bims-mitdis 2025-06-08 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2025–06–08
37 papers selected by
Catalina Vasilescu, Helmholz Munich

Biallelic NSUN3 Variants Cause Diverse Phenotypic Spectrum Disease: From Isolated Optic Atrophy to Severe Early-Onset Mitochondrial Disorder.
Base editors model mitochondrial disease.
Mitochondrial tRNA processing defects reprogram mitochondrial and cellular homeostasis.
Powering new therapeutics with precision mitochondrial editing.
Cellular metabolic state controls mitochondrial RNA kinetics.
Evaluating the feasibility of gene replacement strategies to treat MTRFR deficiency.
ROMO1 overexpression protects the mitochondrial cysteinome from oxidations in aging.
Tissue-Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency.
Cross-comparison of strains used for mitochondrial imaging in Caenorhabditis elegans during aging.
The low endoribonuclease activity and lack of rNMP preference of human mitochondrial topoisomerase 1 protect against ribonucleotide-dependent deletions.
Qualitative study of fatigue in adults with primary mitochondrial disease: Development of the PROMIS Fatigue Mitochondrial Disease Short Form.
Impaired Complex I dysregulates neural/glial precursors and corpus callosum development revealing postnatal defects in Leigh Syndrome mice.
Parkin-dependent ubiquitination of TAX1BP1 directs efficient autophagic removal of defective mitochondria.
Understanding the impact of mitochondrial DNA mutations on aging and carcinogenesis (Review).
The Role of Metabolic Testing in the Diagnostic Evaluation of Adult NORSE: A Retrospective, Single-Centre Study.
Reduced DJ-1-F1Fo ATP synthase association correlates with midbrain dopaminergic neuron vulnerability in idiopathic Parkinson's disease.
Role of mitochondrial quality control in neurodegenerative disease progression.
Ndufs4-/- mice: a testing ground for longevity interventions.
The antibacterial factor APOL3 couples lysosomal damage to mitochondrial DNA efflux and type I IFN induction.
A cold-inducible phospholipid-protein interaction in brown fat mitochondria optimizes thermogenic capacity.
Glucose restriction induces degeneration of neurons with mitochondrial DNA depletion by altering ER-mitochondria calcium transfer.
Apoptosis-inducing factor (AIF) at the crossroad of cell survival and cell death: implications for cancer and mitochondrial diseases.
Investigating the sources of variable impact of pathogenic variants in monogenic metabolic conditions.
har-1/CHCHD10 mutations induce neurodegeneration and mitochondrial fragmentation in Caenorhabditis elegans.
Success of Coenzyme Q10 in Treating Steroid-Resistant Nephrotic Syndrome in Jordan: A Case Series.
Mitochondrial Calcium Uniporter is Required for Thermogenic Adaptation Mediated by Reactive Oxygen Species Signaling.
Functional analysis of pathological mutations in DNA topoisomerase 3A.
SARM1 activation induces reversible mitochondrial dysfunction and can be prevented in human neurons by antisense oligonucleotides.
The developing retina undergoes mitochondrial remodeling via PINK1/PRKN-dependent mitophagy.
mTOR inhibition triggers mitochondrial fragmentation in cardiomyocytes through proteosome-dependent prohibitin degradation and OPA-1 cleavage.
Stem cell therapies advance in Parkinson's disease and beyond.
Bi-allelic variants in TM2D3 cause a severe syndromic neurodevelopmental disorder associated with endoplasmic reticulum and mitochondrial abnormalities.
Precision multiplexed base editing in human cells using Cas12a-derived base editors.
A mitochondrial disease model is generated and corrected using engineered base editors in rat zygotes.
Programmable RNA acetylation with CRISPR-Cas13.
An AI-assisted fluorescence microscopic system for screening mitophagy inducers by simultaneous analysis of mitophagic intermediates.
Type II kinase inhibitors that target Parkinson's disease-associated LRRK2.

Invest Ophthalmol Vis Sci. 2025 Jun 02. 66(6): 17

Biallelic NSUN3 Variants Cause Diverse Phenotypic Spectrum Disease: From Isolated Optic Atrophy to Severe Early-Onset Mitochondrial Disorder.

Neringa Jurkute, Heiko Brennenstuhl, Monika Kustermann, Lindsey Van Haute, Christian D Mutti, Enrico Bugiardini, Takayuki Handa, Masaru Shimura, Axel Petzold, James Acheson, Anthony G Robson, William L Macken, Michael G Hanna, Robert D S Pitceathly, Ashirwad Merve, Urania Kotzaeridou, Stefan Kölker, Michael Freilinger, Marcus Erdler, Reginald E Bittner, Johannes A Mayr, Yasushi Okazaki, Kei Murayama, Holger Prokisch, Andrew R Webster, Michal Minczuk, Gavin Arno, Berthold Pemp, Georg F Hoffmann, Wolfgang M Schmidt, Patrick Yu-Wai-Man.

Purpose: Primary mitochondrial disorders (PMDs) are a clinically heterogeneous group of genetic disorders that can affect many tissues, with a broad phenotypic spectrum ranging from isolated organ involvement to severe early-onset multisystem disease. Visual loss from optic atrophy is a frequent clinical manifestation of mitochondrial cytopathies. This study aimed to identify the missing heritability in previously unsolved cases of suspected isolated or syndromic optic neuropathy. Based on three recent reports on biallelic NSUN3 variants causing early-onset PMD, we explored in detail the genetic and clinical spectrum of NSUN3-associated disease.
Methods: Affected individuals were analyzed by exome or genome sequencing. In silico variant analysis and functional assays were performed to investigate the consequences of the identified variants. Detailed phenotyping data were collected from medical records and direct questioning after the identification of candidate-likely pathogenic variants.
Results: Interrogation of exome and genome sequencing data led to the identification of six candidate NSUN3 variants in eight affected individuals from five unrelated families (including a previously reported case). A broad phenotypic spectrum was observed ranging from isolated optic atrophy to severe early-onset PMD. Identified NSUN3 variants impairing NSUN3 activity are located within the S-adenosylmethionine-dependent methyltransferases domain and loss of function variants were associated with a more severe phenotype. Remarkably, bilateral optic atrophy was a unifying clinical feature observed in almost all affected individuals.
Conclusions: Pathogenic or likely pathogenic biallelic variants in NSUN3 disrupt mt-tRNAMet methylation and mitochondrial translation leading to mitochondrial disease ranging from mild isolated optic atrophy to a severe multisystemic phenotype with possible limited life expectancy.

DOI: https://doi.org/10.1167/iovs.66.6.17
Nat Biotechnol. 2025 Jun 03.

Base editors model mitochondrial disease.

Patrick Buchholz, Jens Boch.

DOI: https://doi.org/10.1038/s41587-025-02706-9
J Biol Chem. 2025 Jun 03. pii: S0021-9258(25)02184-2. [Epub ahead of print] 110334

Mitochondrial tRNA processing defects reprogram mitochondrial and cellular homeostasis.

Gao Zhu, Yunfan He, Xincheng Li, Yun Xiao, Huisen Zhan, Maoli Duan, Min-Xin Guan.

Mitochondrial tRNA processing defects have been associated with some clinical presentations including deafness. Especially, a deafness-linked m.7516delA mutation impaired the 5' end processing of RNA precursors and mitochondrial translation. In this study, we investigated the mechanism by m.7516delA mutation induced-deficiencies mitigate organellular and cellular integrity. The m.7516delA mutation downregulated the expression of nucleus encoding subunits and upregulated assemble factors of complex IV and altered the assembly and activities of oxidative phosphorylation (OXPHOS) complexes. The impairment of OXPHOS alleviated mitochondrial quality control processes, including the imbalanced mitochondrial dynamics via increasing fission with abnormal mitochondrial morphology. The m.7516delA mutation upregulated both ubiquitin-dependent and independent mitophagy pathways, evidenced by increasing levels of Parkin, BNIP3, NIX and MFN2-ubiquitination and altering interaction between MFN2 and MUL1 or Parkin, to facilitate the degradation of severely damaged mitochondria. Strikingly, the m.7516delA mutation activated integrated stress response (ISR) pathway, evidenced by upregulation of GCN2, P-GCN2, p-eIF2α, CHOP, ATF4 and elevating the nucleus-location of ATF5 to minimizes the damages in defective mitochondria. Both activation of ISR and PINK1/Parkin mitophagy pathways ameliorate the cell homeostasis via elevating the autophagy process and upregulating apoptotic pathways. Our findings provide new insights into underlying aberrant RNA processing-induced dysfunctions reprogrammed organelles and cellular integrity.

DOI: https://doi.org/10.1016/j.jbc.2025.110334
Nat Biotechnol. 2025 Jun 03.

Powering new therapeutics with precision mitochondrial editing.

DOI: https://doi.org/10.1038/s41587-025-02693-x
bioRxiv. 2025 May 27. pii: 2025.05.13.653903. [Epub ahead of print]

Cellular metabolic state controls mitochondrial RNA kinetics.

Sean D Reardon, Clarisa Bautista, Shannon C Cole, Julien Cicero, Tatiana V Mishanina.

Human mitochondrial genome encodes essential genes for the oxidative phosphorylation (OXPHOS) complexes. These genes must be transcribed and translated in coordination with nuclear-encoded OXPHOS components to ensure correct stoichiometry during OXPHOS complex assembly in the mitochondria. While much is known about nuclear gene regulation during metabolic stresses like glucose deprivation, little is known about the accompanying transcriptional response in mitochondria. Using microscopy, roadblocking qPCR, and transcriptomics, we studied mitochondrial transcription in cells subjected to glucose deprivation, which is known to cause nuclear transcription downregulation and to activate the integrated stress response (ISR). We found that glucose deprivation stabilizes mitochondrial RNAs and slows mitochondrial transcription, effects that are quickly reversed with glucose reintroduction. Although transcriptomics revealed strong upregulation of the ISR, mitochondrial RNA stabilization was not upregulated by pharmacological activation of the ISR, but was promoted by inhibition of glycolysis, unveiling a direct connection between metabolism and regulation of mitochondrial gene expression.

DOI: https://doi.org/10.1101/2025.05.13.653903
Dis Model Mech. 2025 May 01. pii: dmm052120. [Epub ahead of print]18(5):

Evaluating the feasibility of gene replacement strategies to treat MTRFR deficiency.

Samia L Pratt, Mariana Zarate-Mendez, Lidiia Koludarova, Sonja Jansson, Mikko Airavaara, Irena Hlushchuk, David Coleman, Caleb Heffner, Rita Horvath, Brendan J Battersby, Robert W Burgess.

  Mitochondrial translation release factor in rescue (MTRFR) catalyzes a termination step in protein synthesis, facilitating release of the nascent chain from mitoribosomes. Pathogenic variants in MTRFR cause MTRFR deficiency and are loss-of-function variants. Here, we tested gene replacement as a possible therapeutic strategy. A truncating mutation (K155*) was generated in mice; however, homozygotes die embryonically whereas mice heterozygous for this K155* allele are normal. We also generated transgenic strains expressing either wild-type human MTRFR or a partially functional MTRFR. Despite dose-dependent phenotypes from overexpression in vitro, neither transgene caused adverse effects in vivo. In K155* homozygous mice, the wild-type MTRFR transgene completely rescued the phenotype with only one copy present, whereas the mutant transgene rescued less efficiently. Detailed evaluation of mice rescued with the wild-type MTRFR transgene revealed no abnormalities. In human induced pluripotent stem cell (hiPSC)-derived knockdown neurons, mitochondrial phenotypes were corrected by AAV9-mediated delivery of MTRFR. Thus, we find no toxicity from truncated gene products or overexpression of MTRFR in vivo, and expression of MTRFR corrects phenotypes in both mouse and hiPSC models.

Keywords:   C12ORF65 ; Behr's syndrome; CMT6; Leigh syndrome; MRPL58; Mitochondrial translation

DOI:  https://doi.org/10.1242/dmm.052120
Nat Commun. 2025 Jun 03. 16(1): 5133

ROMO1 overexpression protects the mitochondrial cysteinome from oxidations in aging.

Fengli Xu, Haipeng Huang, Kun Peng, Chongshu Jian, Hao Wu, Zhiwen Jing, Shan Qiu, Ying Chen, Keke Liu, Ling Fu, Yanru Wang, Jing Yang, Xiaotao Duan, Chu Wang, Heping Cheng, Xianhua Wang.

Reactive thiols of proteinaceous cysteines are vital to cell biology by serving as sensor, effector and buffer of environmental redox fluctuations. Being the major source, as well as the prime target, of reactive oxygen species (ROS), mitochondria confront great challenges in preserving their thiol pool. Here we show that ROS modulator 1 (ROMO1), a small inner mitochondrial membrane protein, plays a role in protecting the mitochondrial cysteinome. ROMO1 is redox sensitive and reactive and overexpression can prevent deleterious oxidation of proteinaceous thiols. ROMO1 upregulation leads to a reductive shift of the mitochondrial cysteinome, exerting beneficial effects on mitochondria, such as promoting energy metabolism and Ca2+ uniport while inhibiting vicious membrane permeability transition. Importantly, ROMO1 overexpression reverses mitochondrial cysteinome oxidations in multiple organs and slows functional decline in aged male mice. These findings unravel a redox regulatory mechanism of the mitochondrial cysteinome and mark ROMO1 as a potential target for combating oxidative stress and improving healthspan.

DOI: https://doi.org/10.1038/s41467-025-60503-z
Proteomics. 2025 Jun 01. e13969

Tissue-Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency.

Sibonelo Glen Khumalo, Jeremie Zander Lindeque, Marianne Venter.

  Isolated complex I deficiency (ICD) is commonly associated with mitochondrial diseases and closely mimics subacute necrotising encephalomyelopathy. This disorder is characterised by metabolic perturbations that affect energy metabolism pathways, including fatty acid metabolism. Here, we examined the tissue-specific changes in fatty acid metabolism in the Ndufs4 KO mice by employing mass-spectrometry-based proteomics as a hypothesis-generating approach. We investigated proteomic changes in six tissues, including brain regions (brainstem, cerebellum, olfactory bulb), heart, kidney and liver, focusing on proteins involved in fatty acid metabolism. Although it is expected that most tissues, except for the brain, will utilise fatty acids as alternative energy sources when oxidative phosphorylation (OXPHOS) is deficient, our data revealed a more complex response. In the liver, fatty acid consumption (oxidation) was favoured as expected, but in the heart, fatty acid synthesis was favoured. In the kidney, proteins involved in almost all fatty acid metabolic processes (oxidation and synthesis) were downregulated. Our data demonstrate that metabolic adaptations in fatty acid metabolism to ICD were tissue-specific and often in opposing directions. Understanding the differential adaptations across tissues could inform future treatment targets for mitochondrial disorders.

Keywords:  NDUFS4 knock out; complex I deficiency; fatty acid metabolism; proteomics

DOI:  https://doi.org/10.1002/pmic.13969
Life Sci Alliance. 2025 Aug;pii: e202403189. [Epub ahead of print]8(8):

Cross-comparison of strains used for mitochondrial imaging in Caenorhabditis elegans during aging.

Juri Kim, Naibedya Dutta, Matthew Vega, Andrew Bong, Maxim Averbukh, Rebecca Aviles Barahona, Athena Alcala, Jacob T Holmes, Gilberto Garcia, Ryo Higuchi-Sanabria.

Measurements of mitochondrial morphology are a powerful proxy for assessing mitochondrial health, particularly during aging when organelle dynamics are disrupted. Caenorhabditis elegans provides an ideal system for in vivo mitochondrial imaging, but widely used high-copy transgenic strains can induce artifacts that confound interpretation because of their impact on cellular and organismal health and physiology. Here, we present and validate a suite of C. elegans strains expressing single-copy, matrix-localized GFP in the muscle, intestine, and hypodermis using the MosSCI technology. These strains enable robust, tissue-specific visualization of mitochondrial morphology without the caveats associated with multi-copy reporters. We benchmark their performance against existing models and demonstrate that our mitochondrial reporters are similarly capable of assessing age-associated mitochondrial morphology, while avoiding defects in cellular and physiological health associated with the multi-copy reporters. Furthermore, we assess how aging methods, bacterial diets, and inhibition of fusion and fission machinery impact mitochondrial morphology during aging. Our findings provide a standardized and physiologically relevant platform for studying mitochondrial dynamics during aging in C. elegans.

DOI: https://doi.org/10.26508/lsa.202403189
Nucleic Acids Res. 2025 Jun 06. pii: gkaf475. [Epub ahead of print]53(11):

The low endoribonuclease activity and lack of rNMP preference of human mitochondrial topoisomerase 1 protect against ribonucleotide-dependent deletions.

Cyrielle P J Bader, Erika Miyazaki-Kasho, Josefin M E Forslund, Aiswarya Dash, Malgorzata Wessels, Paulina H Wanrooij.

The incorporation of ribonucleotides (rNMPs) into the nuclear genome leads to severe genomic instability, including strand breaks and short 2-5 bp deletions at repetitive sequences. Curiously, the detrimental effects of rNMPs are not observed for the human mitochondrial genome (mtDNA) that typically contains several rNMPs per molecule. Given that the nuclear genome instability phenotype is dependent on the activity of the nuclear topoisomerase 1 enzyme (hTOP1), and mammalian mitochondria contain a distinct topoisomerase 1 paralog (hTOP1MT), we hypothesized that the differential effects of rNMPs on the two genomes may reflect divergent properties of the two cellular topoisomerase 1 enzymes. Here, we characterized the endoribonuclease activity of hTOP1MT and found it to be less efficient than that of its nuclear counterpart, a finding that was partly explained by its weaker affinity for its DNA substrate. Moreover, while hTOP1 and yeast TOP1 were able to cleave at an rNMP located even outside of the consensus cleavage site, hTOP1MT showed no such preference for rNMPs. As a consequence, hTOP1MT was inefficient at producing the short rNMP-dependent deletions that are characteristic of TOP1-driven genome instability. These findings help explain the tolerance of rNMPs in the mitochondrial genome.

DOI: https://doi.org/10.1093/nar/gkaf475
Mol Genet Metab. 2025 May 26. pii: S1096-7192(25)00144-1. [Epub ahead of print]145(4): 109153

Qualitative study of fatigue in adults with primary mitochondrial disease: Development of the PROMIS Fatigue Mitochondrial Disease Short Form.

Sarah Clifford, Renae J Stefanetti, Roxana Bahar, Magnus J Hansson, Gráinne S Gorman, Amel Karaa.

   BACKGROUND: Fatigue is a debilitating symptom in patients with primary mitochondrial disease nPMD). Developing new treatments that improve fatigue is a patient priority but is hampered by a lack of fit-for-purpose patient-reported outcome measures (PROMs). We aimed to understand the impact of fatigue on the lives of people with PMD and develop a brief PMD-specific PROM to evaluate fatigue in clinical trials.
METHODS: Adults with genetically confirmed PMD and self-reported moderate-to-severe fatigue and myopathy/exercise intolerance participated in a concept elicitation interview to explore their experiences of fatigue. Interview transcripts were coded thematically using MAXQDA™. Characteristics and impacts that emerged from the interviews were mapped to items in the PROMIS® Fatigue item bank. Participants then engaged in a cognitive interview to assess relevance and understandability of PROMIS Fatigue items considered for the PROM.
RESULTS: Twelve adults with PMD (n = 8 women, age 20-75 years) were interviewed. The most frequently reported characteristics of fatigue included tiredness, muscle weakness/fatigue, exhaustion, lack of energy, and mental fatigue. Fatigue affected patients' ability to perform daily life activities, including household chores, leisure activities, physical activity/exercise, and work/school, and negatively affected mood and relationships. Nine items were included in the final PROM based on level of endorsement of underlying concepts elicited by the concept elicitation interviews and relevance, clarity, and ease of answering, as assessed in the cognitive interviews.
CONCLUSION: The nine-item PROMIS Fatigue Mitochondrial Disease Short Form is the first PROM designed specifically to assess fatigue in PMD. This study demonstrates the content validity of the short form, and future longitudinal studies will assess its psychometric properties.

Keywords:  Fatigue; Mitochondrial disease; Patient-reported outcome; Questionnaire validation

DOI:  https://doi.org/10.1016/j.ymgme.2025.109153
bioRxiv. 2025 May 16. pii: 2025.05.16.654318. [Epub ahead of print]

Impaired Complex I dysregulates neural/glial precursors and corpus callosum development revealing postnatal defects in Leigh Syndrome mice.

Sahitya Ranjan Biswas, Porter L Tomsick, Colin Kelly, Brooke A Lester, Julia P Milner, Sara N Henry, Yaris Soto, Samantha Brindley, Nicole DeFoor, Paul D Morton, Alicia M Pickrell.

Leigh syndrome (LS) is a complex, genetic mitochondrial disorder defined by neurodegenerative phenotypes with pediatric manifestation. However, recent clinical studies report behavioral phenotypes in human LS patients that are more reminiscent of neurodevelopmental delays. To determine if disruptions in epochs of rapid brain growth during infancy precede the hallmark brain lesions that arise during childhood, we evaluated neural and glial precursor cellular dynamics in a mouse model of LS. Single cell RNA sequencing along with histological and anatomical assessments were performed in NDUFS4 KO mice and compared with controls to determine the impact of Complex I deficiency on neural stem cells, their neuronal and oligodendroglial progeny, lineage progression, and overt differences in specific brain regions. Our findings show disruptions in all categories, specifically within the subventricular zone and corpus callosum. Given that LS is purely considered a neurodegenerative disease, we propose that mitochondrial dysfunction is a neurodevelopmental signature predating classic diagnosis in LS.

DOI: https://doi.org/10.1101/2025.05.16.654318
bioRxiv. 2025 May 19. pii: 2025.05.16.654474. [Epub ahead of print]

Parkin-dependent ubiquitination of TAX1BP1 directs efficient autophagic removal of defective mitochondria.

Anna Lechado-Terradas, Bianca Lemke, Katharina I Zittlau, Boris Macek, Philipp J Kahle.

In stressed cells, the recessive Parkinson disease (PD) associated gene products PINK1 and parkin mediate the autophagic removal of damaged mitochondria (mitophagy). Upon mitochondrial membrane potential disruption, PINK1 phosphorylation activates the ubiquitin ligase parkin which ubiquitinates various mitochondrial protein substrates. These feed-forward modifications on the mitochondria surface attract ubiquitin-binding autophagy receptors that target ubiquitinated mitochondria to autophagosomes and indirectly contribute to phagophore elongation. Investigating post-translational protein modifications during this process, we detected transient ubiquitination of K549 within the third coiled-coil domain (CC3) of TAX1BP1 in HeLa cells expressing WT but not catalytically inactive parkin. Parkin-dependent ubiquitination did not target TAX1BP1 to proteasomal degradation but was rather indicative of a regulatory modification. In cells with the full complement of autophagy receptors, TAX1BP1 plays only a minor role in mitophagy. However, when expressed as a sole autophagy receptor, both WT and ubiquitination deficient TAX1BP1 were capable of promoting mitophagy, albeit mitochondria degradation was slightly delayed under mutant conditions. Use of the lysosomal inhibitor bafilomycin A indicated classical autophagolysosomal targeting of damaged mitochondria mediated by WT TAX1BP1. However, for the ubiquitination-deficient TAX1BP1, we observed an increased prevalence of enlarged endolysosomal vesicles carrying accumulated TAX1BP1-positive autophagosomes filled with mitochondrial material. Thus, while ubiquitination of the CC3 domain of TAX1BP1 is not essential for complete mitophagy, the lack of CC3 in TAX1BP1 reroutes the degradation flux to a less efficient endolysosmal degradative pathway. Interestingly, the PD gene product VPS35, becomes prominently engaged in this alternative mitophagy pathway.

DOI: https://doi.org/10.1101/2025.05.16.654474
Int J Mol Med. 2025 Aug;pii: 118. [Epub ahead of print]56(2):

Understanding the impact of mitochondrial DNA mutations on aging and carcinogenesis (Review).

Hiroshi Kobayashi, Shogo Imanaka.

  Mitochondria and mitochondrial DNA (mtDNA) are crucial for cellular energy metabolism and the adaptive response to environmental changes. mtDNA collaborates with the nuclear genome to regulate mitochondrial function. Dysfunctional mitochondria and mutations in mtDNA are implicated in a wide range of diseases, including mitochondrial disorders, neurodegenerative conditions, age‑associated pathologies and cancer. While the nuclear genome has been extensively studied for its role in driving the clonal expansion of oncogenes and other aging‑related genetic alterations, knowledge regarding mtDNA remains comparatively limited. However, advances in quantitative analysis have provided information regarding the complex patterns of mtDNA mutations. The present review offers a detailed examination of mtDNA mutations and their classifications in the contexts of aging and cancer, and elucidates the role of mtDNA mutations in these processes. Mutations in mtDNA can be detected as early as the neonatal stage, yet most transition mutations retain a normal cellular phenotype. In contrast to mutations in oncogenes and tumor suppressor genes within the nuclear genome, mtDNA exhibits conserved mutational signatures, irrespective of cancer tissue origin. To adapt to the aging process, mitochondria undergo clonal expansion of advantageous mtDNA mutations, maintaining a dynamic equilibrium among various mitochondrial clones. Over time, however, the loss of strand bias can disrupt this equilibrium, diminishing the pool of adaptive clones. This breakdown in mitochondrial homeostasis may contribute to tumorigenesis. In conclusion, the heterogeneity of mtDNA mutations and the collapse of its homeostasis are pivotal in the progression of age‑related diseases, including cancer, underscoring the importance of mtDNA mutations in health and disease.

Keywords:  aging; carcinogenesis; clonal expansion; mitochondrial DNA; transition mutations

DOI:  https://doi.org/10.3892/ijmm.2025.5559
Eur J Neurol. 2025 Jun;32(6): e70218

The Role of Metabolic Testing in the Diagnostic Evaluation of Adult NORSE: A Retrospective, Single-Centre Study.

Jennifer Kilmer, George Ransley, Elaine Murphy, Michael G Hanna, Robert D S Pitceathly, Sanjeev Rajakulendran, Chiara Pizzamiglio.

   BACKGROUND: New-onset refractory status epilepticus (NORSE) is a diagnostically challenging and severe epileptic presentation in which aetiology is an important predictor of outcome. This retrospective study aimed to investigate the utility of metabolic screening to determine the underlying cause in 42 patients with suspected NORSE, admitted to The National Hospital for Neurology and Neurosurgery, London, between 2004 and 2021.
METHODS: Demographic, clinical, biochemical, and molecular data were collected. Sixty-two per cent of the cohort was classified as cryptogenic (cNORSE), while 38% had symptomatic NORSE (sNORSE).
RESULTS: Despite extensive investigations (100 metabolic-related tests were performed among the 42 cases), inherited disorders of metabolism were not identified as causes for NORSE. Nevertheless, three patients with refractory status epilepticus (RSE), who did not fulfill the diagnostic criteria for NORSE, had a primary mitochondrial disease (PMD). These data help establish criteria that distinguish PMD-related RSE from cNORSE, including pre-existing multisystemic features, a positive family history and/or suggestive MRI findings.
CONCLUSION: The study highlights the challenges in diagnosing NORSE aetiology and the limited utility of extensive testing for inherited metabolic disorders in this patient population. Further research is required to refine diagnostic strategies and enhance our understanding of the heterogeneous aetiology of cNORSE.

Keywords:  NORSE; diagnosis; metabolic workup; mitochondrial diseases; status epilepticus

DOI:  https://doi.org/10.1111/ene.70218
Sci Adv. 2025 Jun 06. 11(23): eads3051

Reduced DJ-1-F1Fo ATP synthase association correlates with midbrain dopaminergic neuron vulnerability in idiopathic Parkinson's disease.

Amina Abulimiti, Haesoo Bae, Anwaar Ali, Shanmuganathan Balakrishnan, Minou Tsujishita, Djordje Gveric, Travis S Tierney, Elizabeth A Jonas, Peter J S Smith, Steve M Gentleman, Kambiz N Alavian.

Disruption in neuronal and synaptic metabolic homeostasis is a key driver of neurodegeneration in Parkinson's disease (PD). Mitochondrial activity, biomass, and efficiency are critical to this balance. While activity and biomass are well characterized in PD pathology, mitochondrial metabolic efficiency remains insufficiently explored. Our previous studies showed that the protein product of PD-associated gene DJ-1 modulates metabolic efficiency through its interaction with the F1Fo-ATP-synthase β subunit (β-sub). Here, using proximity ligation assay (PLA), we compared mitochondrial DJ-1-β-sub association in distinct mesencephalic dopaminergic (mesDA) neuronal subpopulations and their intracellular compartments of PD and control postmortem brains. In PD brains, DJ-1-β-sub-PLA was lower than control in substantia nigra pars compacta (SNpc) somata and neurites but unchanged in ventral tegmental area (VTA) neurons. In PD and control cases, the PLA signal was reduced in distal neurites of SNpc compared to VTA neurons. These intracellular and region-specific differences suggest that impaired mitochondrial efficiency may contribute to the differential vulnerability of mesDA neurons in PD.

DOI: https://doi.org/10.1126/sciadv.ads3051
Front Cell Neurosci. 2025 ;19 1588645

Role of mitochondrial quality control in neurodegenerative disease progression.

Tingting Liu, Weibo Sun, Shuhao Guo, Zhiying Yuan, Minghang Zhu, Jing Lu, Tao Chen, Yuanyuan Qu, Chuwen Feng, Tiansong Yang.

  Neurodegenerative diseases are a diverse group of neurological disorders, in which abnormal mitochondrial function is closely associated with their development and progression. This has generated significant research interest in the field. The proper functioning of mitochondria relies on the dynamic regulation of the mitochondrial quality control system. Key processes such as mitochondrial biogenesis, mitophagy, and mitochondrial dynamics (division/fusion) are essential for maintaining this balance. These processes collectively govern mitochondrial function and homeostasis. Therefore, the mitochondrial quality control system plays a critical role in the onset and progression of neurodegenerative diseases. This article provides a concise overview of the molecular mechanisms involved in mitochondrial biogenesis, mitophagy, and mitochondrial dynamics, explores their interactions, and summarizes current research progress in understanding the mitochondrial quality control system in the context of neurodegenerative diseases.

Keywords:  Alzheimer’s disease; Huntington’s disease; Parkinson’s disease; amyotrophic lateral sclerosis; mitochondrial quality control

DOI:  https://doi.org/10.3389/fncel.2025.1588645
Geroscience. 2025 Jun 05.

Ndufs4-/- mice: a testing ground for longevity interventions.

Jackson Nuss, Matt Kaeberlein, Alessandro Bitto, Anthony S Grillo.

  Mice missing the complex I subunit Ndufs4 of the electron transport chain are widely used as a leading animal model of Leigh syndrome, a pediatric neurodegenerative disorder that leads to premature death. More broadly, this animal model has enabled a better understanding of the pathophysiology of mitochondrial disease and mitochondrial dysfunction in sporadic disorders. Intriguingly, longevity interventions are very effective at treating symptoms of disease in this model. Herein, we introduce the model and its notable features that may help provide insights in longevity research. We performed a retrospective analysis of historical data from our laboratories over the past 10 years regarding the use of this animal model in aging studies, the manifestation and progression of mitochondrial disease, and factors that influence their premature death. We observed a correlation between weight and lifespan in female animals and a sex-independent correlation between the onset of clasping, a typical neurodegenerative symptom, and overall survival. We observed a sexual dimorphism in lifespan with female mice being more resilient despite a similar age of onset of disease symptoms. Lastly, we report increased lifespan and delayed onset of disease symptoms following treatment with 17-alpha-estradiol, a non-feminizing estrogen which can extend lifespan in genetically heterogeneous mice. This analysis serves as a useful guide for researchers utilizing this animal in the discovery of effective interventions for longevity and to prevent the onset of disease. It suggests there may be unprecedented underlying sex-specific differences in patients with Leigh syndrome and further strengthens the connection between normative aging and mitochondrial dysfunction.

Keywords:  Interventions; Longevity; Mitochondrial dysfunction; Vertebrate models

DOI:  https://doi.org/10.1007/s11357-025-01704-8
bioRxiv. 2025 May 19. pii: 2025.05.16.654477. [Epub ahead of print]

The antibacterial factor APOL3 couples lysosomal damage to mitochondrial DNA efflux and type I IFN induction.

Dominic A Ritacco, Hamna Shahnawaz, Antonia Oduguwa, Jacob Hawk, Brianna Vizcaino, Donna Farber, Ryan G Gaudet.

Lysosomal damage is an endogenous danger signal to the cell, but its significance for innate immunity and how specific signaling pathways are engaged by this stressor remain unclear. Here, we uncover an immune-inducible pathway that connects lysosomal damage to mitochondrial DNA (mtDNA) efflux and type I IFN production. Lysosomal damage elicits mitochondrial outer membrane permeabilization (MOMP) via BAK/BAX macropores; however, the inner mitochondrial membrane (IMM) prevents wholesale mtDNA release in resting cells. Priming with type II IFN (IFN-γ) induced the antibacterial effector apolipoprotein L-3 (APOL3), which upon transient lysosomal damage, targets mitochondria undergoing MOMP and selectively permeabilizes the IMM to enhance mtDNA release and activate cGAS/STING signaling. Biochemical and cellular reconstitution revealed that analogous to its bactericidal detergent-like mechanism, APOL3 solubilizes cardiolipin to permeabilize the IMM. Our findings illustrate how cells use an antibacterial protein to expedite the breakdown of endosymbiosis and facilitate a heightened response to injury and infection.

DOI: https://doi.org/10.1101/2025.05.16.654477
bioRxiv. 2025 May 18. pii: 2025.05.15.654206. [Epub ahead of print]

A cold-inducible phospholipid-protein interaction in brown fat mitochondria optimizes thermogenic capacity.

Yuta Shimanaka, Marcus J Tol, Christian Rocha-Roa, Matthew J Jellinek, Liujuan Cui, Aaron Bender, Alexander H Bedard, Madeleine G Milner, Bruno Melillo, Bassem M Shoucri, Adrian Wong, Kevin J Williams, Linsey Stiles, Michael Shum, Thomas A Weston, Whitaker Cohn, Julian P Whitelegge, Itay Budin, Ambre M Bertholet, Benjamin F Cravatt, Stephen G Young, Sander M Houten, Carmen Argmann, David A Ford, Marc Liesa, Orian S Shirihai, Stefano Vanni, Peter Tontonoz.

Cold stress elicits dynamic remodeling of the mitochondrial lipidome in brown adipose tissue (BAT), marked by an increase in arachidonoyl-phosphatidylethanolamine (AA-PE). However, the function of membrane lipid rewiring in thermoregulatory physiology has been a longstanding mystery. Here, we identify LPCAT3 as a cold-regulated O-acyltransferase driving the highly selective accrual of AA-PE in BAT mitochondria. Lipid-based proteomics, molecular dynamics simulations, and bioenergetic analyses reveal that AA-PE partitions at the COX4I1 interface of the Cytochrome c oxidase complex, enhancing electron transport chain (ETC) efficiency. Accordingly, fat-specific Lpcat3 -knockout mice have defects in respiratory-dependent BAT thermogenesis and cold tolerance, despite intact β-adrenergic signaling and UCP1 function. Under cold acclimation, Lpcat3 -/- BAT exhibits ETC dysfunction and activation of the integrated stress-response. Thus, our study illuminates a cold-regulated lipid-protein interaction as a gating factor in UCP1-dependent thermogenesis.

DOI: https://doi.org/10.1101/2025.05.15.654206
Mol Psychiatry. 2025 Jun 03.

Glucose restriction induces degeneration of neurons with mitochondrial DNA depletion by altering ER-mitochondria calcium transfer.

Lingyan Zhou, Feixiang Bao, Jiajun Zheng, Yingzhe Ding, Jiahui Xiao, Jian Zhang, Yongpeng Qin, Liang Yang, Yi Wu, Qi Meng, Manjiao Lu, Qi Long, Lingli Hu, Chong Li, Haitao Wang, Shijuan Huang, Linpeng Li, Junwei Wang, Wuming Wang, Gang Lu, Wai-Yee Chan, Dajiang Qin, Gong Chen, Xingguo Liu.

Mitochondrial DNA (mtDNA) mutations and/or depletion are implicated in epilepsy and many neurodegenerative diseases. However, systematic investigation into how mtDNA alterations relate to epilepsy and neural degeneration is needed. Here, we established a mouse model in which mtDNA depletion is induced by the Herpes Simplex Virus Type 1 (HSV-1) protein UL12.5 in the brain led to an epileptic phenotype characterized by abnormal electroencephalography (EEG) patterns and increased neural excitability in hippocampus. We also found that UL12.5 mediated mtDNA depletion in neurons in vitro (rho-) causes epilepsy-like abnormal EEG. Caloric restriction (CR) or glucose restriction (GR) is a strategy proven to reduce epileptic activity, however GR mimetic 2-deoxy-D-glucose (2-DG), induced degeneration in mtDNA depleted neurons. Mechanistically, mtDNA depletion increased mitochondria-endoplasmic reticulum (ER) contacts, facilitating GR-induced mitochondrial calcium overload. Rho- neurons did not show changes in mitochondrial motility or membrane potential. Our study revealed an unexpected axis of mtDNA depletion, ER-mitochondrial contacts, and calcium overload in the rho- neuron model. Fasting-induced GR causes early motor dysfunction, accelerates epilepsy progression, and worsens neurodegeneration in UL12.5 mice. Importantly, the IP3R inhibitor 2-APB blocks the neurodegeneration induced by fasting. This is the first description of animal and neuronal models of mitochondrial epilepsy. Our findings with these models suggest that GR may not be a viable clinical intervention in patients with mtDNA depletion.

DOI: https://doi.org/10.1038/s41380-025-03069-y
Cell Commun Signal. 2025 Jun 04. 23(1): 264

Apoptosis-inducing factor (AIF) at the crossroad of cell survival and cell death: implications for cancer and mitochondrial diseases.

Tran Ngoc Anh Nguyen, Hong-Toan Lai, Romain Fernandes, Filippo G Dall'Olio, Camille Blériot, Tap Ha-Duong, Catherine Brenner.

  Apoptosis-inducing factor (AIF), a mitochondrial NAD(P)H-dependent oxidoreductase, was initially studied as a cell death inducer in a process later named parthanatos. However, it has been revealed that AIF also participates in mitochondrial bioenergetics through interaction with its partner coiled-coil-helix-coiled-coil-helix domain containing 4 (CHCHD4) and involvement in mitochondrial protein import. These dual roles place AIF between pro-survival and pro-death cell fate decisions. In this review, we first describe the structure and the dual functions of AIF, highlighting its structure-function relationships. We then report previously identified AIFM1 mutations and their clinical phenotypes. Finally, we discuss the relevance of AIF in cancer and the potential of targeting this protein for the treatment of cancer.

Keywords:  Apoptosis-inducing factor (AIF); Cancer; Cell death; Mitochondrial diseases; Mitochondrial protein import

DOI:  https://doi.org/10.1186/s12964-025-02272-2
Nat Commun. 2025 Jun 05. 16(1): 5223

Investigating the sources of variable impact of pathogenic variants in monogenic metabolic conditions.

Angela Wei, Richard Border, Boyang Fu, Sinéad Cullina, Nadav Brandes, Seon-Kyeong Jang, Sriram Sankararaman, Eimear E Kenny, Miriam S Udler, Vasilis Ntranos, Noah Zaitlen, Valerie A Arboleda.

Over three percent of people carry a dominant pathogenic variant, yet only a fraction of carriers develop disease. Disease phenotypes from carriers of variants in the same gene range from mild to severe. Here, we investigate underlying mechanisms for this heterogeneity: variable variant effect sizes, carrier polygenic backgrounds, and modulation of carrier effect by genetic background (marginal epistasis). We leveraged exomes and clinical phenotypes from the UK Biobank and the Mt. Sinai BioMe Biobank to identify carriers of pathogenic variants affecting cardiometabolic traits. We employed recently developed methods to study these cohorts, observing strong statistical support and clinical translational potential for all three mechanisms of variable carrier penetrance and disease severity. For example, scores from our recent model of variant pathogenicity were tightly correlated with phenotype amongst clinical variant carriers, they predicted effects of variants of unknown significance, and they distinguished gain- from loss-of-function variants. We also found that polygenic scores modify phenotypes amongst pathogenic carriers and that genetic background additionally alters the effects of pathogenic variants through interactions.

DOI: https://doi.org/10.1038/s41467-025-60339-7
MicroPubl Biol. 2025 ;2025

har-1/CHCHD10 mutations induce neurodegeneration and mitochondrial fragmentation in Caenorhabditis elegans.

Audrey Labarre, Ericka Guitard, Gilles Tossing, J Alex Parker.

CHCHD10 encodes a mitochondrial protein that plays a role in cristae morphology and oxidative phosphorylation, with mutations associated with neurodegenerative diseases, including the spectrum of amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). The Caenorhabditis elegans ortholog of CHCHD10 is har-1 , which can be used to model CHCHD10-related neurodegenerative diseases. We focused on two har-1 mutant strains: one featuring a 260 bp deletion ( gk3124 ) and the other with a G73E point mutation ( ad2155 ). Both har-1 mutants displayed progressive paralysis, degeneration of GABAergic motor neurons, and mitochondrial fragmentation. These strains may be valuable tools for investigating pathogenic mechanisms and therapeutic strategies for neurodegenerative diseases.

DOI: https://doi.org/10.17912/micropub.biology.001597
Cureus. 2025 Apr;17(4): e83231

Success of Coenzyme Q10 in Treating Steroid-Resistant Nephrotic Syndrome in Jordan: A Case Series.

Mahdi Q Frehat, Aghadir Alhadidi, Abdallah Almhairat, Lubna Alkhatib, Shawq Al Thaher, Ruba Al Assaf, Moath Al Qawaqenah, Batool Mansour, Faisal Khair.

  Focal segmental glomerulosclerosis (FSGS) is one of the leading causes of primary end-stage kidney disease in the pediatric age group. It is commonly associated with steroid-resistant nephrotic syndrome (SRNS), which ultimately leads to impairment in the function of the glomerular filtration system. Genetic studies have revealed nearly 50 types of gene deficiency disorders linked to the development of both FSGS and SRNS. Among these disorders, primary coenzyme Q10 (CoQ10) deficiency is classified as one of the few types that respond well to treatment. CoQ10 plays a crucial role within the mitochondria, including energy production through the electron transport chain. A network of at least 17 genes is necessary for its synthesis. When mutations occur in the genes responsible for CoQ10 production, a deficiency can develop, leading to mitochondrial dysfunction and reduced cellular energy levels. Since CoQ10 is crucial for mitochondrial function, its deficiency has been recognized as a potential therapeutic target. Increasing evidence suggests that CoQ10 supplementation may provide clinical benefit in treating this condition. We present three pediatric cases of SRNS that did not respond to standard treatment. Despite kidney biopsies revealing FSGS, conventional therapies proved ineffective. The patients were started on CoQ10 supplementation, which led to a complete resolution of nephrotic syndrome. Their kidney function remained within the normal range during follow-up, and proteinuria remained stable, indicating a sustained therapeutic response.

Keywords:  coenzyme q10; end-stage kidney disease; focal segmental glomerulosclerosis; nephrotic syndrome; steroid resistance

DOI:  https://doi.org/10.7759/cureus.83231
J Lipid Res. 2025 May 29. pii: S0022-2275(25)00094-X. [Epub ahead of print] 100834

Mitochondrial Calcium Uniporter is Required for Thermogenic Adaptation Mediated by Reactive Oxygen Species Signaling.

Suji Kim, Seung-Kuy Cha, Kyu-Sang Park, Jun Namkung.

  Mitochondrial Ca2+ influx via mitochondrial calcium uniporter (MCU) accelerates mitochondrial biogenesis and energy metabolism. Nevertheless, the molecular mechanism of MCU-dependent mitochondrial activation and thermogenesis in thermogenic adipose tissues remains elusive. In this study, we demonstrate that MCU governs mitochondrial functions in brown and beige adipocytes via the formation of mitochondrial reactive oxygen species (mtROS). Mice with a brown adipose tissue-specific Mcu knockout (Mcu BKO) mice exhibited decreased oxygen consumption and heat production, accompanied by downregulation of genes related to β-oxidation and thermogenesis. Furthermore, Mcu BKO mice, exhibiting a reduction in mtROS, showed defective thermogenic responses to cold exposure or β-adrenergic stimulation. Downregulation of thermogenic genes including Ucp1 in Mcu BKO mice can be rescued by exogenous ROS through AMP-activated protein kinase (AMPK) activation. Collectively, our results suggest that MCU modulates mtROS formation, which in turn mediates mitonuclear signaling to cellular response with mitochondrial activation.

Keywords:  Adipocytes; Adipose tissue; Lipolysis and fatty acid metabolism; Mitochondria; Obesity; brown

DOI:  https://doi.org/10.1016/j.jlr.2025.100834
Cell Rep. 2025 May 30. pii: S2211-1247(25)00535-2. [Epub ahead of print]44(6): 115764

Functional analysis of pathological mutations in DNA topoisomerase 3A.

Yiqing Wang, Sebastian Kaiser, Javier Martin-Gonzalez, Yuan Li, Lene J Rasmussen, Andres J Lopez-Contreras, Anna H Bizard, Ian D Hickson.

  DNA topoisomerase IIIα (TOP3A) is a highly conserved type IA topoisomerase critical for genome maintenance. Its deletion causes embryonic lethality in many organisms, which has hampered attempts to understand its physiological role. Recently, human subjects with TOP3A mutations were identified who display a Bloom's syndrome (BS)-like phenotype and mitochondrial dysfunction, consistent with TOP3A's roles in the nucleus, alongside the Bloom's helicase, and in mitochondria. Here, we generate a Top3a mutant mouse model mimicking those patient mutations that truncate the C-terminal domain (CTD). In contrast to humans, homozygous Top3a mutant mice lose viability at around 7.5 days post coitum (dpc). Mutant embryos and embryonic stem cells progressively lose mitochondrial DNA. Biochemical analyses indicate that CTD loss impairs DNA binding and plasmid relaxation activity and that the isolated CTD binds both single- and double-stranded DNA substrates. Our findings highlight the CTD's important role in TOP3A function in both the nucleus and mitochondria.

Keywords:  CP: Molecular biology; DNA binding; DNA topology; embryonic development; mitochondrial genome maintenance; mouse models of human disease

DOI:  https://doi.org/10.1016/j.celrep.2025.115764
Neurobiol Dis. 2025 Jun 03. pii: S0969-9961(25)00202-5. [Epub ahead of print] 106986

SARM1 activation induces reversible mitochondrial dysfunction and can be prevented in human neurons by antisense oligonucleotides.

Andrea Loreto, Kaitlyn M L Cramb, Lucy A McDermott, Christina Antoniou, Ilenia Cirilli, Maria Claudia Caiazza, Elisa Merlini, Peter Arthur-Farraj, W Daniel du Preez, Elliot D Mock, Hien T Zhao, David L Bennett, Giuseppe Orsomando, Michael P Coleman, Richard Wade-Martins.

  SARM1 is a key regulator of a conserved program of axon degeneration increasingly linked to human neurodegenerative diseases. Pathological SARM1 activation causes rapid NAD consumption, disrupting cellular homeostasis and leading to axon degeneration. In this study, we develop antisense oligonucleotides (ASOs) targeting human SARM1, demonstrating robust neuroprotection against morphological, metabolic, and mitochondrial impairment in human iPSC-derived dopamine neurons induced by the lethal neurotoxin vacor, a potent SARM1 activator. Furthermore, our findings reveal that axon fragmentation can be prevented, and mitochondrial dysfunction reversed using the NAD precursor nicotinamide, a form of vitamin B3, even after SARM1 activation has occurred, when neurons are already unhealthy. This research identifies ASOs as a promising therapeutic strategy to block SARM1, and provides an extensive characterisation and further mechanistic insights that demonstrate the reversibility of SARM1 toxicity in human neurons. It also identifies the SARM1 activator vacor as a specific and reversible neuroablative agent in human neurons.

Keywords:  ASO; Axon degeneration; Mitochondrial dysfunction; Neuroablative; Nicotinamide; SARM1; Vacor

DOI:  https://doi.org/10.1016/j.nbd.2025.106986
J Mol Biol. 2025 Jun 03. pii: S0022-2836(25)00329-8. [Epub ahead of print] 169263

The developing retina undergoes mitochondrial remodeling via PINK1/PRKN-dependent mitophagy.

Juan Zapata-Muñoz, Juan Ignacio Jiménez-Loygorri, Michael Stumpe, Beatriz Villarejo-Zori, Sandra Alonso-Gil, Petra Terešak, Benan J Mathai, Ian G Ganley, Anne Simonsen, Jörn Dengjel, Patricia Boya.

  Mitophagy, the selective degradation of mitochondria, is essential for retinal ganglion cell (RGC) differentiation and retinal homeostasis. However, the specific mitophagy pathways involved and their temporal dynamics during retinal development and maturation remain poorly understood. Using proteomics analysis of isolated mouse retinas across developmental stages and the mitophagy reporter mouse line, mito-QC, we characterized mitophagy throughout retinogenesis. While mitolysosomes were more prevalent in the mature retina, we observed two distinct mitophagy peaks during embryonic development. The first, independent of PTEN-induced kinase 1 (PINK1) activation, was associated with RGCs. The second, PINK1-dependent peak was triggered after an increase in retinal oxidative stress. This PINK1-dependent, oxidative stress-induced mitophagy pathway is conserved in mice and zebrafish, providing the first evidence of programmed, PINK1-dependent mitophagy during development.

Keywords:  PINK1; autophagy; development; mitophagy; retina

DOI:  https://doi.org/10.1016/j.jmb.2025.169263
Cell Commun Signal. 2025 May 31. 23(1): 256

mTOR inhibition triggers mitochondrial fragmentation in cardiomyocytes through proteosome-dependent prohibitin degradation and OPA-1 cleavage.

Hugo E Verdejo, Valentina Parra, Andrea Del Campo, Cesar Vasquez-Trincado, Damian Gatica, Camila Lopez-Crisosto, Jovan Kuzmicic, Leslye Venegas-Zamora, Ursula Zuñiga-Cuevas, Mayarling F Troncoso, Rodrigo Troncoso, Beverly A Rothermel, Mario Chiong, E Dale Abel, Sergio Lavandero.

   INTRODUCTION: Cardiac mitochondrial function is intricately regulated by various processes, ultimately impacting metabolic performance. Additionally, protein turnover is crucial for sustained metabolic homeostasis in cardiomyocytes.
OBJECTIVE: Here, we studied the role of mTOR in OPA-1 cleavage and its consequent effects on mitochondrial dynamics and energetics in cardiomyocytes.
RESULTS: Cultured rat cardiomyocytes treated with rapamycin for 6-24 h showed a significant reduction in phosphorylation of p70S6K, indicative of sustained inhibition of mTOR. Structural and functional analysis revealed increased mitochondrial fragmentation and impaired bioenergetics characterized by decreases in ROS production, oxygen consumption, and cellular ATP. Depletion of either the mitochondrial protease OMA1 or the mTOR regulator TSC2 by siRNA, coupled with an inducible, cardiomyocyte-specific knockout of mTOR in vivo, suggested that inhibition of mTOR promotes mitochondrial fragmentation through a mechanism involving OMA1 processing of OPA-1. Under homeostatic conditions, OMA1 activity is kept under check through an interaction with microdomains in the inner mitochondrial membrane that requires prohibitin proteins (PHB). Loss of these microdomains releases OMA1 to cleave its substrates. We found that rapamycin both increased ubiquitination of PHB1 and decreased its abundance, suggesting proteasomal degradation. Consistent with this, the proteasome inhibitor MG-132 maintained OPA-1 content in rapamycin-treated cardiomyocytes. Using pharmacological activation and inhibition of AMPK our data supports the hypothesis that this mTOR-PHB1-OMA-OPA-1 pathway impacts mitochondrial morphology under stress conditions, where it mediates dynamic changes in metabolic status.
CONCLUSIONS: These data suggest that mTOR inhibition disrupts mitochondrial integrity in cardiomyocytes by promoting the degradation of prohibitins and OPA-1, leading to mitochondrial fragmentation and metabolic dysfunction, particularly under conditions of metabolic stress.

Keywords:  AMPK; Mitochondrial fusion; OMA1; OPA-1; Prohibitin; Rapamycin; mTOR

DOI:  https://doi.org/10.1186/s12964-025-02240-w
Nat Med. 2025 Jun 04.

Stem cell therapies advance in Parkinson's disease and beyond.

Natalie Healey.

DOI: https://doi.org/10.1038/d41591-025-00036-6
Am J Hum Genet. 2025 May 26. pii: S0002-9297(25)00184-3. [Epub ahead of print]

Bi-allelic variants in TM2D3 cause a severe syndromic neurodevelopmental disorder associated with endoplasmic reticulum and mitochondrial abnormalities.

Claudie Gabillard-Lefort, Caroline Silveira Martinez, Naïg Gueguen, Valérie Desquiret-Dumas, Méline Wery, Louis Legoff, Anne Guimier, Sophie Rondeau, Giulia Barcia, Christine Barnerias, Benjamin Cogne, Thomas Besnard, Elsa Lorino, Jessica Douglas, Olaf Bodamer, Annalisa Vetro, Renzo Guerrini, Simona Balestrini, Valerio Conti, Laura Siri, Arnaud Chevrollier, Céline Bris, Estelle Colin, Vincent Procaccio, Delphine Prunier-Mirebeau, Guy Lenaers, Salim Khiati, Mathilde Nizon, Olivier R Baris.

  We identified via exome sequencing bi-allelic variants in TM2D3 in four affected individuals from four unrelated families with overlapping clinical presentations, including microcephaly, severe global developmental delay with absent speech, autistic features, heart malformation, and dysmorphic facial features. TM2D3 encodes a transmembrane protein present in many tissues, with a higher abundance in the central nervous system, but little is known about its function and cell localization. Here, by using chemical and genetically encoded probes in SNB75 cells, we show that TM2D3 is an endoplasmic reticulum (ER) protein. Further analysis on SNB75 TM2D3-knockout cells as well as skin fibroblasts from affected individuals harboring the recurrent c.503G>A (p.Gly168Asp) allele revealed an impact of TM2D3 on ER-stress response, with dysregulated expression of ATF4, HSPA5, and DDIT3. Transmission electron microscopy highlighted ER swelling as well as unexpected secondary mitochondrial alterations including increased length, cristae width, and ER-mitochondria distance. To gain further insights into the pathomechanisms at play, we performed RNA sequencing from the fibroblasts of the three individuals harboring the p.Gly168Asp variant and four available parents and disclosed 21 differentially expressed genes, including genes coding for extracellular matrix components involved in the migration of neuronal precursors. Altogether, these clinical and experimental data show that bi-allelic TM2D3 variants underlie a severe syndromic neurodevelopmental disorder linked to exacerbated ER-stress sensitivity, secondary mitochondrial alterations, and altered extracellular matrix gene expression.

Keywords:  ER stress; TM2D3; endoplasmic reticulum; extracellular matrix; microcephaly; mitochondria; mitochondrial dynamics; neurodevelopmental disorder

DOI:  https://doi.org/10.1016/j.ajhg.2025.05.004
Nat Commun. 2025 May 31. 16(1): 5061

Precision multiplexed base editing in human cells using Cas12a-derived base editors.

Anabel Y Schweitzer, Etowah W Adams, Michael T A Nguyen, Monkol Lek, Farren J Isaacs.

Base editors enable the direct conversion of target nucleotides without introducing DNA double strand breaks, making them a powerful tool for creating point mutations in a human genome. However, current Cas9-derived base editing technologies have limited ability to simultaneously edit multiple loci with base-pair level precision, hindering the generation of polygenic phenotypes. Here, we test the ability of six Cas12a-derived base editing systems to process multiple gRNAs from a single transcript. We identify base editor variants capable of multiplexed base editing and improve the design of the respective gRNA array expression cassette, enabling multiplexed editing of 15 target sites in multiple human cell lines, increasing state-of-the-art in multiplexing by three-fold in the field of mammalian genome engineering. To reduce bystander mutations, we also develop a Cas12a gRNA engineering approach that directs editing outcomes towards a single base-pair conversion. We combine these advances to demonstrate that both strategies can be combined to drive multiplex base editing with greater precision and reduced bystander mutation rates. Overcoming these key obstacles of mammalian genome engineering technologies will be critical for their use in studying single nucleotide variant-associated diseases and engineering synthetic mammalian genomes.

DOI: https://doi.org/10.1038/s41467-025-59653-x
Nat Biotechnol. 2025 Jun 03.

A mitochondrial disease model is generated and corrected using engineered base editors in rat zygotes.

Liang Chen, Changming Luan, Mengjia Hong, Meng Yuan, Hao Huang, Debo Gao, Xinyuan Guo, Zhengxin Chen, Yongmei Li, Lei Yang, Zongyi Yi, Wensheng Wei, Mingyao Liu, Liangcai Gao, Honghui Han, Dali Li.

Efficient generation and correction of mutations in mitochondrial DNA (mtDNA) is challenging. Here, through embryonic injection of an mtDNA adenine base editor (eTd-mtABE), Leigh syndrome rat models were generated efficiently (up to 74%) in the F0 generation, exhibiting severe defects. To correct this mutation, a precise mtDNA C-to-T base editor was engineered and injected into mutated embryos. It achieved restoration of wild-type alleles to an average of 53%, leading to amelioration of disease symptoms.

DOI: https://doi.org/10.1038/s41587-025-02684-y
Nat Chem Biol. 2025 Jun 02.

Programmable RNA acetylation with CRISPR-Cas13.

Jihwan Yu, Juae Jin, Eury Kwon, Hyunsoo Jang, Sang-Kun Choi, Donggyun Kim, Chaemin Kim, Seungkyu Son, Ki-Jun Yoon, Won Do Heo.

Recent studies claim that N4-acetylcytidine (ac4C) modification of RNA confers crucial regulatory roles, such as increasing translation efficiency and prolonging its half-life. However, the absence of methods for selectively acetylating specific RNA molecules hampers linking ac4C to cell physiology. Here, we developed an efficient molecular tool that incorporates ac4C on a specific transcript of interest. Through protein engineering, we developed a hyperactive variant of N-acetyltransferase 10 (NAT10), designated enhanced NAT10 (eNAT10). When fused to the programmable RNA-targeting protein dCas13, eNAT10 enables robust acetylation of various target RNAs in multiple contexts. RNA acetylation by dCas13-eNAT10 was highly dependent on co-transfected guide RNA, highlighting its specificity. We also describe the programmable RNA chemical modification in vivo using dual-adeno-associated virus. Using our system, we found that acetylation of RNA may modulate the subcellular localization of modified transcripts. We anticipate that our tool will facilitate numerous studies on ac4C functions across different cellular and disease contexts.

DOI: https://doi.org/10.1038/s41589-025-01922-3
Nat Commun. 2025 Jun 04. 16(1): 5179

An AI-assisted fluorescence microscopic system for screening mitophagy inducers by simultaneous analysis of mitophagic intermediates.

Yicheng Wang, Pengfei Song, Heqing Zhou, Pengwei Wang, Yan Li, Zhiyong Shao, Lu Wang, Yan You, Zuhai Lei, Jinhua Yu, Cong Li.

Mitophagy, the selective autophagic elimination of mitochondria, is essential for maintaining mitochondrial quality and cell homeostasis. Impairment of mitophagy flux, a process involving multiple sequential intermediates, is implicated in the onset of numerous neurodegenerative diseases. Screening mitophagy inducers, particularly understanding their impact on mitophagic intermediates, is crucial for neurodegenerative disease treatment. However, existing techniques do not allow simultaneous visualization of distinct mitophagic intermediates in live cells. Here, we introduce an artificial intelligence-assisted fluorescence microscopic system (AI-FM) that enables the uninterrupted recognition and quantification of key mitophagic intermediates by extracting mitochondrial pH and morphological features. Using AI-FM, we identify a potential mitophagy modulator, Y040-7904, which enhances mitophagy by promoting mitochondria transport to autophagosomes and the fusion of autophagosomes with autolysosomes. Y040-7904 also reduces amyloid-β pathologies in both in vitro and in vivo models of Alzheimer's disease. This work offers an approach for visualizing the entire mitophagy flux, advancing the understanding of mitophagy-related mechanisms and enabling the discovery of mitophagy inducers for neurodegenerative diseases.

DOI: https://doi.org/10.1038/s41467-025-60315-1
Sci Adv. 2025 Jun 06. 11(23): eadt2050

Type II kinase inhibitors that target Parkinson's disease-associated LRRK2.

Nicolai D Raig, Katherine J Surridge, Marta Sanz-Murillo, Verena Dederer, Andreas Krämer, Martin P Schwalm, Nicholas M Lattal, Lewis Elson, Deep Chatterjee, Sebastian Mathea, Thomas Hanke, Andres E Leschziner, Samara L Reck-Peterson, Stefan Knapp.

Increased kinase activity of leucine-rich repeat kinase 2 (LRRK2) is associated with Parkinson's disease (PD). Numerous LRRK2-selective type I kinase inhibitors have been developed, and some have entered clinical trials. Here, to our knowledge, we present the first type II kinase inhibitors that target LRRK2. Targeting the inactive conformation of LRRK2 is functionally distinct from targeting the active-like conformation using type I inhibitors. We designed these inhibitors with a combinatorial chemistry approach fusing selective LRRK2 type I and promiscuous type II inhibitors using iterative cycles of synthesis supported by structural biology and activity testing. Our lead compounds are selective and potent toward both LRRK2 and LRRK1, a close relative of LRRK2. Through cellular assays, cryo-electron microscopy structural analysis, and in vitro motility assays, we show that our inhibitors stabilize the open, inactive LRRK2 kinase conformation. These new conformation-specific compounds will be invaluable as tools to study LRRK2's function and regulation and expand the potential therapeutic options for PD.

DOI: https://doi.org/10.1126/sciadv.adt2050