bims-mitdis 2025-09-21 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2025–09–21
forty-one papers selected by
Catalina Vasilescu, Helmholz Munich

Manipulating mitochondrial gene expression.
mtDNA base editing: Mind the gap.
Motor Neuropathy in a Patient With Mitochondrial Disease and a Novel TTC19 Variant: An Underrecognized Phenotypic Feature.
Compartmentalized thymidine phosphorylation by mitochondrial nucleotide kinases TK2 and CMPK2.
InsP3R signaling mediates mitochondrial stress-induced longevity through actomyosin-dependent mitochondrial dynamics.
Mitochondrial Diseases: Molecular Pathogenesis and Therapeutic Advances.
STX4 is indispensable for mitochondrial homeostasis in skeletal muscle.
Interaction of the mitochondrial calcium/proton exchanger TMBIM5 with MICU1.
Role of the mitochondrial regulatory factor CHCHD2 in neurodegenerative diseases.
Biallelic TMEM126B Variants as a Novel Cause of Kidney Failure-Implications for Mitochondrial Genetic Testing in Nephrology.
A novel XPNPEP3 gene variant manifesting as rhabdomyolysis and exercise intolerance.
Meclizine rescues cardiac function and mitochondrial ultrastructure by ATP- and glycolysis-independent mechanisms in a genetic model of mitochondrial energy dysfunction.
Cryo-EM Reveals Regulatory Mechanisms Governing Substrate Selection and Activation of Human LONP1.
Methodological validation of Miro1 retention as a candidate Parkinson's disease biomarker.
Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating.
Mitochondrial DNA damage in substantia nigra pars compacta astrocytes exacerbates dopaminergic neuron loss in a 6-hydroxydopamine mouse model of parkinsonism.
Federated Learning for the pathogenicity annotation of genetic variants in multi-site clinical settings.
MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA.
Peroxisomal metabolism of branched fatty acids regulates energy homeostasis.
Nucleic Acid Sequence Determinants of Transcriptional Pausing by the Human Mitochondrial RNA Polymerase (POLRMT).
Whole mitochondrial genome sequencing in individuals with Leber hereditary optic neuropathy negative for the common pathogenic mitochondrial DNA variants.
Neuroimaging features of familial MT-TK related mitochondrial disease in a child.
Mapping the genetic landscape of iron metabolism uncovers the SETD2 methyltransferase as a modulator of iron flux.
Single-cell Omics Assessment of Mitochondrial Function: Current Status and Future Perspectives.
Mitochondrial RNA in Inflammation.
A reversible feedback mechanism regulating mitochondrial heme synthesis.
Reviving mitochondria to restore the mind: stem cell-based bioenergetic rescue in Parkinson's disease.
Photocatalytic labelling-enabled subcellular-resolved RNA profiling and synchronous multi-omics investigation.
Covariation MS uncovers a protein that controls cysteine catabolism.
A rare genetic variant confers resistance to neurodegeneration across multiple neurological disorders by augmenting selective autophagy.
Cryo-EM structure of the prohibitin complex in open conformation.
Mitochondrial oxidative stress, cellular damages and stem cell aging in premature aging models with complex II electron transport defect.
Hepatocyte FAM210A deficiency disrupts mitochondrial function and triggers juvenile steatosis with compensatory repair in adulthood.
Boosted mitochondria reverse cognitive impairment in mice.
Neurons and astrocytes have distinct organelle signatures and responses to stress.
Genetic background of neurological disorders with basal ganglia calcification.
BDH2-driven lysosome-to-mitochondria iron transfer shapes ferroptosis vulnerability of the melanoma cell states.
Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.
CircNCX1 contributes to mitochondrial fusion in cardiomyocyte by mediating the expression of mitofusin 2.
Mitochondrial organization in the developing proximal tubule is controlled by LRRK2.
Predicting the regulatory genome.

Biol Chem. 2025 Sep 15.

Manipulating mitochondrial gene expression.

Drishan Dahal, Luis D Cruz-Zargoza, Peter Rehling.

  Mitochondria are essential for cellular metabolism, serving as the primary source of adenosine triphosphate (ATP). This energy is generated by the oxidative phosphorylation (OXPHOS) system located in the inner mitochondrial membrane. Impairments in this machinery are linked to serious human diseases, especially in tissues with high energy demands. Assembly of the OXPHOS system requires the coordinated expression of genes encoded by both the nuclear and mitochondrial genomes. The mitochondrial DNA encodes for 13 protein components, which are synthesized by mitochondrial ribosomes and inserted into the inner membrane during translation. Despite progress, key aspects of how mitochondrial gene expression is regulated remain elusive, largely due to the organelle's limited genetic accessibility. However, emerging technologies now offer new tools to manipulate various stages of this process. In this review, we explore recent strategies that expand our ability to target mitochondria genetically.

Keywords:  RNA; gene expression; genetic tools; mitochondria

DOI:  https://doi.org/10.1515/hsz-2025-0170
Mol Cell. 2025 Sep 18. pii: S1097-2765(25)00713-0. [Epub ahead of print]85(18): 3351-3352

mtDNA base editing: Mind the gap.

Jose Domingo Barrera-Paez, Carlos T Moraes.

In this issue of Molecular Cell, Xiang et al.1 provided insights into the mechanism and structure-guided engineering of DdCBE for mitochondrial DNA base editing. More precise editing was achieved by better defining the editing window.

DOI: https://doi.org/10.1016/j.molcel.2025.08.028
J Peripher Nerv Syst. 2025 Sep;30(3): e70060

Motor Neuropathy in a Patient With Mitochondrial Disease and a Novel TTC19 Variant: An Underrecognized Phenotypic Feature.

Daniele Mandia, Charline Benoit, Tanya Stojkovic, Yann Nadjar.

   BACKGROUND AND AIMS: TTC19 encodes a mitochondrial protein involved in the assembly of complex III of the respiratory chain. Biallelic pathogenic variants cause a rare mitochondrial disorder typically associated with cerebellar ataxia, neuropsychiatric symptoms, and characteristic brain MRI findings within the Leigh syndrome spectrum. Peripheral motor involvement has been described in a minority of cases but has rarely been documented with detailed neurophysiological data. We report a novel TTC19 variant in a patient presenting with a distinctive combination of central and peripheral motor involvement.
CASE REPORT: A male patient of Malian origin presented with cerebellar ataxia and attention deficits from early childhood. During adolescence, he developed additional features including dysarthria, dysphagia, dysexecutive syndrome, and signs of peripheral motor neuropathy. Brain MRI revealed T2-FLAIR hyperintensities in the basal ganglia and brainstem. Genetic testing identified a novel homozygous nonsense variant in TTC19 (c.235G>T, p.(Gly79*)). At age 19, he experienced two acute deteriorations associated with respiratory infections, leading to severe tetraparesis and diaphragmatic weakness. Neurophysiological studies confirmed a diffuse, axonal, pure distal motor neuropathy. Follow-up imaging showed progression and cavitation of brainstem lesions. The patient died from respiratory failure at age 20.
INTERPRETATION: This case, featuring a novel TTC19 variant and detailed electrophysiological data, further supports the presence of pure motor neuropathy within the phenotypic spectrum of TTC19-related disease. The co-occurrence of Leigh syndrome MRI findings and motor neuropathy represents a specific diagnostic clue that may help prioritize genetic testing in patients with overlapping central and peripheral motor involvement.

Keywords:  Leigh syndrome; TTC19; mitochondrial disease; motor neuropathy; respiratory chain complex III

DOI:  https://doi.org/10.1111/jns.70060
J Biol Chem. 2025 Sep 16. pii: S0021-9258(25)02585-2. [Epub ahead of print] 110733

Compartmentalized thymidine phosphorylation by mitochondrial nucleotide kinases TK2 and CMPK2.

Avery S Ward, Vasudeva G Kamath, Chia-Heng Hsiung, Zachary J Lizenby, Alexander G Gillish, D Stave Kohtz, Edward E McKee.

  Deoxynucleotides (dNTPs) in post-mitotic tissues rely on deoxynucleoside salvage pathways in order to repair and replicate nuclear and mitochondrial DNA (mtDNA). Previous work from our laboratory showed in perfused rat heart and isolated mitochondria that the only substrate for TTP synthesis is thymidine. When thymidylate (TMP) is provided to bypass thymidine kinase 2 (TK2) the substrate is readily dephosphorylated to thymidine before salvage occurs suggesting compartmentalization within the heart mitochondrial matrix. The goal of this work extends these findings in the heart to mitochondria from other post-mitotic tissues, including rat liver, kidney, and brain. Using AZT to block mitochondrial thymidine kinase 2, we demonstrate that TMP cannot serve as a precursor for TTP synthesis in isolated mitochondria from any of these tissues unless it is de-phosphorylated to thymidine first. Broken mitochondria incubated with labeled TMP showed similar results as intact mitochondria, suggesting the findings are not related to TMP transport across the inner mitochondrial membrane. Further, using proximity labeling with immunofluorescence microscopy we provide evidence supporting the hypothesis that TMP compartmentation is accounted for by the interaction of TK2 and CMPK2 in the mitochondria. Differential fraction experiments provide additional evidence that association with TK2 allows CMPK2 to display TMPK2 activity. Together, the results indicate that a two-step phosphorylation of thymidine to TDP occurs because the proximity of TK2 and CMPK2 in the mitochondria prevents TMP from diffusing from the two enzymes.

Keywords:  cytidine monophosphate kinase 2; mitochondrial disease; mitochondrial metabolism; nucleoside/nucleotide biosynthesis; nucleoside/nucleotide metabolism; thymidine kinase 2

DOI:  https://doi.org/10.1016/j.jbc.2025.110733
bioRxiv. 2025 Sep 04. pii: 2025.08.30.673265. [Epub ahead of print]

InsP3R signaling mediates mitochondrial stress-induced longevity through actomyosin-dependent mitochondrial dynamics.

Gaomin Feng, Elizabeth M Ruark, Alexandra G Mulligan, Eric K F Donahue, Anthony Hoang, Brianne Jacquet-Cribe, Li Peng, Kristopher Burkewitz.

Certain forms of mitochondrial impairment confer longevity, while mitochondrial dysfunction arising from aging and disease-associated mutations triggers severe pathogenesis. The adaptive pathways that distinguish benefit from pathology remain unclear. Here we reveal that longevity induced by mitochondrial Complex I/ nuo-6 mutation in C. elegans is dependent on the endoplasmic reticulum (ER) Ca 2+ channel, InsP3R. We find that the InsP3R promotes mitochondrial respiration, but the mitochondrial calcium uniporter is dispensable for both respiration and lifespan extension in Complex I mutants, suggesting InsP3R action is independent of matrix Ca 2+ flux. Transcriptomic profiling and imaging reveal a previously unrecognized role for the InsP3R in regulating mitochondrial scaling, where InsP3R impairment results in maladaptive hyper-expansion of dysfunctional mitochondrial networks. We reveal a conserved InsP3R signaling axis through which calmodulin and actomyosin remodeling machineries, including Arp2/3, formin FHOD-1, and MLCK, constrain mitochondrial expansion and promote longevity. Disruption of actin remodeling or autophagy mimics InsP3R loss. Conversely, driving fragmentation ameliorates mitochondrial expansion and rescues longevity, supporting a model in which InsP3R-dependent actin remodeling sustains mitochondrial turnover. These findings establish an inter-organelle signaling axis by which ER calcium release orchestrates mitochondrial-based longevity through cytoskeletal effectors.

DOI: https://doi.org/10.1101/2025.08.30.673265
MedComm (2020). 2025 Sep;6(9): e70385

Mitochondrial Diseases: Molecular Pathogenesis and Therapeutic Advances.

Jialun Mei, Peng Ding, Chuan Gao, Jian Zhou, Zhiwei Li, Changqing Zhang, Junjie Gao.

  Mitochondrial diseases are a heterogeneous group of inherited disorders caused by pathogenic variants in mitochondrial DNA (mtDNA) or nuclear genes encoding mitochondrial proteins, culminating in defective oxidative phosphorylation and multisystem involvement. Key pathogenic mechanisms include heteroplasmy driven threshold effects, excess reactive oxygen species, disrupted mitochondrial dynamics and mitophagy, abnormal calcium signaling, and compromised mtDNA repair, which together cause tissue-specific energy failure in high demand organs. Recent advances have expanded the therapeutic landscape. Precision mitochondrial genome editing-using mitochondrial zinc finger nucleases, mitochondrial transcription activator-like effector nucleases, DddA-derived cytosine base editor, and other base editing tools-enables targeted correction or rebalancing of mutant genomes, while highlighting challenges of delivery and off-target effects. In parallel, metabolic modulators (e.g., coenzyme Q10, idebenone, EPI-743) aim to restore bioenergetics, and mitochondrial replacement technologies and transplantation are being explored. Despite these promising strategies, major challenges remain, including off-target effects, precise delivery, and ethical considerations. Addressing these issues through multidisciplinary research and clinical translation holds promise for transforming mitochondrial disease management and improving patient outcomes. By bridging the understanding of mitochondrial dysfunction with advanced therapeutic interventions, this review aims to shed light on effective solutions for managing these complex disorders.

Keywords:  base editing; gene therapy; genetic medicine; mitochondrial DNA (mtDNA); mitochondrial diseases; mitochondrial gene editing; therapeutic strategies

DOI:  https://doi.org/10.1002/mco2.70385
bioRxiv. 2025 Sep 03. pii: 2025.09.02.673840. [Epub ahead of print]

STX4 is indispensable for mitochondrial homeostasis in skeletal muscle.

Joseph M Hoolachan, Rekha Balakrishnan, Erika M McCown, Karla E Merz, Chunxue Zhou, Elizabeth Bloom-Saldana, Patrick T Fueger, Angelica Hamilton, Tali Kiperman, Ke Ma, Eunjin Oh, Lei Jiang, Patrick Pirrotte, Orian Shirihai, Debbie C Thurmond.

Background: Mitochondrial homeostasis is vital for optimal skeletal muscle integrity. Mitochondrial quality control (MQC) mechanisms that are essential for maintaining proper functions of mitochondria include mitochondrial biogenesis, dynamics and mitophagy. Previously, Syntaxin 4 (STX4) traditionally considered a cell surface protein known for glucose uptake in skeletal muscle, was also identified at the outer mitochondrial membrane. STX4 enrichment was sufficient to reverse Type 2 diabetes-associated mitochondrial damage in skeletal muscle by inactivation of mitochondrial fission. However, whether STX4 could modulate skeletal muscle mitochondrial homeostasis through MQC mechanisms involving mitochondrial biogenesis or mitophagy remains to be determined.
Methods: To determine the requirements of STX4 in mitochondrial structure, function and MQC processes of biogenesis and mitophagy, we implemented our in-house generated inducible skeletal muscle-specific STX4-knockout (skmSTX4-iKO) mice ( Stx4 fl/fl ; Tg(HSA-rtTA/TRE-Cre )/B6) and STX4-depleted immortalized L6.GLUT4myc myotubes via siRNA knockdown (siSTX4).
Results: We found that non-obese skmSTX4-iKO male mice (>50% reduced STX4 abundance, Soleus and Gastrocnemius ***p<0.001, Tibialis anterior (TA) ****p<0.0001) developed insulin resistance (**p<0.01), together with reduced energy expenditure (AUC *p<0.05), respiratory exchange ratio (AUC **p<0.01), and grip strength (*p<0.05). STX4 ablation in muscle also impaired mitochondrial oxygen consumption rate (****p<0.0001). Mitochondrial morphological damage was heterogenous in STX4 depleted muscle, presenting with small fragmented mitochondria (****p<0.0001) and deceased electron transport chain (ETC) abundance (CI ***p<0.001, CII *p<0.05, CIV **p<0.01) in oxidative soleus muscle, while glycolytic TA fibers display enlarged swollen mitochondria (****p<0.0001) with no change in ETC abundance. Notably, >60% reduction of STX4 in siSTX4 L6.GLUT4myc myotubes (****p<0.0001) also decreased ETC abundance (CI ****p<0.0001, CII ****p<0.0001, CIV *p<0.05) without changes in mitochondrial glucose metabolism, as shown by [U- 13 C] glucose isotope tracing. For MQC, both skmSTX4-iKO male mice (*p<0.05) and siSTX4 L6.GLUT4myc myotubes (*p<0.05) showed decreased mitochondrial DNA levels alongside reduced mRNA expression of mitochondrial biogenesis genes Ppargc1a (PGC1-α, *p<0.05) and Tfam (*p<0.05) in skmSTX4-iKO soleus muscle and PGC1-α (mRNA *p<0.05, protein ***p<0.001), NRF1 (mRNA and protein *p<0.05) and Tfam (mRNA *p<0.05) in siSTX4 L6.GLUT4myc myotubes. Furthermore, live cell imaging using mt-Keima mitophagy biosensor in siSTX4 L6.GLUT4myc cells revealed significantly impaired mitochondrial turnover by mitophagy (*p<0.05) and mitochondria-lysosome colocalization (*p<0.05). STX4 depletion also reduced canonical mitophagy markers, PINK1 and PARKIN in both skmSTX4-iKO muscle (PARKIN *p<0.05, PINK1 **p<0.01) and siSTX4 L6.GLUT4myc myotubes (PARKIN ****p<0.0001, PINK1 *p<0.05).
Conclusions: Our study demonstrated STX4 as a key mitochondrial regulator required for mitochondrial homeostasis in skeletal muscle.

DOI: https://doi.org/10.1101/2025.09.02.673840
Commun Biol. 2025 Sep 19. 8(1): 1348

Interaction of the mitochondrial calcium/proton exchanger TMBIM5 with MICU1.

Li Zhang, Benjamin Gottschalk, Felicia Dietsche, Sara Bitar, Diones Bueno, Liliana Rojas-Charry, Anshu Kumari, Vivek Garg, Wolfgang F Graier, Axel Methner.

Ion transport within mitochondria influences their structure, energy production, and cell death regulation. TMBIM5, a conserved calcium/proton exchanger in the inner mitochondrial membrane, contributes to mitochondrial structure, ATP synthesis, and apoptosis regulation. The relationship of TMBIM5 with the mitochondrial calcium uniporter complex formed by MCU, MICU1-3, and EMRE remains undefined. We generated Tmbim5-deficient Drosophila that exhibit disrupted cristae architecture, premature mitochondrial permeability transition pore opening, reduced calcium uptake, and mitochondrial swelling - resulting in impaired mobility and shortened lifespan. Crossing these with flies lacking mitochondrial calcium uniporter complex proteins was generally detrimental, but partial MICU1 depletion ameliorated the Tmbim5-deficiency phenotype. In human cells, MICU1 rescues morphological defects in TMBIM5-knockout mitochondria, while TMBIM5 overexpression exacerbates size reduction in MICU1-knockout mitochondria. Both proteins demonstrated opposing effects on submitochondrial localization and coexisted in the same macromolecular complex. Our findings establish a functional interplay between TMBIM5 and MICU1 in maintaining mitochondrial integrity, with implications for understanding calcium homeostasis mechanisms.

DOI: https://doi.org/10.1038/s42003-025-08839-6
Front Neurosci. 2025 ;19 1639651

Role of the mitochondrial regulatory factor CHCHD2 in neurodegenerative diseases.

Xinyu Guo, Peiyu Xu, Chen Liang, Yuntao Li.

  Mitochondria are essential organelles within cells, and their dysfunction is associated with many neurodegenerative disorders. The protein CHCHD2, which is situated in the intermembrane space of mitochondria, plays a pivotal role in mitochondrial function. Its knockdown or mutation is linked to mitochondrial impairment. Although research suggests that CHCHD2 is involved in the mechanisms underlying various neurodegenerative diseases, there is a notable absence of comprehensive studies that integrate different mutation types, pathogenic mechanisms, and targeted treatment strategies. This paper provides a review of CHCHD2's structure and function, mutant varieties, biological models, and relevant therapies. We conclude that CHCHD2 is critical for maintaining mitochondrial homeostasis, facilitating cell migration, and regulating apoptosis. Mutations in CHCHD2 may influence the mechanisms of neurodegenerative diseases through both loss-of-function and gain-of-function effects, with overexpression possibly reversing pathological processes and mitochondrial dysfunction. Furthermore, elamipretide, a novel drug that targets mitochondria, has shown efficacy in partially alleviating mitochondrial defects resulting from CHCHD2 mutations. These insights could inform the identification of therapeutic targets in neurodegenerative diseases and shape future research on CHCHD2.

Keywords:  CHCHD2; mitochondria; mutation; neurodegenerative disorders; structural and functional abnormalities

DOI:  https://doi.org/10.3389/fnins.2025.1639651
Clin Genet. 2025 Sep 19.

Biallelic TMEM126B Variants as a Novel Cause of Kidney Failure-Implications for Mitochondrial Genetic Testing in Nephrology.

Zachary T Sentell, Anthony C T Cheung, Felicia Russo, Chantal Bernard, Rita Suri, Andrey V Cybulsky, Daniela Buhas, Thomas M Kitzler.

  An adult with kidney failure had compound-heterozygous TMEM126B variants causing mitochondrial complex I deficiency. This expands TMEM126B to mitochondrial nephropathy and supports including mitochondrial genes in renal genetic testing.

Keywords:   TMEM126B ; genetic testing; kidney failure; mitochondrial complex I deficiency; mitochondrial nephropathy

DOI:  https://doi.org/10.1111/cge.70073
J Neuromuscul Dis. 2025 Sep 15. 22143602251352986

A novel XPNPEP3 gene variant manifesting as rhabdomyolysis and exercise intolerance.

Katia Staedler, Juliette Nectoux, Corinne Metay, Alban Lermine, Rocio-Nur Villar-Quiles, Teresinha Evangelista, Clemence Labasse, Emmanuelle Lacène, Tanya Stojkovic.

  Biallelic mutations in XPNPEP3 gene, encoding a mitochondrial peptidase, mainly cause nephronophthisis, but associated muscle involvement remains poorly described. We report here a 44-year-old male presenting since childhood with exercise intolerance and recurrent rhabdomyolysis. Electroneuromyography revealed a sensory axonal neuropathy and brain MRI showed white matter lesions in the posterior cranial fossa. Muscle biopsy revealed ragged-red fibers, COX negative fibers and abnormal mitochondria in electron microscopy. Whole genome sequencing identified a homozygous frameshift variant in the XPNPEP3 gene. Our results expand the spectrum associated with XPNPEP3 variants, including metabolic myopathy with subclinical central and peripheral nervous system involvement.

Keywords:  XPNPEP3; mitochondrial myopathies; muscular diseases; myalgia; rhabdomyolysis

DOI:  https://doi.org/10.1177/22143602251352986
bioRxiv. 2025 Sep 07. pii: 2025.09.03.674000. [Epub ahead of print]

Meclizine rescues cardiac function and mitochondrial ultrastructure by ATP- and glycolysis-independent mechanisms in a genetic model of mitochondrial energy dysfunction.

Nasab Ghazal, Banjamin Huang, Luke J Shoemaker, Victor Faundez, Jennifer Q Kwong.

Primary mitochondrial cardiomyopathies are an unmet clinical challenge, as there are no therapies that directly address the underlying mitochondrial dysfunction. We previously reported that the cardiomyocyte-specific deletion of the mitochondrial phosphate carrier (SLC25A3), which imports phosphate required for ATP synthesis, produces a model of mitochondrial cardiomyopathy in which total cardiac ATP levels are preserved despite defective mitochondrial ATP production. This was accompanied by increased glycolytic activity and reduced mitochondrial flux, leading us to hypothesize that pharmacologically enhancing glycolysis might be protective when the mitochondrial energy machinery is intrinsically impaired. To test this, we turned to meclizine, an FDA-approved antihistamine previously shown to shift metabolism toward glycolysis. Chronic meclizine treatment in SLC25A3-deficient mice attenuated cardiac hypertrophy, improved systolic function, and restored mitochondrial ultrastructure. Unexpectedly, meclizine suppressed glycolytic enzyme expression and reduced lactate accumulation, suggesting that meclizine does not induce a glycolytic shift in SLC25A3-deleted hearts. Instead, proteomic and functional analyses revealed preservation of mitochondrial cristae architecture via MICOS upregulation and improved NAD+/NADH homeostasis through uncoupled electron flux and NAD+ regeneration. Together, these findings identify meclizine as a clinically approved compound that promotes cardioprotection in mitochondrial disease not by driving glycolysis, but by preserving mitochondrial membrane organization and redox balance, highlighting mitochondrial quality and NAD+ redox homeostasis as therapeutic targets for primary mitochondrial cardiomyopathies.

DOI: https://doi.org/10.1101/2025.09.03.674000
bioRxiv. 2025 Sep 06. pii: 2025.09.05.674599. [Epub ahead of print]

Cryo-EM Reveals Regulatory Mechanisms Governing Substrate Selection and Activation of Human LONP1.

Jeffrey T Mindrebo, Lauren Alexandrescu, Jennifer R Baker, Garret Wang, Gabriel C Lander.

The human AAA+ protease LONP1 plays a central role in maintaining mitochondrial proteostasis. LONP1 processes a vast array of substrates, ranging from damaged or unfolded proteins to specific subunits stably integrated into respiratory complexes. Previous cryo-EM studies of LONP1 uncovered two distinct conformational states corresponding to inactive or active forms of the enzyme. While these states have shed light on the intricacies of LONP1 substrate translocation and proteolytic processing, little is known about the decision-making involved in LONP1 substrate engagement and subsequent initiation of its unfoldase activity. Here, we use cryo-EM to determine a novel ADP-bound, C3-symmetric intermediate state of LONP1 (LONP1C3) with putative substrate "fold-sensing" capabilities. Our biochemical and structural data indicate that LONP1C3 is an on-pathway intermediate and that is stabilized by interaction with folded substrates. Moreover, we identify additional symmetric and asymmetric conformational states, including a two-fold symmetric split-hexamer conformation, that we associate with the transition from LONP1C3 to LONP1ENZ. We propose that the C3-state regulates substrate selection and enables LONP1 to efficiently surveil the matrix proteome to ensure selective removal of damaged and dysfunctional proteins as well as privileged LONP1 substrates. These findings collectively provide further mechanistic insights into LONP1 substrate recruitment and engagement and inform on its diverse roles in maintaining homeostasis within the mitochondria.

DOI: https://doi.org/10.1101/2025.09.05.674599
NPJ Parkinsons Dis. 2025 Sep 15. 11(1): 270

Methodological validation of Miro1 retention as a candidate Parkinson's disease biomarker.

Layla Drwesh, Giuseppe Arena, Daniel J Merk, Daniele Ferrante, Vyron Gorgogietas, Thomas Gasser, Anne Grünewald, Patrick May, Kathrin Brockmann, Rejko Krüger, Richard Wüst, Christian Johannes Gloeckner, Julia C Fitzgerald.

Mitochondrial markers help stratify Parkinson's disease (PD) patients. We use high-throughput blotting to quantify Miro1, Mfn2, and VDAC levels in fibroblasts, blood cells, and iPSC-derived neurons. Miro1 is specifically retained in PD cells but degraded in healthy ones after mitochondrial depolarization. We correlate Miro1 retention scores with pathogenic mutations, genetic background, age, and clinical data. This scalable assay and quantifiable score for mitochondrial-PD support biomarker development and pharmacological screening.

DOI: https://doi.org/10.1038/s41531-025-01115-8
J Chem Inf Model. 2025 Sep 18.

Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating.

Luka Simsive, Oleksii Zdorevskyi, Vivek Sharma.

Energy coupling processes in respiratory complex I, a large redox-driven proton pump in the inner mitochondrial membrane, remain one of the most enigmatic problems in modern bioenergetics. Recent high-resolution cryo-EM structures of complex I revealed extensive hydration in the interior of the protein, including the buried E channel, which is an acidic charged conduit that bridges the quinone binding cavity with the extended membrane domain of the enzyme. Despite the general agreement that E channel participates in proton transfer, the absence of proton density in the cryo-EM maps poses a significant challenge to develop viable models of proton pumping. By adhering to the hypothesis that E channel catalyzes transfer of proton(s) from the quinone binding cavity to the membrane-bound proton pumping site(s), we performed hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations using the ∼2.4 Å cryo-EM structure of mitochondrial complex I fromMus musculus. By combining classical atomistic MD simulations with hybrid QM/MM free energy calculations, we identify several energetically favorable Grotthuss-competent proton transfer paths in the E channel region. As part of the long-range coupling in complex I, our calculations show that protonation of a single acidic amino acid residue in the distal MM surroundings can alter the dynamics of proton transfer in the E channel region. Additionally, we pinpoint the gating function of a highly conserved tyrosine residue in the E channel, which undergoes conformational flipping to establish an energetically favorable proton transfer path. In the context of the redox-coupled proton pumping mechanism of complex I, we propose a stepping-stone model of proton transfer through the E channel.

DOI: https://doi.org/10.1021/acs.jcim.5c01365
bioRxiv. 2025 Sep 03. pii: 2025.08.30.673287. [Epub ahead of print]

Mitochondrial DNA damage in substantia nigra pars compacta astrocytes exacerbates dopaminergic neuron loss in a 6-hydroxydopamine mouse model of parkinsonism.

Daniela A Ayala, Grace M Hall, Eliana Tijerina, Luisa Lopez, Zaid Khan, Devanshi Paliwal, Anu Anand, Mendell Rimer, Rahul Srinivasan.

Parkinson's disease (PD) is the fastest growing neurological disorder with no known cure. Our ability to develop disease-modifying treatments that slow down the loss of substantia nigra pars compacta (SNc) dopaminergic (DA) neurons is hindered by a dearth of knowledge on roles for non-neuronal elements such as astrocytes during PD pathogenesis. More specifically, the extent to which mitochondrial DNA (mtDNA) damage in SNc astrocytes contributes to SNc DA neuron loss during PD remains unknown. To address this knowledge gap, we utilized an adeno-associated virus (AAV) called Mito-PstI that expresses the restriction enzyme PstI as an approach to damage mtDNA in SNc astrocytes and assess the effect of astrocytic mtDNA damage on SNc DA neuron function and viability in mice. Mito-PstI-induced mtDNA damage in SNc astrocytes disrupted mitochondrial morphology, caused increased wrapping of SNc astrocytic processes around SNc DA neurons, and abnormally increased dopamine release by SNc DA neuron axonal terminals within the dorsolateral striatum (DLS). In addition, mice injected with Mito-PstI in the SNc showed increased spontaneous and apomorphine-induced rotations contralateral to the side with SNc Mito-PstI injections. In further experiments, we used a parkinsonian mouse model with low dose 6-hydroxydopamine (6-OHDA) injection into the DLS to show that Mito-PstI expression in SNc astrocytes caused a worsening of 6-OHDA-induced spontaneous contralateral rotational behavior, and exacerbated SNc DA neuron loss. These results suggest that mitochondria in SNc astrocytes are not only critical for the function of SNc DA neurons, but are also a new target for developing disease-modifying strategies against PD.
Main Points: Mito-PstI expression in mouse SNc astrocytes increases dopamine releaseMito-PstI expression in SNc astrocytes worsens contralateral rotational behavior in miceMito-PstI expression in SNc astrocytes increases DA neuron loss in 6-OHDA mice.

DOI: https://doi.org/10.1101/2025.08.30.673287
Bioinformatics. 2025 Sep 19. pii: btaf523. [Epub ahead of print]

Federated Learning for the pathogenicity annotation of genetic variants in multi-site clinical settings.

Nigreisy Montalvo, Francisco Requena, Emidio Capriotti, Antonio Rausell.

MOTIVATION: Rare diseases collectively affect 5% of the population. However, fewer than 50% of rare disease patients receive a molecular diagnosis after whole genome sequencing. Supervised machine Learning is a valuable approach for the pathogenicity scoring of human genetic variants. However, existing methods are often trained on curated but limited central repositories, resulting in poor accuracy when tested on external cohorts. Yet, large collections of variants generated at hospitals and research institutions remain inaccessible to machine-learning purposes because of privacy and legal constraints. Federated learning (FL) algorithms have been recently developed enabling institutions to collaboratively train models without sharing their local datasets.
RESULTS: Here, we present a proof-of-concept study evaluating the effectiveness of federated learn-ing for the clinical classification of genetic variants. A comprehensive array of diverse FL strategies was assessed for coding and non-coding Single Nucleotide Variants as well as Copy Number Variants. Our results showed that federated models generally achieved com-parable or superior performance to traditional centralized learning. In addition, federated models reached a robust generalization to independent sets with smaller data fractions as compared to their centralized model counterparts. Our findings support the adoption of FL to establish secure multi-institutional collaborations in human variant interpretation.
AVAILABILITY: All source code required to reproduce the results presented in this manuscript, implemented in Python, is available under the GNU General Public License v3 at https://github.com/RausellLab/FedLearnVar.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btaf523
bioRxiv. 2025 Sep 05. pii: 2025.09.05.674553. [Epub ahead of print]

MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA.

Linhan Wang, Nikolaos Poulis, Deepak Srivastava, Seth L Shipman.

Genetically encoded DNA recorders convert transient biological events into stable genomic mutations, offering a means to reconstruct past cellular states. However, current approaches to log historical events by modifying genomic DNA have limited capacity to record the magnitude of biological signals within individual cells. Here, we introduce MitoScribe, a mitochondrial DNA (mtDNA)-based recording platform that uses mtDNA base editors (DdCBEs) to write graded biological signals into mtDNA as neutral, single-nucleotide substitutions at a defined site. Taking advantage of the hundreds to thousands of mitochondrial genome copies per cell, we demonstrate MitoScribe enables reproducible, highly sensitive, non-destructive, durable, and high-throughput measurements of molecular signals, including hypoxia, NF-κB activity, BMP and Wnt signaling. We show multiple modes of operation, including multiplexed recordings of two independent signals, and coincidence detection of temporally overlapping signals. Coupling MitoScribe with single-cell RNA sequencing and mitochondrial transcript enrichment, we further reconstruct signaling dynamics at the single-cell transcriptome level. Applying this approach during the directed differentiation of human induced pluripotent stem cells (iPSCs) toward mesoderm, we show that early heterogeneity in response to a differentiation cue predicts the later cell state. Together, MitoScribe provides a scalable platform for high-resolution molecular recording in complex cellular contexts.

DOI: https://doi.org/10.1101/2025.09.05.674553
Nature. 2025 Sep 17.

Peroxisomal metabolism of branched fatty acids regulates energy homeostasis.

Xuejing Liu, Anyuan He, Dongliang Lu, Donghua Hu, Min Tan, Abenezer Abere, Parniyan Goodarzi, Bilal Ahmad, Brian Kleiboeker, Brian N Finck, Mohamed Zayed, Katsuhiko Funai, Jonathan R Brestoff, Ali Javaheri, Patricia Weisensee, Bettina Mittendorfer, Fong-Fu Hsu, Paul P Van Veldhoven, Babak Razani, Clay F Semenkovich, Irfan J Lodhi.

Brown and beige adipocytes express uncoupling protein 1 (UCP1), a mitochondrial protein that dissociates respiration from ATP synthesis and promotes heat production and energy expenditure. However, UCP1-/- mice are not obese1-5, consistent with the existence of alternative mechanisms of thermogenesis6-8. Here we describe a UCP1-independent mechanism of thermogenesis involving ATP-consuming metabolism of monomethyl branched-chain fatty acids (mmBCFA) in peroxisomes. These fatty acids are synthesized by fatty acid synthase using precursors derived from catabolism of branched-chain amino acids9 and our results indicate that β-oxidation of mmBCFAs is mediated by the peroxisomal protein acyl-CoA oxidase 2 (ACOX2). Notably, cold exposure upregulated proteins involved in both biosynthesis and β-oxidation of mmBCFA in thermogenic fat. Acute thermogenic stimuli promoted translocation of fatty acid synthase to peroxisomes. Brown-adipose-tissue-specific fatty acid synthase knockout decreased cold tolerance. Adipose-specific ACOX2 knockout also impaired cold tolerance and promoted diet-induced obesity and insulin resistance. Conversely, ACOX2 overexpression in adipose tissue enhanced thermogenesis independently of UCP1 and improved metabolic homeostasis. Using a peroxisome-localized temperature sensor named Pexo-TEMP, we found that ACOX2-mediated fatty acid β-oxidation raised intracellular temperature in brown adipocytes. These results identify a previously unrecognized role for peroxisomes in adipose tissue thermogenesis characterized by an mmBCFA synthesis and catabolism cycle.

DOI: https://doi.org/10.1038/s41586-025-09517-7
Biochemistry. 2025 Sep 17.

Nucleic Acid Sequence Determinants of Transcriptional Pausing by the Human Mitochondrial RNA Polymerase (POLRMT).

An H Hsieh, Tatiana V Mishanina.

Transcription by RNA polymerase (RNAP) lies at the heart of gene expression in all organisms. The speed with which RNAPs produce RNA is tuned, in part, by signals in the transcribed nucleic acid sequences, which temporarily arrange RNAPs into a paused conformation that is unable to extend the RNA. In turn, the altered transcription kinetics of paused RNAPs determine the three-dimensional shape into which RNA ultimately folds and promote or inhibit cotranscriptional events. While pause sequence determinants have been characterized for multisubunit RNAPs in bacteria and in eukaryotic nuclei, this information is lacking for the single-subunit, T-odd phage-like RNAP of human mitochondria, POLRMT. Here, we developed a robust nucleic acid scaffold system to reconstitute POLRMT transcription in vitro and identified multiple transcriptional pause sites on the human mitochondrial DNA (mtDNA). Using one of the pause sequences as a representative, we performed a suite of mutational studies to pinpoint the nucleic acid elements that enhance, weaken, or completely abolish POLRMT pausing. Based on these mutational results, we constructed a consensus pause motif expected to cause strong pausing for POLRMT: 5'-R-10NNNNNNNGT-1G+1-3', where -1 is the 3' nascent RNA nucleotide in the POLRMT active site, +1 is the incoming NTP to be added to the nascent RNA, R is A or G, and N is any base. Strikingly, most of the consensus pause elements in this motif are the same for multisubunit prokaryotic and nuclear RNAPs, hinting at potentially shared features of the pausing mechanism despite the structural differences between polymerases. Finally, a search of the human mtDNA for this pause motif revealed multiple predicted pause sites with potential roles in mitochondrial cotranscriptional processes.

DOI: https://doi.org/10.1021/acs.biochem.5c00236
Front Neurol. 2025 ;16 1584748

Whole mitochondrial genome sequencing in individuals with Leber hereditary optic neuropathy negative for the common pathogenic mitochondrial DNA variants.

Sundaramurthy Srilekha, Selvakumar Ambika, Nagarajan Hemavathy, Dharani Vidhya, Patrick Yu-Wai-Man.

   Purpose: This study aimed to explore the role of additional mitochondrial DNA (mtDNA) variants in the development of Leber hereditary optic neuropathy (LHON) by screening the entire mitochondrial genome in individuals who had previously tested negative for the three common mtDNA variants: m.3460G > A (MT-ND1), m.11778G > A (MT-ND4), and m.14484 T > C (MT-ND6), by conventional Sanger sequencing.
Methods: Forty-one individuals with a suspected clinical diagnosis of LHON were recruited from the neuro-ophthalmology clinic. Each participant had undergone a comprehensive neuro-ophthalmic examination, including slit lamp examination, indirect ophthalmoscopy, visual field perimetry, optical coherence tomography, and MRI of the brain and orbits. Targeted re-sequencing was conducted using next-generation sequencing (NGS) on the HiSeqX 10 platform (Illumina, San Diego, California) with a 2 × 150 bp paired-end configuration. The sequencing reads were aligned to the human mitochondrial genome sequence (hg19). Variants were filtered with the VariMAT tool (v.2.3.9). Haplogroup analysis was performed using Haplogrep 2 (v2.0). To assess the deleteriousness of nonsynonymous variations, bioinformatics prediction tools such as PolyPhen2, SIFT, CADD, and Mutation Assessor were utilized. In addition, while tools like Consurf, PredictSNP, DynaMut, ENCoM, DUET, SDM, mCSM, were employed to evaluate evolutionary conservation, pathogenicity, structural stability, and functional impact.
Results: Whole mitochondrial genome sequencing of 41 clinically suspected LHON cases identified a total of 1,518 mtDNA variants. Of these, 822 were located in the coding regions, including 555 synonymous and 273 non-synonymous variants. Two heteroplasmic disease-causing variants (m.11778G > A and m.3460G > A) were identified in one individual each (90.0 and 63.6%, respectively). Additionally, rare mtDNA variants listed in Mitomap were found in five individuals (5/41, 12.1%), namely, MT-ND1 (m.3335 T > C, m.3394 T > C, m.3395A > G), MT-ND4L (m.10680G > A), and MT-ND6 (m.14502 T > C), with variants in MT-ND1 being the most prevalent (3/41, 7.3%).
Conclusion: Our study of a well-characterized Indian LHON cohort uncovered rare mtDNA variants that should be considered when assessing undiagnosed optic neuropathy cases. Additionally, it underscores the effectiveness of NGS in identifying heteroplasmic mtDNA variants. This indicates that whole mitochondrial genome sequencing via NGS is a more efficient and preferred approach for routine molecular genetic testing.

Keywords:  bioinformatics analysis; haplogroup analysis; homoplasmy; next generation sequencing; rare variants

DOI:  https://doi.org/10.3389/fneur.2025.1584748
BMJ Case Rep. 2025 Sep 18. pii: e265230. [Epub ahead of print]18(9):

Neuroimaging features of familial MT-TK related mitochondrial disease in a child.

Leia Salongo, Ben Nguyen, John Ross Crawford.



Keywords:  Neuro genetics; Neuroimaging; Sleep disorders (neurology)

DOI:  https://doi.org/10.1136/bcr-2025-265230
Sci Adv. 2025 Sep 19. 11(38): eadw9095

Mapping the genetic landscape of iron metabolism uncovers the SETD2 methyltransferase as a modulator of iron flux.

Anthony W Martinelli, Chun-Pei Wu, Tristan Vornbäumen, Hudson W Coates, Louise H Jordon, Niek Wit, Jia J Sia, Anneliese O Speak, James A Nathan.

Cellular iron levels must be tightly regulated to ensure sufficient iron for essential enzymatic functions while avoiding the harmful generation of toxic species. Here, to better understand how iron levels are controlled, we carry out genome-wide mutagenesis screens in human cells. Alongside mapping known components of iron sensing, we determine the relative contributions of iron uptake, iron recycling, ferritin breakdown, and mitochondrial flux in controlling the labile iron pool. We also identify SETD2, a histone methyltransferase, as a chromatin modifying enzyme that controls intracellular iron availability through ferritin breakdown. Functionally, we show that SETD2 inhibition or cancer-associated SETD2 mutations render cells iron deficient, thereby driving resistance to ferroptosis and potentially explaining how some tumors evade antitumoral immunity.

DOI: https://doi.org/10.1126/sciadv.adw9095
Genomics Proteomics Bioinformatics. 2025 Sep 17. pii: qzaf081. [Epub ahead of print]

Single-cell Omics Assessment of Mitochondrial Function: Current Status and Future Perspectives.

Xu Zhang, Peng An, Zhengyang Zhang, Yanling Hao, Xiaoxian Guo, Yinhua Zhu, Zhenglong Gu, Yongting Luo, Junjie Luo.

  In recent years, single-cell omics technologies have seen significant advancements, offering new insights into the study of mitochondria. These technologies are particularly suitable for investigating mitochondria due to their capacity to address intracellular and intercellular heterogeneity. In this review, we categorize the mitochondrial dysfunction and variability identified in both pathological and physiological contexts through single-cell omics assessments. We examine the cutting-edge single-cell omics technologies and track the evolution of studies on mitochondria, highlighting the transition from low-throughput to high-throughput capabilities and from single data types to the integration of multiple genomic and phenomic profiles. Furthermore, we emphasize the applications of single-cell mitochondrial assessment methods in exploring mechanisms, disease screening and prevention, and their potential impacts on lineage tracing, drug discovery, and genetic counseling. Insights gained from single-cell technologies may lead to the development of novel therapeutic strategies, offering promising avenues for addressing diseases associated with mitochondrial dysfunction. Lastly, we identify the limitations of current methodologies and propose areas of focus for future research.

Keywords:  Heterogeneity; Mitochondria; Omics; Pathogenic mechanism; Single-cell

DOI:  https://doi.org/10.1093/gpbjnl/qzaf081
Int J Biol Sci. 2025 ;21(12): 5378-5392

Mitochondrial RNA in Inflammation.

Jian Chen, Chen You, Haibo Xie, Qixing Zhu.

  Mitochondria are dynamic organelles integral to cellular energy metabolism and homeostasis. Beyond their traditional roles, a growing body of evidence underscores the importance of mitochondria as pivotal regulators of innate immune signaling pathways. Recently, mitochondrial RNA (mtRNA) has been identified as a novel modulator of inflammatory responses. mtRNA is detected by intracellular pattern recognition receptors (PRRs), which subsequently activate the mitochondrial antiviral-signaling protein (MAVS) and the interferon regulatory factor 3 (IRF3)/nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling axis, as well as inflammasome pathways. This activation leads to the production of type I interferons and pro-inflammatory cytokines. Furthermore, mtRNA facilitates the propagation of inflammatory signals through exosome-mediated intercellular transfer. Among the various forms of mtRNA, mitochondrial double-stranded RNA (mt-dsRNA) is particularly prone to activating inflammatory responses due to its distinctive double-helical structure. The aberrant accumulation of mt-dsRNA is strongly linked autoimmune diseases, degenerative disease, Liver Disease, kidney disease, cancers, cardiovascular diseases, and respiratory ailments. This review proposes innovative therapeutic strategies aimed at degrading pathological mtRNA or interrupting inflammatory pathways by targeting critical regulatory nodes in mtRNA metabolism and its downstream inflammatory processes.

Keywords:  Inflammation; Mitochondrial; mt-dsRNA.; mtRNA

DOI:  https://doi.org/10.7150/ijbs.119841
bioRxiv. 2025 Sep 09. pii: 2025.06.09.658730. [Epub ahead of print]

A reversible feedback mechanism regulating mitochondrial heme synthesis.

Iva Chitrakar, Alexis B Roberson, Pedro H Ayres-Galhardo, Breann L Brown.

Proper heme biosynthesis is essential for numerous cellular functions across nearly all life forms. In humans, dysregulated heme metabolism is linked to multiple blood diseases, neurodegeneration, cardiovascular disease, and metabolic disorders. Erythroid heme production begins with the rate-limiting enzyme Aminolevulinic Acid Synthase (ALAS2) in the mitochondrion. Although prior studies discuss the regulation of ALAS2 in the nucleus and cytoplasm, its modulation as a mature mitochondrial matrix enzyme remains poorly understood. We report that heme binds mature human ALAS2 with high affinity, acting as a reversible mixed inhibitor that reduces enzymatic activity. Structure-based modeling reveals two flexible regions of ALAS2 interact with heme, locking the enzyme in an inactive conformation and occluding the active site. Our work reveals a negative feedback mechanism for heme synthesis, offering insights into the spatial regulation of ALAS2 and the maturation of the essential heme cofactor.

DOI: https://doi.org/10.1101/2025.06.09.658730
Neurodegener Dis Manag. 2025 Sep 19. 1-11

Reviving mitochondria to restore the mind: stem cell-based bioenergetic rescue in Parkinson's disease.

Supriya Shidhaye, Anis Ahmad Chaudhary, Mayuri Gajghate, Priyanka Singanwad, Milind Umekar, Neha Raut, Hassan Ahmad Rudayni, Rashmi Trivedi.

  Parkinson's disease is a neurodegenerative disorder of aging with dopaminergic neuronal degeneration in the substantia nigra leading to motor dysfunction. Mitochondrial dysfunction is central to its pathophysiology, leading to oxidative stress, derangement of energy metabolism, and induction of neuronal apoptosis. Current therapeutic interventions are symptomatic but fail to stop disease progression. Stem cell-based regenerative strategies have been recognized as potential disease-modifying treatments. Mitochondria-augmented stem cell therapy offers a new mechanism for the correction of cellular bioenergetic deficits. Through genetic manipulations or preconditioning protocols, mesenchymal stem cells and induced pluripotent stem cells are engineered to enhance mitochondrial function and transfer. The engineered cells enable delivery of functional mitochondria into damaged neurons through tunneling nanotubes or extracellular vesicles, promoting ATP production, inhibiting reactive oxygen species, and restoring mitophagy. Preclinical models have demonstrated improved neuronal survival and motor function, and novel technologies like CRISPR gene editing and 3D bioprinting offer improved translational relevance.

Keywords:  Parkinson’s disease; mesenchymal stem cells; mitochondrial dysfunction; mitochondrial transfer; neurorestoration; stem cell therapy

DOI:  https://doi.org/10.1080/17582024.2025.2562741
Nat Chem. 2025 Sep 16.

Photocatalytic labelling-enabled subcellular-resolved RNA profiling and synchronous multi-omics investigation.

Yunpeng Bi, Lishan Yu, Qidong Deng, Linghao Kong, Fuhu Guo, Yuchen Zhang, Ruixiang Wang, Peng R Chen, Jun Liu, Xinyuan Fan.

Understanding cellular functions in health and disease requires dissecting spatiotemporal variations in the subcellular transcriptome. Existing methods for mitochondrial RNA profiling suffer from limitations, including low resolution, contamination and dependence on genetic manipulation. Here we present a bioorthogonal photocatalytic labelling and sequencing strategy (CAT-seq) that enables high-resolution, in situ profiling of mitochondrial RNA in living cells without genetic manipulation. We identified a quinone methide probe for efficient RNA labelling. Rigorous validation and optimization enabled CAT-seq to successfully profile mitochondrial RNA and track RNA dynamics in HeLa cells. We further applied CAT-seq to the challenging RAW 264.7 macrophages, revealing an underlying mitochondrial translational remodelling pathway. By leveraging the chemistry of quinone methide warheads, we established an orthogonal labelling system enabling synchronous RNA and protein multi-omics profiling within the same sample. Together, assisted by bioorthogonal photocatalytic chemistry, CAT-seq offers a general, non-genetic and well-compatible approach for subcellular-resolved RNA and multi-omics investigations, particularly in studies of intact primary living samples that are otherwise challenging to access.

DOI: https://doi.org/10.1038/s41557-025-01946-1
Nature. 2025 Sep 17.

Covariation MS uncovers a protein that controls cysteine catabolism.

Haopeng Xiao, Martha Ordonez, Emma C Fink, Taylor A Covington, Hilina B Woldemichael, Junyi Chen, Mika Sarkin Jain, Milan H Rohatgi, Shelley M Wei, Nils Burger, Muneeb A Sharif, Julius Jan, Yaoyu Wang, Jonathan J Petrocelli, Katherine Blackmore, Amanda L Smythers, Bingsen Zhang, Matthew Gilbert, Hakyung Cheong, Sumeet A Khetarpal, Arianne Smith, Dina Bogoslavski, Yu Lei, Laura Pontano Vaites, Fiona E McAllister, Nick Van Bruggen, Katherine A Donovan, Edward L Huttlin, Evanna L Mills, Eric S Fischer, Edward T Chouchani.

The regulation of metabolic processes by proteins is fundamental to biology and yet is incompletely understood. Here we develop a mass spectrometry (MS)-based approach that leverages genetic diversity to nominate functional relationships between 285 metabolites and 11,868 proteins in living tissues. This method recapitulates protein-metabolite functional relationships mediated by direct physical interactions and local metabolic pathway regulation while nominating 3,542 previously undescribed relationships. With this foundation, we identify a mechanism of regulation over liver cysteine utilization and cholesterol handling, regulated by the poorly characterized protein LRRC58. We show that LRRC58 is the substrate adaptor of an E3 ubiquitin ligase that mediates proteasomal degradation of CDO1, the rate-limiting enzyme of the catabolic shunt of cysteine to taurine1. Cysteine abundance regulates LRRC58-mediated CDO1 degradation, and depletion of LRRC58 is sufficient to stabilize CDO1 to drive consumption of cysteine to produce taurine. Taurine has a central role in cholesterol handling, promoting its excretion from the liver2, and we show that depletion of LRRC58 in hepatocytes increases cysteine flux to taurine and lowers hepatic cholesterol in mice. Uncovering the mechanism of LRRC58 control over cysteine catabolism exemplifies the utility of covariation MS to identify modes of protein regulation of metabolic processes.

DOI: https://doi.org/10.1038/s41586-025-09535-5
Neuron. 2025 Sep 12. pii: S0896-6273(25)00624-5. [Epub ahead of print]

A rare genetic variant confers resistance to neurodegeneration across multiple neurological disorders by augmenting selective autophagy.

Katherine R Croce, Christopher Ng, Serihy Pankiv, Eddy Albarran, Peter Langfelder, Ana Ramos de Jesus, Glenn M Duncan, Nan Wang, Anna Basile, Caitlin McHugh, Nicole A Litt, Alina Li, Sophia Friedman, Etty P Cortes, Michael C Zody, X William Yang, Jun B Ding, Jean Paul G Vonsattel, Anne Simonsen, David E Housman, Nancy S Wexler, Ai Yamamoto.

  The study of disease modifiers is a powerful way to identify patho-mechanisms associated with disease. Using the strong genetic traits of Huntington's disease (HD), we identified a rare, single-nucleotide polymorphism (SNP) in WDFY3 associated with a delayed age of onset of up to 23 years. Remarkably, the introduction of the orthologous SNP into mice recapitulates this neuroprotection, significantly delaying neuropathological and behavioral dysfunction in two models of HD. The SNP increases expression of the protein autophagy-linked Fab1, YOTB, Vac1, and EEA1 (FYVE) protein (Alfy), an autophagy adaptor protein for the clearance of aggregated proteins, whose ectopic overexpression is sufficient to capture the neuroprotective effects of the variant. Increasing Alfy expression protects not only against HD but also against the toxicity due to phospho-α-synuclein and AT8-positive accumulation. By combining human and mouse genetics, we have uncovered a pathway that protects against multiple proteinopathies, revealing a much-sought-after, shared therapeutic target across a broad range of neurodegenerative diseases.

Keywords:  Huntington’s disease; Parkinson’s disease; WDFY3/Alfy; autophagy; neurodegeneration; proteinopathy; selective autophagy; synuclein; tauopathy

DOI:  https://doi.org/10.1016/j.neuron.2025.08.018
Proc Natl Acad Sci U S A. 2025 Sep 23. 122(38): e2512430122

Cryo-EM structure of the prohibitin complex in open conformation.

Sixing Hong, Zeyuan Guan, Liying Zhang, Jinjin Zhuang, Ling Yan, Yanjun Liu, Zhu Liu, Qiang Wang, Ping Yin.

  Prohibitin 1 (PHB1) and Prohibitin 2 (PHB2), two conserved prohibitin members, are primarily localized to the mitochondrial inner membrane (MIM) to form a nanoscale macromolecular prohibitin complex. This prohibitin complex can facilitate the spatial organization of proteins and lipids, thus maintaining cellular metabolism and homeostasis, but its architecture remains largely unknown. Here, we report the cryo-EM structure of a prohibitin complex at 2.8 Å resolution, which contains 11 PHB1-PHB2 heterodimers. This complex displays a bell-like cage, consisting of a lid and a wall, which creates an intermembrane space-facing compartment for the MIM. The lid of the cage is stably assembled, and it is responsible for the prohibitin complex formation. In contrast, the wall of the cage is flexible and exhibits lateral openings, providing a channel for intramembrane exchange of proteins and lipids. These findings provide a structural basis for understanding the scaffold role of the prohibitin complex in organizing intramembrane proteins and lipids.

Keywords:  cryo-EM; membrane microdomain; mitochondria; prohibitin complex; scaffold

DOI:  https://doi.org/10.1073/pnas.2512430122
J Clin Biochem Nutr. 2025 Sep 01. 77(2): 101-112

Mitochondrial oxidative stress, cellular damages and stem cell aging in premature aging models with complex II electron transport defect.

Takamasa Ishii, Kayo Yasuda, Masaki Miyazawa, Hiromi Onouchi, Sumino Yanase, Naoaki Ishii.

  Mitochondria which are the major intracellular reactive oxygen species (ROS) sources produce especially superoxide anion (O2 •-) as a byproduct of energy production. It has been well known that O2 •- is converted from oxygen (O2) and is overproduced by excessive electron leakage from the mitochondrial electron transport chain (ETC), mainly complexes I and III. However we have previously reported that several point mutations (specifically G71E in C. elegans, I71E in Drosophila and V69E in mouse) in succinate dehydrogenase C subunit (SDHC) of complex II cause mitochondrial electron transport defect leading to O2 •- overproduction from mitochondria. These mutations can cause endogenous oxidative stress resulting in tumorigenesis and apoptosis as well as premature death. Recently, we have also demonstrated that premature aging of hematopoietic stem cell with a mutation in SDHC is developed after the growth phase and normal development. Here, we review cellular damages by complex II electron transport defect-induced endogenous oxidative stress in premature aging models.

Keywords:  aging; apoptosis; complex II; mitochondria; oxidative stress

DOI:  https://doi.org/10.3164/jcbn.25-62
bioRxiv. 2025 Sep 04. pii: 2025.09.02.673111. [Epub ahead of print]

Hepatocyte FAM210A deficiency disrupts mitochondrial function and triggers juvenile steatosis with compensatory repair in adulthood.

Yubo Wang, Leah Chu, Yumei Zhou, Zihao Jin, Kyoungrae Kim, Katie Heiden, Miguel A Gutierrez-Monreal, Junxiao Ren, Yufen Li, Zhiyong Cheng, Kari B Basso, Karyn A Esser, Terence E Ryan, Feng Yue.

Mitochondrial dynamics are central to maintaining liver metabolic homeostasis, yet the mechanisms that safeguarding mitochondrial integrity during development and metabolic dysfunction remain poorly defined. Here, we identify Family with sequence similarity 210 member A (FAM210A) as a hepatocyte-enriched mitochondrial regulator essential for postnatal liver maturation. Hepatocyte-specific deletion of Fam210a ( Fam210a HKO ) in mice caused early growth restriction, reduced body and liver mass, and pronounced hepatic steatosis with glycogen depletion. These defects were accompanied by lower postprandial glucose levels in the fasted-refeeding state, impaired oxidative phosphorylation, reduced mtDNA content, and abnormal cristae architecture. Transcriptomic and proteomic profiling revealed broad suppression of fatty acid, sterol, and bile acid metabolism, with concomitant glutathione stress responses. Mechanistically, FAM210A deficiency disrupted the YME1L-OPA1 axis, driving excessive OPA1 cleavage and cristae destabilization. Strikingly, these juvenile defects were transient and resolved by adulthood, underpinned by enhanced hepatocyte proliferation and mitochondrial biogenesis, consistent with a compensatory stress-adaptive response via the activation of ISR signaling. Together, these findings uncover FAM210A as a developmental safeguard of mitochondrial remodeling in hepatocytes and indicate compensatory programs with therapeutic relevance for chronic liver disease.

DOI: https://doi.org/10.1101/2025.09.02.673111
Nat Biotechnol. 2025 Sep;43(9): 1425

Boosted mitochondria reverse cognitive impairment in mice.

Iris Marchal.

DOI: https://doi.org/10.1038/s41587-025-02823-5
Cell Rep. 2025 Sep 15. pii: S2211-1247(25)01051-4. [Epub ahead of print]44(9): 116280

Neurons and astrocytes have distinct organelle signatures and responses to stress.

Shannon N Rhoads, Weizhen Dong, Chih-Hsuan Hsu, Ngudiankama R Mfulama, Ridhi Yarlagadda, Joey V Ragusa, Michael Ye, Andy Henrie, Maria Clara Zanellati, Graham H Diering, Todd J Cohen, Sarah Cohen.

  Neurons and astrocytes play critical yet divergent roles in brain physiology and neurological conditions. Intracellular organelles are integral to cellular function. However, an in-depth characterization of organelles in live neural cells has not been performed. Here, we use multispectral imaging to simultaneously visualize six organelles-endoplasmic reticulum (ER), lysosomes, mitochondria, peroxisomes, Golgi, and lipid droplets-in live primary rodent neurons and astrocytes. We generate a dataset of 173 z stack and 98 time-lapse images, accompanied by quantitative "organelle signature" analysis. Comparative analysis reveals a clear cell-type specificity in organelle morphology and interactions. Neurons are characterized by prominent mitochondrial composition and interactions, while astrocytes contain more lysosomes and lipid droplet interactions. Additionally, neurons display a more robust organelle response than astrocytes to acute oxidative or ER stress. Our data provide a systems-level characterization of neuron and astrocyte organelles that can be a reference for understanding cell-type-specific physiology and disease.

Keywords:  CP: Cell biology; CP: Neuroscience; Golgi; astrocytes; endoplasmic reticulum; lipid droplets; lysosomes; microscopy; mitochondria; neurons; organelles; peroxisomes

DOI:  https://doi.org/10.1016/j.celrep.2025.116280
J Neurol. 2025 Sep 14. 272(9): 632

Genetic background of neurological disorders with basal ganglia calcification.

Maha Yektay Farahmand, Joel Wallenius, Johan Wasselius, Olof Gråhamn, Andreas Puschmann, Andreea Ilinca.

   BACKGROUND: Bilateral basal ganglia calcifications (BGCs), if severe, are known hallmarks for idiopathic BGC disease (IBGC), but if milder, are often considered radiological findings of unknown significance. In previous studies, only a minority of patients with BGC had monogenic forms of IBGC.
METHODS: We studied consecutive patients from a tertiary neurology clinic with bilateral BGCs of variable severity, and their families. We analyzed known IBGC genes, and an extended panel of genes linked to monogenic stroke and metabolic conditions. Clinical, radiological, and genetic data were collected, including vascular risk factors, cerebrovascular events, imaging findings (total calcification score, white matter hyperintensities, ischemic/hemorrhagic lesions), and relevant family history.
RESULTS: Twenty-four families with BGCs and neurological symptoms were analyzed. Disease-causing variants were identified in 14 families (58.3%). Eight patients had IBGC (variants in SLC20A2, PDGFB, MYORG), 4 had mitochondrial disease (MT-TL1), and 2 had monogenic vascular conditions (GAL, MAP3K6). Three variants were novel. BGC severity was highest in IBGC cases, while vascular and mitochondrial cases had milder calcifications. White matter hyperintensities were seen in 94.7% of cases and correlated highly with the total calcification score. Clinical vascular events had occurred in 41.7% cases. No monogenic cause was found in 10 patients, although many of these showed clinical or radiological features suggestive of monogenic disease.
CONCLUSIONS: Bilateral BGCs can occur in many neurogenetic disorders apart from IBGCs, and a broader genetic search increases the diagnostic yield. Patients with BGCs frequently had clinical cerebrovascular events, which emphasizes the role of cerebrovascular pathology in BGCs.

Keywords:  Basal ganglia calcifications; Monogenic neurological disorders; Stroke; White matter hyperintensities; Whole genome sequencing

DOI:  https://doi.org/10.1007/s00415-025-13344-1
Nat Metab. 2025 Sep 16.

BDH2-driven lysosome-to-mitochondria iron transfer shapes ferroptosis vulnerability of the melanoma cell states.

Francesca Rizzollo, Abril Escamilla-Ayala, Nicola Fattorelli, Natalia Barbara Lysiak, Sanket More, Pablo Hernández Varas, Lucia Barazzuol, Chris Van den Haute, Joris Van Asselberghs, David Nittner, Jonathan Coene, Vivek Venkataramani, Bernhard Michalke, Christine Gaillet, Tatiana Cañeque, Irwin Davidson, Steven H L Verhelst, Peter Vangheluwe, Tito Calì, Jean-Christophe Marine, Raphaël Rodriguez, Julie Bonnereau, Patrizia Agostinis.

Iron sustains cancer cell plasticity, yet it also sensitizes the mesenchymal, drug-tolerant phenotype to ferroptosis. This posits that iron compartmentalization must be tightly regulated. However, the molecular machinery governing organelle Fe(II) compartmentalization remains elusive. Here, we show that BDH2 is a key effector of inter-organelle Fe(II) redistribution and ferroptosis vulnerability during melanoma transition from a melanocytic (MEL) to a mesenchymal-like (MES) phenotype. In MEL cells, BDH2 localizes at the mitochondria-lysosome contacts (MLCs) to generate the siderophore 2,5-dihydroxybenzoic acid (2,5-DHBA), which ferries iron into the mitochondria. Fe(II) transfer by BDH2 supports mitochondrial bioenergetics, which is required to maintain lysosomal acidification and MLC formation. Loss of BDH2 alters lysosomal pH and MLC tethering dynamics, causing lysosomal iron sequestration, which primes MES cells for ferroptosis. Rescuing BDH2 expression, or supplementing 2,5-DHBA, rectifies lysosomal pH and MLCs, protecting MES cells from ferroptosis and enhancing their ability to metastasize. Thus, we unveil a BDH2-dependent mechanism that orchestrates inter-organelle Fe(II) transfer, linking metabolic regulation of lysosomal pH to the ferroptosis vulnerability of the mesenchymal, drug-tolerant cancer cells.

DOI: https://doi.org/10.1038/s42255-025-01352-4
Genome Med. 2025 Sep 18. 17(1): 100

Evaluating genome sequencing strategies: trio, singleton, and standard testing in rare disease diagnosis.

Daniel Kaschta, Christina Post, Franziska Gaass, Milad Al-Tawil, Vincent Arriens, Saranya Balachandran, Tobias Bäumer, Valerie Berge, Friederike Birgel, Andreas Dalski, Maike Dittmar, Andre Franke, Sören Franzenburg, Janina Fuß, Bettina Gehring, Rebecca Gembicki, Bianca Greiten, Kristin Grohte, Britta Hanker, Kristian Händler, Lana Harder, Yorck Hellenbroich, Theresia Herget, Gloria Herrmann, Olaf Hiort, Kirstin Hoff, Birga Hoffmann, Nadine Hornig, Irina Hüning, Monika Kautza-Lucht, Juliane Köhler, Anna-Sophie Liegmann, Jasmin Lisfeld, Britt-Sabina Löscher, Nils G Margraf, Michelle Meyenborg, Anna Möllring, Hiltrud Muhle, Eva Maria Murga Penas, Henning Nommels, Dzhoy Papingi, Imke Poggenburg, Jelena Pozojevic, Philip Rosenstiel, Andreas Recke, Kimberly Roberts, Laelia Rösler, Franka Rust, Maj-Britt Salewski, Katharina Schau-Römer, Christian Schlein, Varun K A Sreenivasan, Louiza Toutouna, Caroline Utermann-Thüsing, Amelie T van der Ven, Alexander E Volk, Janne Wehnert, Sandra Wilson, Rixa Woitschach, Veronica Yumiceba, Christine Zühlke, Alexander Münchau, Norbert Brüggemann, Inga Vater, Almuth Caliebe, Inga Nagel, Malte Spielmann.

   BACKGROUND: Short-read genome sequencing (GS) is among the most comprehensive genetic testing methods available, capable of detecting single-nucleotide variants, copy-number variants, mitochondrial variants, repeat expansions, and structural variants in a single assay. Despite its technical advantages, the full clinical utility of GS in real-world diagnostic settings remains to be fully established.
METHODS: This study systematically compared singleton GS (sGS), trio GS (tGS), and exome sequencing-based standard-of-care (SoC) genetic testing in 416 patients with rare diseases in a blinded, prospective study. Three independent teams with divergent baseline expertise evaluated the diagnostic yield of GS as a unifying first-tier test and directly compared its variant detection capabilities, learning curve, and clinical feasibility. The SoC team had extensive prior experience in exome-based diagnostics, while the sGS and tGS teams were newly trained in GS interpretation. Diagnostic yield was assessed through both prospective and retrospective analyses.
RESULTS: In our prospective analysis, tGS achieved the highest diagnostic yield for likely pathogenic/pathogenic variants at 36.1% in the newly trained team, surpassing the experienced SoC team at 35.1% and the newly trained sGS team at 28.8%. To evaluate which variants could technically be identified and account for differences in team experience, we conducted a retrospective analysis, achieving diagnostic yields of 36.7% for SoC, 39.1% for sGS, and 40.0% for tGS. The superior yield of GS was attributed to its ability to detect deep intronic, non-coding, and small copy-number variants missed by SoC. Notably, tGS identified three de novo variants classified as likely pathogenic based on recent GeneMatcher collaborations and newly published gene-disease association studies.
CONCLUSIONS: Our findings demonstrate that GS, particularly tGS, outperforms SoC in diagnosing rare diseases, with sGS providing a more cost-effective alternative. These results suggest that GS should be considered a first-tier genetic test, offering an efficient, single-step approach to reduce the diagnostic odyssey for patients with rare diseases. The trio approach proved especially valuable for less experienced teams, as inheritance data facilitated variant interpretation and maintained high diagnostic yield, while experienced teams achieved comparable results with singleton analysis alone.

Keywords:  Diagnostic yield; Exome sequencing; Genome sequencing; Rare disease; Standard of care

DOI:  https://doi.org/10.1186/s13073-025-01516-7
Int J Biol Macromol. 2025 Sep 17. pii: S0141-8130(25)08295-9. [Epub ahead of print] 147738

CircNCX1 contributes to mitochondrial fusion in cardiomyocyte by mediating the expression of mitofusin 2.

Heng Zhang, Jiaxin Li, Yu Wang, Qi Li, Lin Song, Mengyang Li.

  Mature mammalian cardiomyocytes highly utilize fatty acid-dependent aerobic respiration to produce energy effectively. However, even embryonic and neonatal cardiomyocytes prefer anaerobic glycolysis. The underlying molecular mechanism of this transformation during cardiomyocyte maturation hasn't been fully understood. Circular RNA-circNCX1 (also named circSLC8A1) is enriched in cardiomyocytes and previously demonstrated to inhibit cardiomyocyte proliferation. Here, our study further indicates that circNCX1 is also essential for mitochondria maturation in cardiomyocytes. It was observed that circNCX1 facilitates mitochondrial fusion and closure of the mitochondrial permeability transition pore, leading to an increase in mitochondrial function and metabolic remodeling in cardiomyocytes. Mechanistically, circNCX1 functions in a mitofusin 2 (MFN2)-dependent manner. It up-regulates MFN2 by inhibiting the expression of miR-16-5p. At the animal level, cardiomyocyte-specific silencing of circNCX1 can simultaneously cause mitochondrial dynamics dysfunction and activate cardiomyocyte proliferation, resulting in non-pathological cardiac enlargement with preserved heart function. In summary, our study revealed the regulatory mechanism of circNCX1 on cardiomyocyte maturation and its therapeutic potential in heart disease treatment.

Keywords:  Cardiomyocyte maturation; Circular RNA; MFN2; Metabolic remodeling; Mitochondria; circNCX1; miR-16

DOI:  https://doi.org/10.1016/j.ijbiomac.2025.147738
bioRxiv. 2025 Sep 04. pii: 2025.09.02.673829. [Epub ahead of print]

Mitochondrial organization in the developing proximal tubule is controlled by LRRK2.

Mohsina Anjum Khan, Kyle Bond, Elyse Grilli, Daniel Cameron, Liyang Zhao, Sunder Sims-Lucas, Andrew P McMahon, Thomas J Carroll, Leif Oxburgh.

The proximal tubule of the nephron resorbs water, amino acids and glucose, and its energy demands are high. Formation of the cellular machinery for energy production is an essential step in proximal tubule epithelial cell (PTC) differentiation, and this report focuses on how mitochondria in nascent PTCs are redistributed from their initial apical position to their ultimate basolateral location. We found that mitochondria move from the apical to basolateral side of the PTC coincident with the initiation of lumen flow and that proximal tubules deficient in filtration (aglomerular mice and kidney organoids) maintain their mitochondria in the apical position, indicating that flow is necessary and sufficient for localization. Further, we show that mitochondrial localization depends on the activity of LRRK2 in vitro and in vivo . Modeling the effect of fluid flow on PTCs demonstrates that LRRK2 activity is regulated by fluid shear stress, providing an explanation for how onset of flow in the newly differentiated proximal tubule may trigger the apical-to-basolateral dissemination of mitochondria that forms the template for subsequent PTC maturation. Our findings indicate that mitochondrial redistribution is one component of a cellular program in the nascent PTC that drives function and that this process is regulated by flow.

DOI: https://doi.org/10.1101/2025.09.02.673829
Nat Rev Genet. 2025 Oct;26(10): 659-660

Predicting the regulatory genome.

Sarthak Tiwari, Alireza Karbalayghareh, Christina S Leslie.

DOI: https://doi.org/10.1038/s41576-025-00887-2