas that will help advance the understanding of neuronal phosphatidylethanolamine mechanisms and identify phosphatidylethanolamine-targeted therapeutic strategies for combating such brain diseases.
    Keywords:  ; Alzheimer's disease; Parkinson's disease; autophagy; cognitive dysfunction; hereditary spastic paraplegia; neuronal phospholipid trafficking; phosphatidylserine decarboxylase; phosphatidylserine transport; tauopathy
    DOI:  https://doi.org/10.4103/NRR.NRR-D-25-00201
  18. Autophagy. 2025 Jul 07.
      Loss-of-function mutations in the PINK1 and PRKN genes are the most common cause of early-onset Parkinson disease (PD). The encoded enzymatic pair selectively identifies, labels, and targets damaged mitochondria for degradation via the macroautophagy/autophagy-lysosome system (mitophagy). This pathway is cytoprotective and efforts to activate mitophagy are pursued as therapeutic avenues to combat PD and other neurodegenerative disorders. When mitochondria are damaged, the ubiquitin kinase PINK1 accumulates and recruits PRKN from the cytosol to activate the E3 ubiquitin ligase from its auto-inhibited conformation. We have previously designed several mutations that effectively derepress the structure of PRKN and activate its enzymatic functions in vitro. However, it remained unclear how these PRKN-activating mutations would perform endogenously in cultured neurons or in vivo in the brain. Here, we gene-edited neural progenitor cells and induced pluripotent stem cells to express PRKN-activating mutations in dopaminergic cultures. All tested PRKN-activating mutations indeed enhanced the enzymatic activity of PRKN in the absence of exogenous stress, but their hyperactivity was linked to their own PINK1-dependent degradation. Strikingly, in vivo in a mouse model expressing an equivalent activating mutation, we find the same relationship between PRKN enzymatic activity and protein stability. We conclude that PRKN degradation is the consequence of its structural derepression and enzymatic activation, thus resulting only in a temporary gain of activity. Our findings imply that pharmacological activation of endogenous PRKN will lead to increased turnover and suggest that additional considerations might be necessary to achieve sustained E3 ubiquitin ligase activity for disease treatment.
    Keywords:  Autophagy; PINK1; Parkin; mitophagy; parkinson’s disease
    DOI:  https://doi.org/10.1080/15548627.2025.2531025
  19. Adv Sci (Weinh). 2025 Jul 08. e04175
      Alzheimer's disease (AD) is defined by β-amyloid plaques and tau-containing neurofibrillary tangles, but the ensuing cellular derangements that culminate in neurodegeneration remain elusive. Here, a mechanistic link between two AD pathophysiological hallmarks: energy insufficiency and oxidative stress is revealed. It is demonstrated that mitochondrial function and glutathione (GSH) flux are coupled, impacting neuronal ferroptosis susceptibility. Analysis of proteomic data from the inferior temporal cortex of 625 subjects along a continuum of clinical and pathological changes in AD, reveals a prominent depletion of mitochondrial proteins. Biogenetic insufficiency in AD is reflected by a concurrent loss of GSH, which requires 2 ATP for its synthesis, and genetic and pharmacologic ATP depletion models confirm that ATP is rate-limiting for GSH. Accordingly, an unbiased association analysis uncovers mitochondrial proteins in positive correlation with total GSH (t-GSH) in AD subjects. But mitochondria also consume GSH via the SLC25A39 transporter. It is found that mitochondrial inhibition either increases or decreases ferroptosis susceptibility in cellular models, depending on contextual factors that dictate whether mitochondria act as a net GSH producer or consumer, respectively. Mitochondria therefore control GSH flux, and loss of energy output is consequently demonstrated as a liability for ferroptosis in AD.
    Keywords:  ATP; alzheimer's disease; bioenergetics; ferroptosis; glutathione; mitochondria; neurodegeneration
    DOI:  https://doi.org/10.1002/advs.202504175
  20. Front Aging. 2025 ;6 1585508
      Mitochondrial-driven diseases encompass a diverse group of single-gene and complex disorders, all linked to mitochondrial dysfunction, with significant impacts on human health. While there are rare mitochondrial diseases in which the primary defect resides in mutations in mitochondrial DNA, it is increasingly clear that acquired mitochondrial dysfunction, both genetically- and epigenetically-mediated, complicates common complex diseases, including diabetes, cardiovascular disease and ischemia reperfusion injury, cancer, pulmonary hypertension, and neurodegenerative diseases. It is also recognized that mitochondrial abnormalities not only act by altering metabolism but, through effects on mitochondrial dynamics, can regulate numerous cellular processes including intracellular calcium handling, cell proliferation, apoptosis and quality control. This review examines the crucial role of preclinical models in advancing our understanding of mitochondrial genetic contributions to these conditions. It follows the evolution of models of mitochondrial-driven diseases, from earlier in vitro and in vivo systems to the use of more innovative approaches, such as CRISPR-based gene editing and mitochondrial replacement therapies. By assessing both the strengths and limitations of these models, we highlight their contributions to uncovering disease mechanisms, identifying therapeutic targets, and facilitating novel discoveries. Challenges in translating preclinical findings into clinical applications are also addressed, along with strategies to enhance the accuracy and relevance of these models. This review outlines the current state of the field, the future trajectory of mitochondrial disease modeling, and its potential impact on patient care.
    Keywords:  CRISPR/Cas9; conplastic mouse; cybrid; mitochondrial replacement therapy (MRT); mitochondrial-driven diseases; mitochondrial-nuclear eXchange (MNX) mice; organoid; preclinical models
    DOI:  https://doi.org/10.3389/fragi.2025.1585508
  21. Biophys Physicobiol. 2025 ;22(2): e220012
      Mitochondria isolated from cells are essential tools in biological research. However, many mitochondria are often damaged during the isolation process. Although cryopreservation can greatly improve the usability of isolated mitochondria, it typically leads to significant loss of activity following freezing and thawing. In this study, we present our own techniques for mitochondrial isolation and cryopreservation to overcome these challenges. Our isolation method begins by selectively weakening the plasma membrane through the incorporation of digitonin, under conditions that do not increase membrane permeability. The plasma membrane is then selectively ruptured to release mitochondria. Notably, mitochondria contract within the cell before the plasma membrane ruptures, a process that facilitates their extraction. The isolated mitochondria showed polarized inner membranes in approximately 90% of the population. Compared to mitochondria isolated by homogenization, they retained more intermembrane space proteins and exhibited greater outer membrane integrity. For cryopreservation, rapid thawing was critical to maintaining mitochondrial activity after freeze-thaw cycles. When thawing was completed in under 1.5 minutes, the proportion of polarized mitochondria decreased by only about 10%. These findings suggest that our isolation and cryopreservation protocols are promising for applications requiring intact, functional mitochondria.
    Keywords:  cryopreservation; isolation; mitochondria
    DOI:  https://doi.org/10.2142/biophysico.bppb-v22.0012
  22. FEBS J. 2025 Jul 07.
      Organelles were once regarded as discrete entities, but it is now established that they interact through specialized membrane contacts maintained by protein tethers and lipid interactions. Among these, mitochondria-endoplasmic reticulum contact sites (MERCS) emerged as hubs for calcium signaling, lipid metabolism, and mitochondrial dynamics. Here, we critically appraise current methodologies for MERC visualization and quantification, survey the molecular toolbox for their selective perturbation, and highlight common experimental pitfalls. We also discuss key conceptual issues-defining MERCs on structural and functional grounds, addressing redundancy among tethering factors, and distinguishing primary MERC-mediated effects from secondary cellular responses. Finally, we propose that an integrative strategy combining imaging, precise biochemical isolation, proteomics, and functional assays will be essential to resolve outstanding questions about MERC dynamics in physiology and pathology.
    Keywords:  endoplasmic reticulum; imaging; membrane contact sites; mitochondria; mitochondria–ER contact sites
    DOI:  https://doi.org/10.1111/febs.70184
  23. Sci Adv. 2025 Jul 11. 11(28): eadw1883
      Cell competition is a conserved fitness quality control that eliminates cells that are less fit than their neighbors. How winner cells induce the elimination of losers is poorly understood. We tackle this question by studying the onset of embryonic differentiation in mice, where cell competition eliminates 35% of embryonic cells. These loser cells have mitochondrial dysfunction, which we show causes amino acid deprivation and activation of the integrated stress response (ISR), a pathway essential for their survival. We demonstrate that l-proline is a key amino acid sensed by the ISR and that proline represses the ISR and drives their elimination. These results indicate that cell competition acts as a previously unidentified tissue-sparing mechanism, regulated by the availability of extracellular amino acids, that allows for the elimination of dysfunctional cells when amino acids are plentiful but ensures their survival in nutrient-poor environments.
    DOI:  https://doi.org/10.1126/sciadv.adw1883
  24. Pediatr Res. 2025 Jul 09.
       IMPACT: DNM1L mutations impair mitochondrial fission, leading to cardiomyocyte energy deficits and contractile dysfunction, and reveal a cardiac role for DNM1L beyond neurological disease. iPSC-cardiomyocytes derived from patients with DNM1L mutations demonstrate mitochondrial defects and cardiomyopathy phenotypes, offering a robust model to dissect disease mechanisms and identify personalised therapies. Disrupted mitochondrial dynamics directly lead to calcium mishandling and contractile dysfunction, positioning fission/fusion pathways as promising therapeutic targets in cardiomyopathy treatment.
    DOI:  https://doi.org/10.1038/s41390-025-04278-5
  25. Small Methods. 2025 Jul 06. e2500674
      Mitochondria are micrometer-sized organelles, yet are pivotal for the activity, function, and fate of mammalian cells. Recent findings further reveal that mitochondrial homeostasis plays an active role in regulating lung cell disorders, inspiring a novel strategy to treat pulmonary disease by restoring the imbalanced mitochondrial homeostasis. Pioneering studies have shown the potentials of this strategy for the treatment of pulmonary fibrosis (PF), chronic obstructive pulmonary disease (COPD), and acute respiratory distress syndrome (ARDS), which currently lack efficient medicines. However, there has been no comprehensive summary of this innovative strategy in pulmonary disease treatment. Therefore, the present review aims to provide an overview of the mechanism and advances in pulmonary disease treatment by restoring mitochondrial homeostasis. Particularly, some of the latest therapeutic strategies, including antioxidant therapy, mitochondrial quality controlling, and mitochondrial replenishment therapy (MRT), are introduced to show the potent capability of mitochondria to regulate cellular disorders in different types of lung cells. This review is believed to provide a general understanding of the mitochondria involved in pathogenesis and is intended to inspire the development of novel therapeutic methods against pulmonary diseases, focusing on regulating impaired mitochondrial homeostasis.
    Keywords:  antioxidants; homeostasis; mitochondria; mitochondria transfer; pulmonary diseases
    DOI:  https://doi.org/10.1002/smtd.202500674
  26. bioRxiv. 2025 Jul 04. pii: 2025.06.30.662412. [Epub ahead of print]
      Metabolic flexibility, the capacity to adapt fuel utilization in response to nutrient availability, is essential for maintaining energy homeostasis and preventing metabolic disease. Here, we investigate the role of Ulk1 phosphorylation at serine 555 (S555), a site regulated by AMPK, in coordinating metabolic switching following short-term caloric restriction and fasting. Using Ulk1(S555A) global knock-in mice, we show loss of S555 phosphorylation impairs glucose oxidation in skeletal muscle and liver during short-term CR, despite improved glucose tolerance. Metabolomic, transcriptomic, and mitochondrial respiration analyses reveal a compensatory reliance on glucogenic amino acids, particularly alanine and serine, in Ulk1(S555A) mice, with sustained amino acid oxidation during fasting and blunted mitochondrial response to energetic stress. These findings establish Ulk1(S555) phosphorylation as a critical regulatory event linking nutrient stress to substrate switching and highlights an underappreciated role of Ulk1 in maintaining metabolic flexibility.
    DOI:  https://doi.org/10.1101/2025.06.30.662412
  27. Cell Mol Neurobiol. 2025 Jul 11. 45(1): 68
      This review aims to investigate the potential role of estrogen in various mitochondrial diseases, such as Leber's Hereditary Optic Neuropathy and Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episodes, focusing on its effects on aging, oxidative stress, mitochondrial biogenesis, and mitophagy. Mitochondrial diseases have become important in modern medical research due to their complex genetic background and diverse clinical manifestations. Studies in recent years have shown that estrogen plays an essential role in physiological regulation and may also affect the health status of cells by regulating mitochondrial function, which in turn affects the occurrence and development of diseases. However, there is still a lack of systematic review of estrogen's specific mechanisms and roles in these diseases. This review will synthesize the relevant literature to explore the association between estrogen and mitochondrial diseases and its possible therapeutic prospects, aiming to provide a theoretical basis and reference for future research.
    Keywords:  Aging; Estrogen; Mitochondrial biogenesis; Mitochondrial disease; Mitophagy; Oxidative stress
    DOI:  https://doi.org/10.1007/s10571-025-01592-8
  28. Biochem Biophys Res Commun. 2025 Jul 01. pii: S0006-291X(25)00993-3. [Epub ahead of print]777 152278
      Leigh syndrome (LS), a primary mitochondrial disease frequently caused by complex I (CI) deficiency, has been associated with hepatic dysfunction and impaired metabolic homeostasis. Despite this, the impact of mitochondrial dysfunction on hepatic xenobiotic detoxification pathways remains poorly understood. This study investigated the glycine conjugation pathway-central to the metabolism of dietary xenobiotics such as benzoate, salicylate, and medium-chain fatty acids (MCFAs)-in a whole-body Ndufs4 knockout (Ndufs4-/-) mouse model of LS. Transcriptomic analysis revealed a significant downregulation of the xenobiotic/medium chain fatty acid: CoA ligases (Acsm1 and Acsm2) and glycine N-acyltransferase (Glyat) in the livers of Ndufs4-/- mice, suggesting impaired activation and conjugation of xenobiotics. This was corroborated by reduced GLYAT (EC2.3.1.13) enzymatic activity and a marked decrease in hepatic hexanoylglycine levels. These findings imply that CI deficiency attenuates glycine conjugation capacity, potentially compromising the liver's ability to metabolise xenobiotic and dietary substrates. Given the role of glycine conjugation in detoxification, our data highlight a metabolic vulnerability in LS that may influence dietary and pharmacological interventions. Adjusting dietary intake of conjugation substrates may therefore be crucial in the clinical management of mitochondrial disease.
    Keywords:  ACSM; GLYAT; Glycine N-Acyltransferase; Glycine conjugation; Leigh syndrome; Xenobiotic detoxification; Xenobiotic/medium chain fatty acid: CoA ligases
    DOI:  https://doi.org/10.1016/j.bbrc.2025.152278
  29. bioRxiv. 2025 Apr 11. pii: 2025.04.09.647991. [Epub ahead of print]
      Nicotinamide adenine dinucleotide (NAD + ) is an essential redox cofactor and signaling molecule linked to age-dependent metabolic decline, with its compartmentalization regulated by the mitochondrial carrier SLC25A51. The mechanisms contributing to declining NAD + levels during aging and the consequences of altered NAD + homeostasis across tissues are poorly understood. Here, we show that SLC25A51 is upregulated in aging and aging-associated conditions, particularly in senescent cells. In a mouse model of beta-cell senescence, upregulated SLC25A51 was associated with beta-cell identity loss, senescence progression, and a reduced NAD + /NADH ratio. SLC25A51 was elevated following p16 INK4a -, replicative-, irradiation-, and H 2 O 2 -induced senescence, with NRF2 implicated as a potential transcriptional regulator. Overexpression of SLC25A51, but not a transport-dead mutant, induced senescence factors, while its deletion prevented this effect. Beta-cell-specific deletion of SLC25A51 lowered p16 INK4a levels in pancreatic islets, circulating insulin, and glucose levels, improving insulin sensitivity and indicating its role in cellular senescence and the metabolic control of beta-cell function.
    DOI:  https://doi.org/10.1101/2025.04.09.647991
  30. J Paediatr Child Health. 2025 Jul 05.
       BACKGROUND: Using genomic sequencing technology at population scale as a screening test holds the promise of improving outcomes for individuals with rare diseases through early detection and timely access to precision medicine. However, the incorporation of genomics into established newborn screening programmes raises many challenges, ranging from technical feasibility and scalability through to ethical concerns regarding consent and data management. Empirical evidence and implementation experience from large-scale studies are required to guide future policy.
    METHODS: We provide a narrative summary of genomic newborn screening studies currently underway in Australia.
    FINDINGS: We summarise six research studies currently underway in Australia, which explore the application of genomic technologies in the newborn screening context. These studies have taken varying approaches to generating evidence about the implementation of genomic newborn screening and have formed a national consortium, the Genomic Screening Consortium for Australian Newborns (GenSCAN), with the aim of sharing experiences and enabling collective learning.
    CONCLUSIONS: Over the next decade, we can expect substantial evidence to be generated nationally and internationally to inform future policy decisions on whether to incorporate genomic sequencing into newborn screening programmes.
    Keywords:  genetics; genomics; neonatology; newborn screening; rare disease
    DOI:  https://doi.org/10.1111/jpc.70131
  31. J Gen Virol. 2025 Jul;106(7):
      As intracellular parasites, viruses must hijack and often rewire organelles, signalling pathways and the bioenergetics machinery of the infected cell to replicate their genome, produce viral proteins and assemble new viral particles. Mitochondria are key eukaryotic organelles often referred to as the cell's powerhouse. They control many fundamental cellular processes, from metabolism and energy production to calcium homeostasis and programmed cell death. Importantly, mitochondrial membranes are also critical sites for the integration and amplification of antiviral innate immune responses. Overall, mitochondria are therefore both supporting the virus life cycle by sustaining energy production, metabolism and synthesis of macromolecules and part of the cell's first line of defence against viruses. This review summarizes recent findings on viral manipulations of mitochondria and their functions. We explore the evolving understanding of how mitochondrial dynamics is targeted to regulate innate immunity, evasion strategies used to avoid mitochondrial-associated mechanisms that impair replication and the role of mitochondrial functions such as generating reactive oxygen species or regulating the electron transport chain during infection. Overall, we provide a comprehensive view of how viruses modulate mitochondrial function to promote replication.
    Keywords:  innate immunity; mitochondria; mitochondrial unfolded protein response (UPRmt)
    DOI:  https://doi.org/10.1099/jgv.0.002128
  32. Cytotechnology. 2025 Aug;77(4): 139
      Mitochondrial medicine has shown great promise as a therapeutic approach for treating currently incurable diseases. Preclinical studies highlight its safety and efficacy, but significant challenges remain in translating these therapies from bench to bedside. Key unresolved issues include understanding the mechanisms behind the reparative potential of transplanted mitochondria, such as their viability and functionality in an extracellular environment, especially under elevated calcium ion concentrations. Additionally, challenges related to mitochondrial sourcing, delivery methods, and ethical considerations need to be addressed for broader clinical adoption. This review analyses these challenges and explores strategies to overcome them, including refining mitochondrial sourcing, delivery techniques, and storage solutions. We also emphasise the need for rigorous ethical guidelines and regulatory frameworks to ensure safe and global implementation, paving the way for mitochondrial medicine's broader clinical use.
    Keywords:  Mitochondrial biology; Mitochondrial dysfunction; Mitochondrial medicine; Mitochondrial transplantation; Regenerative medicine
    DOI:  https://doi.org/10.1007/s10616-025-00805-8
  33. FASEB Bioadv. 2025 Jul;7(7): e70030
      Cell homeostasis and metabolic control require the efficient function of mitochondria and implementation of quality control pathways following damage. Cells have various discrete pathways of mitochondrial quality control (mitoQC) to maintain the healthy network. PINK1 and Parkin are two key players in mitoQC, most highly associated with the ubiquitin-dependent capture and degradation of whole mitochondria by autophagy. However, these proteins have alternative roles in repair routes directing locally damaged cargo to the lysosome, such as the mitochondrial-derived vesicle (MDV) pathway. We aimed to clarify the role of PINK1 and determine how its loss of function impacts mitochondrial dynamics and quality control. Results indicate PINK1 knockout (KO) has little impact on whole mitochondrial turnover in response to damage in SH-SY5Y cells, whereas both PINK1 and Parkin KO cells have healthy mitochondrial networks with efficient ATP production. However, TOM20 positive outer-membrane and damage-induced PDH-positive inner-membrane MDVs are elevated in PINK1 KO cells. Although, in contrast to Parkin KO, this is not due to a defect in trafficking to a LAMP1-positive compartment and may instead indicate increased damage-induced flux. In comparison, loss of Atg5-dependent mitophagy has no effect on whole mitochondrial turnover and only results in a limited elevation in inner-membrane MDVs in response to damage, indicating autophagy-independent mechanisms of whole mitochondrial turnover and a minor compensatory increase in damage-induced MDVs. Therefore, these data suggest PINK1 and Parkin are dispensable for whole mitochondrial turnover, but following their perturbation have disparate effects on the MDV pathway.
    Keywords:  Parkinson's; lysosome; membrane trafficking; mitochondria; mitochondrial quality control; vesicle transport
    DOI:  https://doi.org/10.1096/fba.2024-00200
  34. J Am Chem Soc. 2025 Jul 08.
      Mitochondrial fission is controlled by dynamin-like proteins, the dysregulation of which is correlated with diverse diseases. Fission dynamin-like proteins are GTP hydrolysis-driven mechanoenzymes that self-oligomerize into helical structures that constrict membranes to achieve fission while also remodeling membranes by inducing negative Gaussian curvature, which is essential for the completion of fission. Despite advances in optical and electron imaging technologies, the underlying mechanics of mitochondrial fission remain unclear due to the multiple times involved in the dynamics of mechanoenzyme activity, oligomer disassembly, and membrane remodeling. Here, we examine how multiscale phenomena in dynamin Drp1 synergistically influence membrane fission using a mechanical model calibrated with small-angle X-ray scattering structural data and informed by a machine learning analysis of the Drp1 sequence, and tested the concept using optogenetic mechanostimulation of mitochondria in live cells. We find that free dynamin-like proteins can trigger a "snap-through instability" that enforces a shape transition from an oligomer-confined cylindrical membrane to a drastically narrower catenoid-shaped neck within the spontaneous hemi-fission regime, in a manner that depends critically on the length of the confined tube. These results indicate how the combination of assembly and paradoxically disassembly of dynamin-like proteins can lead to diverse pathways to scission.
    DOI:  https://doi.org/10.1021/jacs.5c06352
  35. Cell Rep. 2025 Jul 01. pii: S2211-1247(25)00693-X. [Epub ahead of print] 115922
      Virus-infected cells often exhibit dramatic cellular changes accompanied by altered mitochondrial function. The contribution of factors shaping the inner mitochondrial membrane (IMM) and cristae architecture to viral replication is insufficiently understood. Single-cell transcriptomics applying vesicular stomatitis virus infection suggests involvement of factors determining IMM architecture following infection. Consistently, inhibition of the F1FO adenosine triphosphate (ATP) synthase reduces viral replication, which is associated with oligomerization of this complex and altered IMM structure. Moreover, deletion of mitochondrial contact site and cristae organizing system (MICOS) complex by targeting MIC60 results in reduced viral replication. Generation of Mic60inv/invCD11c-Cre+ mice uncovers reduced crista junctions and viral replication in bone marrow-derived dendritic cells. Consequently, reduced viral replication in CD11c-expressing cells limits prolonged immune activation. Altogether, by linking the F1FO ATP synthase and the MICOS complex to viral replication and immune activation, we describe links between the mitochondrial structure-metabolism and the immune response against viral infection.
    Keywords:  BMDC; CP: Cell biology; CP: Microbiology; MIC60; MICOS; immunometabolism; innate immunity; inner mitochondrial membrane; itaconate; mitochondria; viral infection
    DOI:  https://doi.org/10.1016/j.celrep.2025.115922
  36. Beilstein J Nanotechnol. 2025 ;16 951-967
      Mitochondrial network dynamics play a key role in enabling cells to adapt to environmental changes. Fusion and fission of mitochondria, as well as their contact with other organelles, are central processes. Consequently, the outer membrane, which separates the mitochondrion from the cytoplasm, has become a focus of investigation. We analysed metabolically active mitochondria from HeLa cells using scanning ion conductance microscopy to generate nanoscopically resolved, three-dimensional topographies. Our measurements reveal the diversity of mitochondrial shapes. Moreover, a morphodynamic effect was identified, the magnitude of which depends on mitochondrial viability. This method, applied for the first time to mitochondria, shows potential for visualising the morphodynamic responses of mitochondria to their local environment. The similarities between the nanopipette in the measurement setup and the microtubules in the cellular context are discussed as the basis for the hypothesis.
    Keywords:  HeLa; metabolically active; mitochondria; morphodynamics; scanning ion conductance microscopy
    DOI:  https://doi.org/10.3762/bjnano.16.73
  37. J Inherit Metab Dis. 2025 Jul;48(4): e70060
      3-hydroxy acylcarnitines (3-OH-ACs) are key biomarkers for screening of long-chain 3-hydroxyacyl-CoA dehydrogenase and trifunctional protein deficiencies (LCHADD/TFPD). The utility of this biomarker for disease monitoring in identified patients remains debated, and recent suggestions have highlighted the potential use of lipidomics for diagnosis, monitoring, prognosis, and/or identification of new biomarkers. We evaluated the use of omics in LCHADD/TFPD patients by analyzing plasma acylcarnitine profiles, metabolomics, and lipidomics, combined with genotype, visual assessments, and dietary records. Fasting plasma from 39 participants with LCHADD/TFPD and 32 control subjects were analyzed through untargeted metabolomic and lipidomic analyses. In LCHADD/TFPD participants, acylcarnitine profiling, visual and retinal function assessments were performed, and 3-day diet records were collected. Relationships between acylcarnitines, metabolomics, lipidomics, along with visual outcomes and dietary intake were investigated. Plasma of LCHADD/TFPD participants exhibited elevated 3-OH-ACs, which correlated with genotype and visual outcomes. Metabolomics successfully distinguished LCHADD/TFPD from controls, and the biggest divergence was observed in lipid pathways. Metabolomic profiles tightly correlated with 3-OH-ACs, genotype, and visual outcomes. Lower concentrations of total lipids and some individual lipid species such as phosphoethanolamines (PE) were detected in LCHADD/TFPD, except for elevations in several certain triglycerides. LCHADD/TFPD participants followed a diet low in long-chain fat (LCFA) as recommended. LCFA intake did not correlate with either plasma 3-OH-ACs or metabolomics. 3-OH-ACs are strong consistent biomarkers of LCHADD/TFPD that are associated with clinical parameters of vision and genotype. We did not observe a relationship between dietary LCFA intake and 3-OH-ACs.
    Keywords:  3‐hydroxy acylcarnitines; 3‐hydroxy fatty acids; fatty acid oxidation; fatty acid oxidation disorders; lipidomics; long‐chain 3‐hydroxyacyl‐CoA dehydrogenase deficiency; metabolomics
    DOI:  https://doi.org/10.1002/jimd.70060
  38. Commun Med (Lond). 2025 Jul 10. 5(1): 286
       BACKGROUND: Primary coenzyme Q (CoQ) deficiency is a severe mitochondrial disorder characterized by diverse clinical manifestations due to multiple pathomechanisms. Although CoQ10 supplementation remains the standard treatment, its therapeutic efficacy is limited by poor bioavailability and restricted tissue distribution, especially to the central nervous system.
    METHODS: In this study, we investigated the therapeutic potential of combining CoQ10 with vanillic acid (VA), a structural analog of 4-hydroxybenzoic acid, in both murine and human models of primary CoQ deficiency, through phenotypic, biochemical, and molecular analyses.
    RESULTS: In Coq9R239X mice, we demonstrate that co-administration of CoQ10 and VA significantly extends lifespan and improves motor function beyond the effects observed with either compound alone. Mechanistically, this enhanced therapeutic efficacy results from the complementary actions of both compounds, i.e., CoQ10 increases quinone pools in peripheral tissues and modulates one-carbon metabolism, particularly in the liver, while VA reduces DMQ accumulation in the kidney and liver and exhibits potent anti-neuroinflammatory properties, leading to a reduction in gliosis. The co-treatment shows remarkable tissue-specific responses, with the liver displaying the most pronounced metabolic adaptations. In this tissue, the combined therapy restores the expression of genes involved in sulfide oxidation and one-carbon metabolism pathways. We further validate these findings in human COQ7-deficient fibroblasts, where the co-treatment normalizes key metabolic pathways more effectively than individual treatments.
    CONCLUSIONS: Our findings demonstrate that combining CoQ10 with VA effectively addresses multiple pathogenic mechanisms in CoQ deficiency, resulting in enhanced therapeutic outcomes. This therapeutic strategy could represent a more effective and feasible treatment approach for mitochondrial disorders, particularly those involving CoQ deficiency and neurological manifestations.
    DOI:  https://doi.org/10.1038/s43856-025-01000-8
  39. Neurobiol Dis. 2025 Jul 04. pii: S0969-9961(25)00235-9. [Epub ahead of print]213 107019
      Charcot-Marie-Tooth disease type 4 A ((CMT4A), an autosomal recessive neuropathy, is caused by mutations in ganglioside-induced differentiation-associated protein 1 (GDAP1). GDAP1 resides in the outer mitochondrial membrane facing the cytosol and is involved in mitochondrial dynamics and function. Its perturbation affects mitochondrial shape, contact sites, redox homeostasis and cellular metabolism. In response to GDAP1 knockdown in a human neuronal cell line, we found increased mitochondrial turnover, biogenesis and mitophagy. This was associated with more lysosomal proteins in mitochondrial fractions including BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3) and its homolog BNIP3-like (BNIP3L) - proteins involved in the recruitment of autophagy machinery via direct interaction. Flies with neural Gdap1 knockdown also exhibited upregulated levels of the sole BNIP3 ortholog. Neural expression of human BNIP3 reduced the detrimental effects of Gdap1 knockdown on eclosion and climbing ability in adult flies, while simultaneous knockdown of both genes was detrimental. These findings suggest that increased BNIP3-driven mitophagy may act as a protective mechanism, partially counteracting the cellular dysfunction caused by GDAP1 loss of function, and highlight the potential of targeting mitophagy pathways as a therapeutic strategy for CMT4A.
    Keywords:  BNIP3; Charcot-Marie-tooth (CMT) disease; Drosophila; GDAP1; Mitophagy
    DOI:  https://doi.org/10.1016/j.nbd.2025.107019
  40. Curr Opin Genet Dev. 2025 Jul 04. pii: S0959-437X(25)00068-1. [Epub ahead of print]93 102376
      The mitochondrial genome (mtDNA) can accumulate deleterious mutations that lead to disease. Animals have evolved strategies to eliminate mtDNA mutations in the maternal germ line, increasing the likelihood that their progeny inherit healthy mitochondria. Here, we provide an overview of mitochondrial quality control in the germ line, focusing on recent findings in mammals, Drosophila, and C. elegans. We discuss three strategies for quality control: elimination of sperm mtDNA, which prevents transmission of paternal mtDNA to progeny; the genetic bottleneck, which reduces the effective number of mtDNAs in germ cells, potentially exposing mutations to selection; and purifying selection, which selects for healthier mtDNAs. Finally, we discuss outstanding questions in the field and technical advances needed to address them.
    DOI:  https://doi.org/10.1016/j.gde.2025.102376
  41. Clin Genet. 2025 Jul 09.
      SLC25A42 encodes a mitochondrial carrier that is responsible for the import of CoA into mitochondria. Biallelic pathogenic variants in SLC25A42 have been associated with a recently described mitochondrial disorder characterized by encephalomyopathy with variable severity. To date, 24 affected individuals from 16 different families have been reported. Most are of Arab descent who harbor the founder variant in SLC25A42 (c.871A>G, p.Asn291Asp). In this report, we present 23 additional individuals from 19 unrelated families and their clinical, radiological, and molecular findings. We show again that SLC25A42-related mitochondrial disorder is associated with extremely variable severity. Some individuals with mild presentation may be unrecognized, while others are prone to metabolic decompensations with neuro-regression and irreversible neurological insult, making early diagnosis important.
    Keywords:  SLC25A42; autosomal recessive (AR) trait; consanguinity; lactic acidosis; mitochondria
    DOI:  https://doi.org/10.1111/cge.70021
  42. Am J Hum Genet. 2025 Jul 04. pii: S0002-9297(25)00243-5. [Epub ahead of print]
      Genomic medicine requires a robust evidence base of variant phenotypic impacts, which remains incomplete even in extensively studied genes with monogenic disease associations. Here, we evaluated the broad potential of using population cohort data to identify evidence that can be used in variant assessment. Across 41 genes related to 18 clinically actionable monogenic phenotypes, we calculated variant-level odds ratios of disease enrichment using data from 469,803 UK Biobank participants. We found significant differences in odds ratio values between ClinVar-labeled pathogenic and benign variants in 11 phenotypes, spanning both common and rare disorders. To facilitate clinical translation, we calibrated the strength of evidence provided by variant-level odds ratios to align with American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) interpretation guidelines (PS4 criterion) and found that odds ratios may reach "moderate," "strong," or "very strong" evidence, varying by phenotype and gene. Overall, we found that 2.6% (N = 12,350) of participants harbor a rare variant of uncertain significance (VUS) with at least moderate evidence of pathogenicity-an indication of potentially unrecognized disease risk. Finally, by incorporating computational and functional data alongside population-based odds ratios, we identified variants that met the criteria for clinical reclassification. Notably, using this approach, we identified that 12.4% of rare VUSs in LDLR seen in participants meet diagnostic criteria to be classified as likely pathogenic, demonstrating its potential to scale the reclassification of VUSs.
    Keywords:  ACMG/AMP sequence variant interpretation guidelines; PS4 evidence; UK Biobank; VUS; clinical variant classification; disease enrichment for rare coding variants; odds ratio; statistical genetics; variant interpretation; variant of uncertain significance
    DOI:  https://doi.org/10.1016/j.ajhg.2025.06.012
  43. Expert Rev Clin Pharmacol. 2025 Jul 09.
       INTRODUCTION: Long-chain fatty acid oxidation disorders (LC-FAODs) are rare inherited metabolic defects that present across the lifespan with skeletal, cardiac, and hepatic complications due to deficiency of energy production. Historically, medium-chain triglycerides (MCT) were used in their management of LC-FAODs, but individuals still developed symptoms due to depletion of tricarboxylic acid (TCA) cycle substrates.
    AREAS COVERED: This review covers the pathophysiology of LC-FAODs, highlighting the rationale for the use of triheptanoin (Dojolvi®), an MCT consisting of three 7-carbon fatty acids, in the nutritional management of LC-FAODs.
    EXPERT OPINION: Triheptanoin is an anaplerotic source of calories for treatment of LC-FAODs, providing a source of substrates to sustain the TCA cycle, gluconeogenesis, and energy production. Use of triheptanoin prior to its regulatory approval demonstrated significant clinical benefit. Clinical benefit was thereafter demonstrated in clinical trials, with a positive cardiac effect in a double-blinded, randomized controlled comparison to MCT, and improvement in major clinical events in open label extension studies. Side effects of triheptanoin are primarily GI intolerance similar to conventional MCT oil. Use prior to onset of symptoms in severe disease is recommended. Its use is not limited to LC-FAODs with active studies looking at its potential benefit in other conditions.
    Keywords:  Cardiomyopathy; Fatty acid oxidation; carnitine acylcarnitine transferase deficiency; carnitinepalmitoyltransferase 1 deficiency; carnitinepalmitoyltransferase 2 deficiency; fatty acid oxidation diorders; mitochondria trifunctional protein deficiency; recurrent rhabdomyolysis; trihepianoin; very long acyl-CoA dehydrogenase deficiency
    DOI:  https://doi.org/10.1080/17512433.2025.2528835
  44. Brain. 2025 Jul 07. pii: awaf182. [Epub ahead of print]
      Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the selective loss of motor neurons. Proteasome dysfunction in ALS is considered to cause the accumulation of protein aggregates, which leads to motor neuron degeneration; however, the resilience of motor neurons to ALS pathology might be impaired long before the appearance of protein aggregates. Intriguingly, sensory dorsal root ganglion (DRG) neurons are not susceptible to ALS pathology despite their processes coexisting with axons of motor neurons in the same spinal nerves. Both DRG neurons and motor neurons in ALS model mice express activating transcription factor 3 (ATF3), a well-known marker of nerve injury and disease progression, suggesting that both types of neurons respond to ALS pathology. However, it remains unknown why only DRG neurons are resilient to ALS pathological damage. To address this issue, we used a nerve injury model in combination with unique injury-induced genetically engineered mice, in which genetic control with an Atf3 regulatory element enables proteasome ablation and mitochondrial visualization specifically in damaged neurons. Using the strategy, we found that DRG neurons are resistant to damage in proteasome-deficient conditions, whereas spinal motor neurons degenerate in the same conditions. This might be because DRG neurons lack the typical axon initial segment (AIS), which normally exists in mature neurons and acts as a gate for the selective transport of cargo to axons. The absence of a typical AIS in DRG neurons facilitated increased entry of mitochondria into the axon upon injury, with or without proteasome function. In contrast, damaged motor neurons lacking the proteasome failed to disassemble the AIS, which prevented increased mitochondrial influx into axons and led to energy depletion and degeneration. In the absence of the AIS, DRG neurons in the ALS mouse model are able to deliver sufficient mitochondria into the axon to prevent pathological damage. However, impaired proteasome function in ALS motor neurons results in retention of the AIS gate and failure of mitochondrial transport to axons. This is a possible reason why DRG neurons have greater resilience to ALS pathological damage compared with spinal motor neurons. Collectively, this study opens new directions for the understanding of neurodegenerative diseases at early stages of disturbed protein homeostasis.
    Keywords:  Rpt3 (Pmsc4); amyotrophic lateral sclerosis; axonal transport; neurodegeneration; neuronal injury; proteostasis
    DOI:  https://doi.org/10.1093/brain/awaf182
  45. Proc Natl Acad Sci U S A. 2025 Jul 15. 122(28): e2509003122
      Glycogen is the largest energy reserve in the brain, but the specific role of glycogen in supporting neuronal energy metabolism in vivo is not well understood. We established a system in Caenorhabditis elegans to dynamically probe glycolytic states in single cells of living animals via the use of the glycolytic sensor HYlight and determined that neurons can dynamically regulate glycolysis in response to activity or transient hypoxia. We performed an RNAi screen and identified that PYGL-1, an ortholog of the human glycogen phosphorylase, is required in neurons for glycolytic plasticity. We determined that neurons employ at least two mechanisms of glycolytic plasticity: glycogen-dependent glycolytic plasticity (GDGP) and glycogen-independent glycolytic plasticity. We uncover that GDGP is employed under conditions of mitochondrial dysfunction, such as transient hypoxia or in mutants for mitochondrial function. We find that the loss of GDGP impairs glycolytic plasticity and is associated with defects in synaptic vesicle recycling during hypoxia. Together, our study reveals that, in vivo, neurons can directly use glycogen as a fuel source to sustain glycolytic plasticity and synaptic function.
    Keywords:  C. elegans; glycogen utilization; glycolytic biosensor; glycolytic plasticity; neuronal metabolism
    DOI:  https://doi.org/10.1073/pnas.2509003122
  46. Proc Natl Acad Sci U S A. 2025 Jul 15. 122(28): e2421886122
      Autophagic dysfunction is a hallmark of neurodegenerative disease, leaving neurons vulnerable to the accumulation of damaged organelles and aggregated proteins. However, the late onset of diseases suggests that compensatory quality control mechanisms may be engaged to delay these deleterious effects. Neurons expressing common familial Parkinson's disease-associated mutations in the leucine-rich repeat kinase 2 (LRRK2) exhibit defective autophagy. Here, we demonstrate that both primary murine neurons and human induced Pluripotent Stem Cells (iPSC)-derived neurons harboring pathogenic LRRK2 upregulate the secretion of extracellular vesicles. We used unbiased proteomics to characterize the secretome of LRRK2G2019S neurons and found that autophagic cargos including mitochondrial proteins were enriched. Based on these observations, we hypothesize that autophagosomes are rerouted toward secretion when cell-autonomous degradation is compromised to mediate clearance of undegraded cellular waste. Immunoblotting confirmed the release of autophagic cargos and live-cell imaging demonstrated that secretory autophagy is upregulated in LRRK2G2019S neurons. We also found that LRRK2G2019S neurons upregulate the release of exosomes containing microRNAs. Live-cell imaging confirmed that this upregulation of exosomal release is dependent on hyperactive LRRK2 activity, while pharmacological experiments indicate that this release staves off apoptosis. Finally, we show that markers of both vesicle populations are upregulated in plasma from mice expressing pathogenic LRRK2. In sum, we find that neurons expressing pathogenic LRRK2 upregulate secretory autophagy and the compensatory release of exosomes to mediate waste disposal and transcellular communication, respectively. We propose that this increased secretion contributes to the maintenance of cellular homeostasis, delaying neurodegenerative disease progression over the short term while potentially contributing to neuroinflammation over the longer term.
    Keywords:  Parkinson’s disease; autophagy; neurodegeneration; secretion
    DOI:  https://doi.org/10.1073/pnas.2421886122
  47. Cell Death Dis. 2025 Jul 07. 16(1): 499
      Mitochondrial defects are early pathological changes in neurodegenerative disease (ND). Homocysteine (Hcy) is an independent risk factor for ND. However, whether and how Hcy induces mitochondrial defects during the process of neurodegeneration is unclear. Here, we revealed that Hcy interfered with mitochondrial oxidative phosphorylation (OXPHOS) by inhibiting the mitochondrial electron transport chain (ETC) complex I, resulting in increased levels of reactive oxygen species (ROS) in the hippocampus of rats. Specifically, Hcy suppressed Ndufa1 expression, which is essential for complex I assembly and activation, by interfering with its transcription factor Creb1. Moreover, we found that Hcy induced neurodegeneration-like pathological changes in mitochondria in the brain via the inhibition of the NAD+/Sirt1 pathway, including defects in mitochondrial morphology, mitochondrial biogenesis, and mitophagy, ultimately leading to impairments in synapses and cognition, all of which were reversed by Ndufa1 upregulation. Thus, Ndufa1 is a key molecular switch of Hcy-induced mitochondrial damage, and appropriately targeting Ndufa1 or NAD+ replenishment may serve as a novel therapeutic strategy for Hcy-induced neurodegeneration and cognitive impairment.
    DOI:  https://doi.org/10.1038/s41419-025-07834-3
  48. J Cell Sci. 2025 Jul 01. pii: jcs263954. [Epub ahead of print]138(13):
      Functional residuomics explores how individual amino acid residues influence protein function, interactions and cellular homeostasis, shifting the focus from gene-level mutations to residue-level alterations. Unlike gene-centric approaches, residuomics systematically examines missense mutations across the proteome, linking small changes in amino acid sequences to organelle dynamics and tissue phenotypes. By integrating mutagenesis with high-throughput phenotyping, this approach connects atomic-scale changes to larger biological systems, offering valuable insights for clinical diagnostics and therapeutic development. Advances in saturation genome editing (SGE) and multiplexed assays of variant effect (MAVEs) show the potential of residuomics in addressing human genetic variation and improving precision medicine. Despite challenges in scalability and data interpretation, innovations in genetic tools, diploid models and machine learning are unlocking the full potential of residuomics in modern cell biology.
    Keywords:  Functional residuomics
    DOI:  https://doi.org/10.1242/jcs.263954
  49. Cell Calcium. 2025 Jul 03. pii: S0143-4160(25)00061-2. [Epub ahead of print]130 103052
      VDAC1, a large conductance channel in the outer mitochondrial membrane, plays a crucial role in mitochondrial physiology. VDAC1 supports cellular metabolism and survival by serving as a mitochondrial Ca2+-uptake and ATP-exit system. Conversely, VDAC1 also contributes to apoptosis by forming oligomeric pores mediating cytochrome c release. Recently, Oflaz et al., EMBO J, 2025, identified the Ca2+-binding protein Annexin A5 as a dynamic, Ca2+-dependent switch that enhances VDAC1's Ca2+-transport function while at the same time preventing pro-apoptotic VDAC1 oligomer formation.
    DOI:  https://doi.org/10.1016/j.ceca.2025.103052
  50. J Am Chem Soc. 2025 Jul 08.
      Dynamin-related protein (Drp1) drives mitochondrial fission, dysregulation of which leads to neurodegenerative, metabolic, and apoptotic disorders. The precise mechanism of fission completion is unclear. One prevailing model is based on GTP-driven assembly of Drp1 helices that increase confinement via force generation. However, constriction to nanoscopic tubule radii appears necessary but not sufficient for scission. The other is based on GTP-driven disassembly of a constricting Drp1 scaffold that drives a membrane disturbance, but the relation of disassembly to scission and GTP hydrolysis remain uncertain. Elucidation of mitochondrial fission is complicated by the multiple time-involved in the dynamics of mechanoenzyme activity, oligomer disassembly, and membrane remodeling. Using machine learning, synchrotron X-ray scattering, and a theoretical model, our data support a model where progressive GTP hydrolysis enables free Drp1s to increase their capacity for inducing membrane negative Gaussian curvature (NGC). Furthermore, we identify Drp1 variants that diminish this progressive capacity. Machine learning reveals that predicted NGC-generating sequences of the Drp1 oligomer are not in contact with the confined lipid tube and that scission-enhancing membrane remodeling is triggered by free Drp1 released upon disassembly.
    DOI:  https://doi.org/10.1021/jacs.4c15836
  51. Cell. 2025 Jul 03. pii: S0092-8674(25)00680-4. [Epub ahead of print]
      Protein engineering enables artificial protein evolution through iterative sequence changes, but current methods often suffer from low success rates and limited cost effectiveness. Here, we present AI-informed constraints for protein engineering (AiCE), an approach that facilitates efficient protein evolution using generic protein inverse folding models, reducing dependence on human heuristics and task-specific models. By sampling sequences from inverse folding models and integrating structural and evolutionary constraints, AiCE identifies high-fitness single and multi-mutations. We applied AiCE to eight protein engineering tasks, including deaminases, a nuclear localization sequence, nucleases, and a reverse transcriptase, spanning proteins from tens to thousands of residues, with success rates of 11%-88%. We also developed base editors for precision medicine and agriculture, including enABE8e (5-bp window), enSdd6-CBE (1.3-fold improved fidelity), and enDdd1-DdCBE (up to 14.3-fold enhanced mitochondrial activity). These results demonstrate that AiCE is a versatile, user-friendly mutation-design method that outperforms conventional approaches in efficiency, scalability, and generalizability.
    Keywords:  AiCE; base editor optimization; evolutionary coupling; genome editing; high-fitness mutations; inverse folding; protein evolution; structure-informed constraints
    DOI:  https://doi.org/10.1016/j.cell.2025.06.014
  52. J Transl Med. 2025 Jul 08. 23(1): 754
      Parkinson's disease (PD) is a neurodegenerative disease with severe movement problems. Current treatments mainly focus on symptom management by reducing dopaminergic pathways in the brain. Despite these therapies, ongoing disease progression undermines the effectiveness of prevalent approaches, necessitating exploring alternative methods anchored on genetic factors, notably the leucine-rich repeat kinase 2 (LRRK2) gene. Exploring LRRK2 gene pathogenesis has highlighted various mechanisms that may contribute to treating PD, including protein accumulation, altered cytoskeletal dynamics, neuro-inflammation, autophagy, and mitochondrial dysfunction. Based on the findings, there is an actual correlation between elevated levels of LRRK2 and the biomarkers and assays of PD. Furthermore, research results have suggested inhibiting LRRK2 as a therapeutic intervention targeting pathogenic mechanisms with varying degrees of efficacy. Our review wants to understand how LRRK2 works in the body and its relationship with the occurrence of PD by providing biochemical evidence, LRRK2 gene mutations and pathology, and the role of this gene in the immune system. We also discuss targeted therapies such as kinase inhibitors and Proteolysis targeting chimera and the application of using the LRRK2 protein to diagnose PD and develop bioassay designs. Finally, we mention the clinical trials conducted and the challenges and safety required.
    Keywords:  Autophagy; LRRK2; Mitochondrial dysfunction; Neuro-inflammation; Neurodegenerative diseases; PROTAC; Parkinson’s disease
    DOI:  https://doi.org/10.1186/s12967-025-06354-0
  53. Curr Med Chem. 2025 Jul 04.
      Mitochondria, the complex powerhouses of eukaryotic cells, lie at the core of energy production, metabolism, and signaling. Mitochondrial dysfunctions underlie a wide range of human diseases, and there is a need for simple and effective tools to target and study these organelles. This review focuses on the applications of mitochondria-targeted cationic probes. It provides an up-to-date review of recent publications investigating the effects of these cationic probes, which are designed to manipulate mitochondrial function and detect dysfunction in different cell lines. In addition, it analyzes the effects of mitochondria-targeted fluorescence cationic probes in vivo and in vitro studies, and their effects in probe studies.
    Keywords:  MMP; Mitochondria; ROS; cancer; cell death; fluorescent probe; pH.; viscosity
    DOI:  https://doi.org/10.2174/0109298673368188250613112621
  54. Nat Commun. 2025 Jul 10. 16(1): 6355
      Lipoic acid is an essential cofactor in five mitochondrial multiprotein complexes. In each complex, it is tethered in an amide linkage to the side chain of a conserved lysyl residue on a lipoyl carrier protein or lipoyl domain to afford the lipoyl cofactor. Lipoyl synthase catalyzes the last step in the biosynthesis of the lipoyl cofactor, the addition of two sulfur atoms to carbons 6 and 8 of an octanoyllysyl residue of the H protein, the lipoyl carrier protein of the glycine cleavage system. Lipoyl synthase, a member of the radical S-adenosylmethionine superfamily, contains two [Fe4S4] clusters, one of which is sacrificed during catalysis to supply the appended sulfur atoms. Herein, we use X-ray crystallography to characterize several stages in lipoyl synthase catalysis and present a structure of an intermediate wherein the enzyme is cross-linked to the H protein substrate through a 6-mercaptooctanoyl ligand to a [Fe3S4] cluster.
    DOI:  https://doi.org/10.1038/s41467-025-61393-x
  55. CNS Drugs. 2025 Jul 10.
      Since the publication of the first gene therapy clinical trial in Parkinson's disease (PD) in 2007, rapid advances have resulted in escalating interest in applying this technology to manipulate various cellular processes altered in PD. There is now a rich literature describing the various approaches taken, including modulating aberrant networks, restoring dopamine, and mitigating deleterious effects of known gene mutations or as a restorative therapy. Evidence has accrued supporting feasibility, safety, and tolerability of initial gene therapy approaches, as well as providing initial indications of efficacy in several cases. However, there have also been unexpected challenges, and technology is still evolving, making this an important time point to evaluate what has been learned and to place it in context to support ongoing and future efforts. In this review, we focus on the potential of gene therapy to ameliorate symptoms and modify disease progression in PD. We critically review previous clinical research, we address potential benefits and predicted limitations, and we address pipeline approaches aiming to bring a gene therapy approach to the clinic.
    DOI:  https://doi.org/10.1007/s40263-025-01203-6
  56. J Cell Sci. 2025 Jul 01. pii: jcs263638. [Epub ahead of print]138(13):
      DNA topoisomerases are essential for maintaining DNA topology, gene expression and the accurate transmission of genetic information. Mitochondria possess circular DNA (mtDNA), which, unlike nuclear chromosomes, lacks protective histones and exists in nucleoprotein complexes called nucleoids, which are vital for mtDNA stability. Although the mitochondrial genome encodes essential genes involved in ATP production via oxidative phosphorylation, it does not encode crucial mtDNA maintenance genes and depends entirely on nuclear-encoded proteins for mtDNA maintenance. These include nuclear-encoded topoisomerases (i.e. Top1mt, Top2α, Top2β and Top3α), which alleviate topological stress during mtDNA transcription and replication, and mitochondrial transcription factor A (TFAM), are crucial for ensuring proper nucleoid structure and mtDNA packaging. Furthermore, tyrosyl-DNA phosphodiesterase 1 and 2 (TDP1 and TDP2) participate in the repair of mtDNA damage associated with trapped topoisomerase-mtDNA complexes, which can compromise mtDNA integrity and contribute to neurodegeneration, cancer and premature aging. Drugs that stabilize these protein-DNA adducts (PDAs) to induce mtDNA damage and mitochondrial dysfunction are promising new strategies for cancer therapy. This Review explores the essential roles of mitochondrial topoisomerases, overviews mechanisms involved in mtDNA repair and discusses how mitochondrial fission and mitophagy are employed as a survival strategy for clearing damaged mtDNA.
    Keywords:  DNA repair; Mitochondria; Mitochondrial DNA; Neurological diseases; TDP1; TFAM; Topoisomerase 1
    DOI:  https://doi.org/10.1242/jcs.263638
  57. Sci Rep. 2025 Jul 08. 15(1): 24442
      Following a confirmed genetic diagnosis, rare disease patients and their families encounter significant challenges in accessing diagnostic information and support. Patients and non-specialists are increasingly expected to interpret and share test results; however, existing standards are primarily designed for specialists. These standards fail to address the needs of resource-limited populations where low genomic literacy hampers accurate dissemination of genetic results. This research introduces RareInsight, an open-source, interactive dashboard designed to enhance the accessibility, comprehension, and collaboration of genetic data among patients, caregivers, clinicians, and researchers. Developed using shinydashboard, RareInsight was evaluated using whole exome sequencing data from skeletal dysplasia patients. It allows users to input and view Variant Call Format files and includes a searchable ClinVar variant table with filtering options, providing access to multiple resources based on search terms. RareInsight aims to simplify the dissemination of complex genetic information beyond the clinical setting. This dashboard serves as a pilot study demonstrating the potential of patient-centered interactive dashboards for the rare disease community.
    Keywords:  Bioinformatics; Clinical dashboard; Genetic testing; Rare diseases; Shinydashboard
    DOI:  https://doi.org/10.1038/s41598-025-09744-y
  58. J Biosci. 2025 ;pii: 58. [Epub ahead of print]50
      In Saccharomyces cerevisiae, the iron-sulfur cluster biogenesis late-acting subsystem (Fe-S-IBG) comprises the mitochondrial glutaredoxin (Grx5), Isa1, Isa2, and iron-sulfur cluster assembly factor IBA57 (Iba57) proteins. The Fe-S-IBG subsystem assists in inserting [4Fe-4S] clusters into apoproteins, some of which belong to the electron transport chain (ETC). However, whether the Fe-S-IBG subsystem indirectly stabilizes respiratory supercomplexes and proper ETC function via insertion of [Fe-S] proteins into ETC complexes remains to be elucidated. We compared the effects of ISA2- and GRX5-independent mutations on the insertion of Rip1p, a [2Fe-2S]-containing protein involved in both electron transfer in the bc1 complex and the formation of respiratory supercomplexes. The levels of Rip1p, supercomplex assembly, ETC function, oxidative stress, and resistance of yeast to ethanol stress were evaluated on haploid S. cerevisiae cells with independent mutations of the ISA2 and GRX5 genes. Susceptibility to ethanol was increased in the isa2Δ and grx5Δ mutants, which was associated with enhanced glutathione oxidation due to higher levels of free iron and increased oxidants. Furthermore, the isa2Δ mutant showed decreased Rip1p expression, respiratory dysfunction, and defective respiratory supercomplex formation, which was restored by ISA2 complementation. These results suggest that Isa2p is essential for proper respiratory chain function and resistance to oxidative stress by stabilizing supercomplexes in a manner dependent on Rip1p insertion in the cytochrome bc1 complex.
  59. Bioinform Adv. 2025 ;5(1): vbaf106
      Summary: Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective, we discuss recent computational progress and challenges toward solving this fundamental problem. We describe how cis-regulatory elements are mapped with various genomics assays and how studies of the 3D chromatin organization could help identifying long-range regulatory effects. We discuss how the cis-regulatory sequence rules can be learned and interpreted with sequence-to-function neural networks, with the goal of identifying genetic variants in human disease. We also describe current methods for mapping gene regulatory networks to describe biological processes. We point out current gaps in knowledge along with technical limitations and benchmarking challenges of computational methods. Finally, we discuss newly emerging technologies, such as spatial transcriptomics, and outline strategies for creating a more general model of the cis-regulatory code that is more broadly applicable across cell types and individuals.
    DOI:  https://doi.org/10.1093/bioadv/vbaf106
  60. Mol Metab. 2025 Jul 08. pii: S2212-8778(25)00111-5. [Epub ahead of print] 102204
       OBJECTIVE: Mitochondrial uncouplers are used as chemical tools to study mitochondrial function in vitro and in vivo, and some molecules are in development for the treatment of metabolic diseases. One problem in the field is that any molecule that increases proton transport into the mitochondrial matrix independent of ATP production can be classified as an uncoupler regardless of off-target activities. Therefore, there are dozens of classes of molecules that exhibit a wide spectrum of phenotypes. Herein we directly compared 15 mitochondrial uncouplers side-by-side in a well-defined cell system to better understand their in vitro dose response profiles and the top molecules with suitable pharmacology and safety profiles were compared in db/db mice.
    METHODS: Fifteen mitochondrial uncouplers were characterised in vitro in CHO-K1 cells. The top five candidates were selected for further characterisation in male db/db mice based on their in vitro dose tolerance and / or tolerability. We tested two doses of each mitochondrial uncoupler in mice and benchmarked their efficacy to a lifestyle intervention of 35% calorie restriction as well as to lean db/+ metabolically healthy mice. Eleven groups of mice were fed either; 1) ad libitum - chow (control), 2) chow with 0.15% BAM15 (w/w), 3) chow with 0.2% BAM15 (w/w), 4) chow with 0.1% NEN (w/w), 5) chow with 0.25% NEN (w/w), 6) chow with 0.01% OPC-163493 (w/w), 7) chow with 0.02% OPC-63493 (w/w), 8) chow with 0.015% ES9 (w/w), 9) chow with 0.03% ES9 (w/w), 10) chow with 0.2% NTZ (w/w), and 11) chow with 0.4% NTZ (w/w). Another group of mice was fed chow to receive ∼65% of the average daily food intake of control mice as a model of calorie restriction (CR). Mice were metabolically phenotyped over 4 weeks of treatment with assessment of key readouts including body weight, HbA1c, blood glucose and glucose tolerance tests. At termination, key tissues were collected and plasma was analysed for markers of toxicity.
    RESULTS: Few mitochondrial uncouplers behaved similarly in vitro, with 11 molecules impairing maximal mitochondrial capacity. In vivo, BAM15 dose-dependently improved body weight and metabolic parameters in db/db mice, with 0.2% BAM15 treatment yielding statistically significant improvements in body weight, fat pad weight, glucose tolerance, blood glucose, HbA1c, liver weight and triglyceride content. The next-best treatment was 0.03% ES9 which significantly improved glucose tolerance, blood glucose levels, and HbA1c, but increased body weight, liver size and steatosis relative to db/db controls.
    CONCLUSIONS: Mitochondrial uncouplers BAM15 and ES9 had the greatest dose tolerance range in vitro, while BAM15 had the best overall effects on body weight, glucose control and liver steatosis in db/db mice. This study reveals diverse phenotypes across 15 classes of mitochondrial uncouplers and underscores the need for rigorous evaluation to identify molecules that drive stable mitochondrial respiration without unwanted mitochondrial inhibition or off-target effects. Ultimately, mitochondrial uncouplers should not be generalized and each uncoupler molecule needs to be considered by its own actions in well-defined experimental conditions.
    Keywords:  Mitochondrial uncoupling; diabetes; metabolic disease; obesity
    DOI:  https://doi.org/10.1016/j.molmet.2025.102204
  61. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2025 Mar 28. pii: 1672-7347(2025)03-0511-06. [Epub ahead of print]50(3): 511-516
      Mitochondrial encephalomyopathy is a multisystemic metabolic disorder caused by mutations in mitochondrial or nuclear genes. It commonly presents with stroke-like episodes or myopathy as initial symptoms. This paper reports a young male patient with mitochondrial encephalomyopathy whose early and prominent clinical manifestation was refractory shock, without typical neurological symptoms. The patient initially presented with abdominal pain and lower limb weakness, followed by severe hypotension requiring high-dose vasopressors to maintain blood pressure. His lactate level peaked at 20 mmol/L. After 10 days of symptomatic and supportive treatment, his hypotension resolved; lactate levels returned to normal by day 22. One month later, he still had difficulty weaning from mechanical ventilation and exhibited persistent limb weakness. Genetic testing of the biceps brachii revealed an m.3271T>C mutation in the mitochondrial tRNA gene. Mitochondrial encephalomyopathy may initially present with severe circulatory dysfunction. In patients with lactic acidosis not related to hypoperfusion, mitochondrial disease should be considered, and genetic testing of muscle or other peripheral tissues may improve diagnostic yield.
    Keywords:  abdominal pain; hyperlactacidemia; mitochondrial encephalomyopathy; myasthenia; refractory shock
    DOI:  https://doi.org/10.11817/j.issn.1672-7347.2025.240250
  62. Nat Commun. 2025 Jul 07. 16(1): 6230
      Cells compartmentalize biomolecules in membraneless structures called biomolecular condensates. While their roles in regulating cellular processes are increasingly understood, tools for their synthetic manipulation remain limited. Here, we introduce RELISR (Reversible Light-Induced Store and Release), an optogenetic condensate system that enables reversible storage and release of proteins or mRNAs. RELISR integrates multivalent scaffolds, optogenetic switches, and cargo-binding domains to trap cargo in the dark and release it upon blue-light exposure. We demonstrate its utility in primary neurons and show that light-triggered release of signaling proteins can modulate fibroblast morphology. Furthermore, light-induced release of cargo mRNA results in protein translation both in vitro and in live mice. RELISR thus provides a versatile platform for spatiotemporal control of protein activity and mRNA translation in complex biological systems, with broad potential for research and therapeutic applications.
    DOI:  https://doi.org/10.1038/s41467-025-61322-y
  63. Biochim Biophys Acta Mol Cell Res. 2025 Jul 07. pii: S0167-4889(25)00124-7. [Epub ahead of print] 120019
      Autophagy is a highly conserved cellular catabolic process recognized as an essential pathway for the maintenance of cellular homeostasis. Growing evidence implicates autophagic dysfunction in the pathogenesis of several neurodegenerative disorders, including Alzheimer's disease (AD), thus its modulation might represent an interesting therapeutic tool. Searching for a compound that stimulates autophagic pathway, led us to identify the inhibitor of RPSA receptor, NSC47924. In this study, we show that, NSC47924 down-modulated Akt-mTOR-axis pathway, the master regulator of autophagy, which was abnormally hyperactivated in fibroblasts from genetic AD-affected patients. Consistently, by monitoring the conversion of LC3, we found that inhibition of RPSA enhanced and restored the compromised autophagic flux. Moreover, by qRT-PCR analysis we found that inhibitor treatment upregulated the expression of autophagy-linked genes. Importantly, AD-affected fibroblasts exhibited massive mitochondrial network fragmentation and mitophagy defects, which were restored through the stimulation of autophagy induced by RPSA inhibition. Consistent with an efficient elimination of dysfunctional mitochondria, we found that the turnover of both the mitophagy regulators PINK1 and Parkin and the autophagic receptors p62, NDP52, OPTN, was modulated, thus restoring a highly interconnected organelle's network. In addition, the improvement of mitochondrial morphology correlated with a functional recovery, as assessed by Seahorse analysis and mitochondrial ROS production evaluation. Collectively, our findings suggest that RPSA inhibition stimulates an autophagic pathway promoting the efficient removal of damaged mitochondria, favouring the recovery of cellular homeostasis, and counteracting crucial AD pathogenic mechanisms.
    Keywords:  37/67 kDa non-integrin laminin receptor; APP V717I mutant; Alzheimer's disease; Autophagy; Mitophagy; PS1 M146L mutant; RPSA
    DOI:  https://doi.org/10.1016/j.bbamcr.2025.120019
  64. bioRxiv. 2025 Jul 04. pii: 2025.06.30.662363. [Epub ahead of print]
      Alpha kinase 1 (ALPK1) is a cytosolic sensor of microbial sugar metabolites that activates NF-κB signaling through phosphorylation of the adaptor protein TIFA. Although canonically linked to NF-κB, individuals with gain-of-function ALPK1 mutations also show features of interferon-driven inflammation. Here, we show that ALPK1 activation enhances multiple outputs of the stimulator of interferon genes (STING) pathway, including both canonical and noncanonical responses such as STING proton channel-dependent LC3B lipidation and NLRP3 inflammasome activation. Furthermore, ALPK1 signaling activates eIF2α, an effector of the integrated stress response. Conversely, STING activation increases ALPK1 protein expression and triggers TIFA-Threonine 9 phosphorylation. Clinically, individuals with ALPK1-mediated disease exhibit premature intracranial mineralization and elevated cerebrospinal fluid neopterin, both associated with dysregulated interferon signaling. These findings support a model of bidirectional signaling between ALPK1 and STING, in which microbial and nucleic acid sensing pathways can amplify one another. This crosstalk provides a mechanistic framework for understanding innate immune signaling relevant to both homeostasis and disease.
    DOI:  https://doi.org/10.1101/2025.06.30.662363
  65. Redox Biol. 2025 Jun 28. pii: S2213-2317(25)00258-7. [Epub ahead of print]85 103745
      Increasing evidence has implicated the important role of mitochondrial morphofunctional defects in pathological myocardial hypertrophy and heart failure. Deubiquitinating enzymes (DUBs) are involved in protein stability maintenance and regulate multiple cellular processes, while it remains largely unclear whether DUBs participate in the maintenance of mitochondrial morphofunction. The aim of this study was to investigate the possible link between DUBs and abnormal mitochondrial morphofunction in pressure overload-induced pathological cardiac hypertrophy and explore the underlying molecular mechanism. RNA sequencing results showed that ubiquitin-mediated proteolysis was markedly enriched in pressure overload-induced hypertrophied and failing myocardium, and USP10 was identified as the most significantly downregulated gene among them and correlated with heart failure severity in human heart samples. Restoration of USP10 mitigates cardiac hypertrophy and dysfunction as well as abnormal mitochondrial morphofunction in vitro and in vivo. Immunoprecipitation and mass spectrometry analysis mechanistically revealed that USP10 directly interacted with Mfn2 (a mitochondrial outer membrane protein). Interestingly, the interaction between Mfn2 and USP10 occurred in cytoplasm but not on mitochondria. His-679 in the UCH domain of USP10 exerted deubiquitination to maintain the stability of the Mfn2 by removing the K11/K48 ubiquitin chain and preventing proteasomal pathway degradation, thereby maintaining mitochondrial function and homeostasis. Knockdown or knockout of Mfn2 largely eliminated the cardioprotection of USP10. Additionally, reduced USP10 expression in hypertrophied myocardium was induced by impaired translation of Yy1. Together, our findings provide a USP10-modulated mitochondrial homeostasis mechanism that enhances the stability of cytoplasmic Mfn2 before its translocation to mitochondria. USP10 may represent a novel therapeutic target for combating pressure overstress-induced cardiac hypertrophy and heart failure.
    Keywords:  Heart failure; Mfn2; Mitochondrial morphofunction; Pathological cardiac hypertrophy; USP10
    DOI:  https://doi.org/10.1016/j.redox.2025.103745