bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–01–26
77 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Mitochondrial disease and epilepsy in children.
  2. Mitochondrial protein import stress.
  3. Precise modelling of mitochondrial diseases using optimized mitoBEs.
  4. Derivation and Characterization of Isogenic OPA1 Mutant and Control Human Pluripotent Stem Cell Lines.
  5. Hypotonic Swelling Method for the Isolation of Pure Mitochondria From Primary Human Skeletal Myoblasts for Proteomic Studies.
  6. Role of cardiolipin in skeletal muscle function and its therapeutic implications.
  7. MitoStores: stress-induced aggregation of mitochondrial proteins.
  8. Glycogen homeostasis and mitochondrial DNA expression require motor neuron to muscle TGF-β/Activin signaling in Drosophila.
  9. Fine-tuning tumor immunogenicity with mitochondrial complex I.
  10. Expanding the Concept of Iron Deficiency Using a Mitochondrial Metabolic Approach: Explaining and Preventing Sudden Death.
  11. Fis1 is required for the development of the dendritic mitochondrial network in pyramidal cortical neurons.
  12. Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.
  13. Exerkines and Sarcopenia: Unveiling the Mechanism Behind Exercise-Induced Mitochondrial Homeostasis.
  14. Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm.
  15. MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays.
  16. The mitochondrial choline transporter, SLC25A48, regulates urine and blood choline levels in humans.
  17. GCTransNet: 3D mitochondrial instance segmentation based on Global Context Vision Transformers.
  18. Mitochondria mechanosensing: The powerhouse fueling cellular force signaling.
  19. Selective deficiency of mitochondrial respiratory complex I subunits Ndufs4/6 causes tumor immunogenicity.
  20. Mitochondria and its epigenetic dynamics: Insight into synaptic regulation and synaptopathies.
  21. Discovery of a DNA methylation profile in individuals with Sifrim-Hitz-Weiss syndrome.
  22. A zebrafish model of nicotinamide adenine dinucleotide (NAD+) deficiency-derived congenital disorders.
  23. Hypoxia as a medicine.
  24. Novel c.221+1dup pathogenic variant in AGK gene linked to Sengers syndrome.
  25. Mitochondria complex III-generated superoxide is essential for IL-10 secretion in macrophages.
  26. Mitochondrial NAD+ transporter SLC25A51 linked to human aortic disease.
  27. Long-range PCR as a tool for evaluating mitochondrial DNA damage: Principles, benefits, and limitations of the technique.
  28. The oxygen level in air directs airway epithelial cell differentiation by controlling mitochondrial citrate export.
  29. Discovering and targeting mitochondrial loss in NOTCH1-related aortic aneurysm.
  30. Mitochondrial dysfunction in Alzheimer's disease: Guiding the path to targeted therapies.
  31. Numerous rRNA molecules form the apicomplexan mitoribosome via repurposed protein and RNA elements.
  32. Tissue-specific modulation of NADH consumption as an anti-aging intervention in Drosophila.
  33. Current progress in CRISPR-Cas systems for rare diseases.
  34. Mitochondrial fatty acid oxidation regulates monocytic type I interferon signaling via histone acetylation.
  35. Ionis wins FDA nod for triglyceride-lowering rare disease drug.
  36. Mitochondrial DNA (mtDNA) as fluid biomarker in neurodegenerative disorders: A systematic review.
  37. Bidirectional Mendelian Randomization Analysis of the Association Between Mitochondrial Proteins and Neurodegenerative Diseases.
  38. Mitochondrial regulation of obesity by POMC neurons.
  39. Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients.
  40. Accelerated enzyme engineering by machine-learning guided cell-free expression.
  41. mTOR Ser1261 is an AMPK-dependent phosphosite in mouse and human skeletal muscle not required for mTORC2 activity.
  42. Protocol for real-time assessment of energy metabolism in dissociated mouse retinal photoreceptors using a SeahorseXFe24 analyzer.
  43. Caenorhabditis Elegans as a Model for Environmental Epigenetics.
  44. Programmed neurite degeneration in human central nervous system neurons driven by changes in NAD+ metabolism.
  45. Family and genetic counseling in Leber hereditary optic neuropathy.
  46. Tangled but ordered human mitochondrial tRNA maturation.
  47. Nanoenzyme-Anchored Mitofactories Boost Mitochondrial Transplantation to Restore Locomotor Function after Paralysis Following Spinal Cord Injury.
  48. Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses.
  49. Optogenetic control of mitochondrial aggregation and function.
  50. Landscape of human protein-coding somatic mutations across tissues and individuals.
  51. Hypertrophic Inferior Olivary Nucleus Degeneration and Peri-dentate Hyperintensities in POLG mutation.
  52. Synaptic-mitochondrial transport: mechanisms in neural adaptation and degeneration.
  53. Use of Quantum Dots as Nanotheranostic Agents: Emerging Applications in Rare Genetic Diseases.
  54. A genomic strategy for precision medicine in rare diseases: integrating customized algorithms into clinical practice.
  55. The Lactate-Primed KAT8‒PCK2 Axis Exacerbates Hepatic Ferroptosis During Ischemia/Reperfusion Injury by Reprogramming OXSM-Dependent Mitochondrial Fatty Acid Synthesis.
  56. Mitochondrial quality control: Biochemical mechanism of cardiovascular disease.
  57. Multimodal cell mapping with optimal transport.
  58. Mitochondrial swap from cancer to immune cells thwarts anti-tumour defences.
  59. Exploring the Molecular Interplay Between Oxygen Transport, Cellular Oxygen Sensing, and Mitochondrial Respiration.
  60. Illuminating understudied kinases: a generalizable biosensor development method applied to protein kinase N.
  61. KAT6A acetylation drives metabolic adaptation to mediate cellular growth and mitochondrial metabolism through AMPK interaction.
  62. Emerging Delivery Systems for Enabling Precision Nucleic Acid Therapeutics.
  63. Mitochondrial NAD+ deficiency in vascular smooth muscle impairs collagen III turnover to trigger thoracic and abdominal aortic aneurysm.
  64. TMAO accelerates cellular aging by disrupting endoplasmic reticulum integrity and mitochondrial unfolded protein response.
  65. Cryo-EM structure and regulation of human NAD kinase.
  66. Increased Rate of Unique Mitochondrial DNA Deletion Breakpoints in Young Adults With Early-Life Stress.
  67. KNTC1 introduces segmental heterogeneity to mitochondria.
  68. Dysfunctional BCAA degradation triggers neuronal damage through disrupted AMPK-mitochondrial axis due to enhanced PP2Ac interaction.
  69. Drp1-associated genes implicated in sepsis survival.
  70. Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery.
  71. Translating Time: Challenges, Progress, and Future Directions.
  72. Editorial: Revealing the unconventional mechanisms of mitochondria-targeting drugs in heart-related diseases.
  73. Long-read sequencing revealed complex biallelic pentanucleotide repeat expansions in RFC1-related Parkinson's disease.
  74. Unlocking biological complexity: the role of machine learning in integrative multi-omics.
  75. Protocol for generating protein profiles and distance-based network analysis of murine tissue slices.
  76. Carnitine Palmitoyltransferase II (CPT2) Deficiency in a Patient With Recurrent Rhabdomyolysis: A Case Report.
  77. MnSOD non-acetylation mimic knock-in mice exhibit dilated cardiomyopathy.
  1. Front Neurol. 2024 ;15 1499876
    Mitochondrial disease and epilepsy in children.
    Xuan Zhang, Bo Zhang, Zhiming Tao, Jianmin Liang.
      Mitochondria is the cell's powerhouse. Mitochondrial disease refers to a group of clinically heterogeneous disorders caused by dysfunction in the mitochondrial respiratory chain, often due to mutations in mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) that encodes mitochondrial proteins. This dysfunction can lead to a variety of clinical phenotypes, particularly affecting organs with high energy demands, such as the brain and muscles. Epilepsy is a prevalent neurological disorder in children and is also a frequent manifestation of mitochondrial disease. The exact mechanisms underlying epilepsy in mitochondrial disease remain unclear and are thought to involve multiple contributing factors. This review explores common mitochondrial diseases associated with epilepsy, focusing on their prevalence, seizure types, EEG features, therapeutic strategies, and outcomes. It also summarizes the relationship between the molecular genetics of mitochondrial respiratory chain components and the development of epilepsy.
    Keywords:  coenzyme Q; cytochrome C; epilepsy; genes; mitochondrial complex
    DOI:  https://doi.org/10.3389/fneur.2024.1499876
  2. Nat Cell Biol. 2025 Jan 22.
    Mitochondrial protein import stress.
    Nikolaus Pfanner, Fabian den Brave, Thomas Becker.
      Mitochondria have to import a large number of precursor proteins from the cytosol. Chaperones keep these proteins in a largely unfolded state and guide them to the mitochondrial import sites. Premature folding, mitochondrial stress and import defects can cause clogging of import sites and accumulation of non-imported precursors, representing a critical burden for cellular proteostasis. Here we discuss how cells respond to mitochondrial protein import stress by regenerating clogged import sites and inducing stress responses. The mitochondrial protein import machinery has a dual role by serving as sensor for detecting mitochondrial dysfunction and inducing stress-response pathways. The production of chaperones that fold or sequester precursor proteins in deposits is induced and the proteasomal activity is increased to remove the excess precursor proteins. Together, these pathways reveal how mitochondria are tightly integrated into a cellular proteostasis and stress response network to maintain cell viability.
    DOI:  https://doi.org/10.1038/s41556-024-01590-w
  3. Nature. 2025 Jan 22.
    Precise modelling of mitochondrial diseases using optimized mitoBEs.
    Xiaoxue Zhang, Xue Zhang, Jiwu Ren, Jiayi Li, Xiaoxu Wei, Ying Yu, Zongyi Yi, Wensheng Wei.
      The development of animal models is crucial for studying and treating mitochondrial diseases. Here we optimized adenine and cytosine deaminases to reduce off-target effects on the transcriptome and the mitochondrial genome, improving the accuracy and efficiency of our newly developed mitochondrial base editors (mitoBEs)1. Using these upgraded mitoBEs (version 2 (v2)), we targeted 70 mouse mitochondrial DNA mutations analogous to human pathogenic variants2, establishing a foundation for mitochondrial disease mouse models. Circular RNA-encoded mitoBEs v2 achieved up to 82% editing efficiency in mice without detectable off-target effects in the nuclear genome. The edited mitochondrial DNA persisted across various tissues and was maternally inherited, resulting in F1 generation mice with mutation loads as high as 100% and some mice exhibiting editing only at the target site. By optimizing the transcription activator-like effector (TALE) binding site, we developed a single-base-editing mouse model for the mt-Nd5 A12784G mutation. Phenotypic evaluations led to the creation of mouse models for the mt-Atp6 T8591C and mt-Nd5 A12784G mutations, exhibiting phenotypes corresponding to the reduced heart rate seen in Leigh syndrome and the vision loss characteristic of Leber's hereditary optic neuropathy, respectively. Moreover, the mt-Atp6 T8591C mutation proved to be more deleterious than mt-Nd5 A12784G, affecting embryonic development and rapidly diminishing through successive generations. These upgraded mitoBEs offer a highly efficient and precise strategy for constructing mitochondrial disease models, laying a foundation for further research in this field.
    DOI:  https://doi.org/10.1038/s41586-024-08469-8
  4. Cells. 2025 Jan 17. pii: 137. [Epub ahead of print]14(2):
    Derivation and Characterization of Isogenic OPA1 Mutant and Control Human Pluripotent Stem Cell Lines.
    Katherine A Pohl, Xiangmei Zhang, Johnny Jeonghyun Ji, Linsey Stiles, Alfredo A Sadun, Xian-Jie Yang.
      Dominant optic atrophy (DOA) is the most commonly inherited optic neuropathy. The majority of DOA is caused by mutations in the OPA1 gene, which encodes a dynamin-related GTPase located to the mitochondrion. OPA1 has been shown to regulate mitochondrial dynamics and promote fusion. Within the mitochondrion, proteolytically processed OPA1 proteins form complexes to maintain membrane integrity and the respiratory chain complexity. Although OPA1 is broadly expressed, human OPA1 mutations predominantly affect retinal ganglion cells (RGCs) that are responsible for transmitting visual information from the retina to the brain. Due to the scarcity of human RGCs, DOA has not been studied in depth using the disease affected neurons. To enable studies of DOA using stem-cell-derived human RGCs, we performed CRISPR-Cas9 gene editing to generate OPA1 mutant pluripotent stem cell (PSC) lines with corresponding isogenic controls. CRISPR-Cas9 gene editing yielded both OPA1 homozygous and heterozygous mutant ESC lines from a parental control ESC line. In addition, CRISPR-mediated homology-directed repair (HDR) successfully corrected the OPA1 mutation in a DOA patient's iPSCs. In comparison to the isogenic controls, the heterozygous mutant PSCs expressed the same OPA1 protein isoforms but at reduced levels; whereas the homozygous mutant PSCs showed a loss of OPA1 protein and altered mitochondrial morphology. Furthermore, OPA1 mutant PSCs exhibited reduced rates of oxygen consumption and ATP production associated with mitochondria. These isogenic PSC lines will be valuable tools for establishing OPA1-DOA disease models in vitro and developing treatments for mitochondrial deficiency associated neurodegeneration.
    Keywords:  CRISPR-Cas9 editing; OPA1 gene; dominant optic atrophy; isogenic human pluripotent stem cell lines; mitochondria
    DOI:  https://doi.org/10.3390/cells14020137
  5. J Cell Mol Med. 2025 Jan;29(2): e70370
    Hypotonic Swelling Method for the Isolation of Pure Mitochondria From Primary Human Skeletal Myoblasts for Proteomic Studies.
    Evrim Aksu-Menges, Eray Taha Kumtepe, Gurler Akpinar, Burcu Balci-Hayta.
      Mitochondria play a fundamental role in energy metabolism, particularly in high-energy-demand tissues such as skeletal muscle. Understanding the proteomic composition of mitochondria in these cells is crucial for elucidating the mechanisms underlying muscle physiology and pathology. However, effective isolation of mitochondria from primary human skeletal muscle cells has been challenging due to the complex cellular architecture and the propensity for contamination with other organelles. Here, we compared four different methods to isolate mitochondria from primary human skeletal myoblasts regarding total protein yield, mitochondrial enrichment capacity and purity of the isolated fraction. We presented a modified method that combines differential centrifugation with a hypotonic swelling step and a subsequent purification process to minimise cellular contamination. We validated our method by demonstrating its ability to obtain highly pure mitochondrial fractions, as confirmed by Western Blot with mitochondrial, cytosolic and nuclear markers. We demonstrated that proteomic analysis can be performed with isolated mitochondria. Our approach provides a valuable tool for investigating mitochondrial dynamics, biogenesis and function in the context of skeletal muscle biology in health and disease. This methodological advancement opens new avenues for mitochondrial research and its implications in myopathies, sarcopenia, cachexia and metabolic disorders.
    Keywords:  differential centrifugation; hypotonic swelling method; mitochondria isolation; primary human skeletal myoblasts
    DOI:  https://doi.org/10.1111/jcmm.70370
  6. Cell Commun Signal. 2025 Jan 21. 23(1): 36
    Role of cardiolipin in skeletal muscle function and its therapeutic implications.
    Youngbum Yoo, MyeongHoon Yeon, Mee-Sup Yoon, Young-Kyo Seo.
      Cardiolipin, a unique phospholipid predominantly present in the inner mitochondrial membrane, is critical for maintaining mitochondrial integrity and function. Its dimeric structure and role in supporting mitochondrial dynamics, energy production, and mitophagy make it indispensable for skeletal muscle health. This review provides a comprehensive overview of cardiolipin biosynthesis, remodeling processes, and essential functions within mitochondria. We explore the influences of cardiolipin on the stability of the mitochondrial complexes, cristae formation, and calcium handling, all of which are vital for efficient oxidative phosphorylation and muscle contraction. Skeletal muscle, with its high energy demands, is particularly dependent on cardiolipin for optimal performance. We discuss the impact of aging on cardiolipin levels, which correlates with a decline in mitochondrial function and muscle mass, contributing to conditions such as sarcopenia. Furthermore, we examined the relationship between cardiolipin and endurance exercise, highlighting the effects of exercise-induced increase in cardiolipin levels on the improvement of mitochondrial function and muscle health. The role of Crls1 in cardiolipin synthesis has been emphasized as a potential therapeutic target for the treatment of sarcopenia. Increasing cardiolipin levels through gene therapy, pharmacological interventions, or specific exercise and nutritional strategies holds promise for mitigating muscle atrophy and promoting muscle regeneration. By focusing on the multifaceted role of cardiolipin in mitochondria and muscle health, we aimed to provide new insights into therapeutic approaches for enhancing muscle function and combating age-related muscle decline.
    Keywords:   Crls1 ; Cardiolipin; Exercise; Mitochondrial function; Muscle atrophy; Oxidative phosphorylation; Sarcopenia; Skeletal muscle
    DOI:  https://doi.org/10.1186/s12964-025-02032-2
  7. Biol Chem. 2025 Jan 21.
    MitoStores: stress-induced aggregation of mitochondrial proteins.
    Pragya Kaushik, Johannes M Herrmann, Katja G Hansen.
      Most mitochondrial proteins are synthesized in the cytosol and post-translationally imported into mitochondria. If the rate of protein synthesis exceeds the capacity of the mitochondrial import machinery, precursor proteins can transiently accumulate in the cytosol. The cytosolic accumulation of mitochondrial precursors jeopardizes cellular protein homeostasis (proteostasis) and can be the cause of diseases. In order to prevent these toxic effects, most non-imported precursors are rapidly degraded by the ubiquitin-proteasome system. However, cells employ a second layer of defense which is the facilitated sequestration of mitochondrial precursor proteins in transient protein aggregates. The formation of such structures is triggered by nucleation factors such as small heat shock proteins. Disaggregases and chaperones can liberate precursors from cytosolic aggregates to pass them on to the mitochondrial import machinery or, under persistent stress conditions, to the proteasome for degradation. Owing to their role as transient buffering systems, these aggregates were referred to as MitoStores. This review articles provides a general overview about the MitoStore concept and the early stages in mitochondrial protein biogenesis in yeast and, in cases where aspects differ, in mammalian cells.
    Keywords:  aggregates; mitochondria; mitostores; proteasome; protein targeting; quality control
    DOI:  https://doi.org/10.1515/hsz-2024-0148
  8. iScience. 2025 Jan 17. 28(1): 111611
    Glycogen homeostasis and mitochondrial DNA expression require motor neuron to muscle TGF-β/Activin signaling in Drosophila.
    Heidi Bretscher, Michael B O'Connor.
      Maintaining metabolic homeostasis requires coordinated nutrient utilization between intracellular organelles and across multiple organ systems. Many organs rely heavily on mitochondria to generate (ATP) from glucose, or stored glycogen. Proteins required for ATP generation are encoded in both nuclear and mitochondrial DNA (mtDNA). We show that motoneuron to muscle signaling by the TGFβ/Activin family member Actβ positively regulates glycogen levels during Drosophila development. Remarkably, we find that levels of stored glycogen are unaffected by altering cytoplasmic glucose catabolism. Instead, loss of Actβ reduces levels of nuclearly encoded genes required for mtDNA replication, transcription, and translation and mtDNA levels. Direct RNAi knockdown of nuclearly encoded mtDNA expression factors in muscle also results in decreased glycogen stores. Lastly, expressing an activated form of the type I receptor Baboon in muscle restores both glycogen and mtDNA levels in actβ mutants, thereby confirming a direct link between Actβ signaling, glycogen homeostasis, and mtDNA expression factors.
    Keywords:  Cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2024.111611
  9. Nat Cancer. 2025 Jan 17.
    Fine-tuning tumor immunogenicity with mitochondrial complex I.
    Désirée Schatton, Christian Frezza.
      
    DOI:  https://doi.org/10.1038/s43018-024-00874-2
  10. Pediatr Blood Cancer. 2025 Jan 21. e31561
    Expanding the Concept of Iron Deficiency Using a Mitochondrial Metabolic Approach: Explaining and Preventing Sudden Death.
    Christineil Thompson.
      
    Keywords:  athlete; cardiac arrest; iron deficiency; mitochondria; nutrition
    DOI:  https://doi.org/10.1002/pbc.31561
  11. bioRxiv. 2025 Jan 07. pii: 2025.01.07.631801. [Epub ahead of print]
    Fis1 is required for the development of the dendritic mitochondrial network in pyramidal cortical neurons.
    Klaudia Strucinska, Parker Kneis, Travis Pennington, Katarzyna Cizio, Patrycja Szybowska, Abigail Morgan, Joshua Weertman, Tommy L Lewis.
      Mitochondrial ATP production and calcium buffering are critical for metabolic regulation and neurotransmission making the formation and maintenance of the mitochondrial network a critical component of neuronal health. Cortical pyramidal neurons contain compartment-specific mitochondrial morphologies that result from distinct axonal and dendritic mitochondrial fission and fusion profiles. We previously showed that axonal mitochondria are maintained at a small size as a result of high axonal mitochondrial fission factor (Mff) activity. However, loss of Mff activity had little effect on cortical dendritic mitochondria, raising the question of how fission/fusion balance is controlled in the dendrites. Thus, we sought to investigate the role of another fission factor, fission 1 (Fis1), on mitochondrial morphology, dynamics and function in cortical neurons. We knocked down Fis1 in cortical neurons both in primary culture and in vivo , and unexpectedly found that Fis1 depletion decreased mitochondrial length in the dendrites, without affecting mitochondrial size in the axon. Further, loss of Fis1 activity resulted in both increased mitochondrial motility and dynamics in the dendrites. These results argue Fis1 exhibits dendrite selectivity and plays a more complex role in neuronal mitochondrial dynamics than previously reported. Functionally, Fis1 loss resulted in reduced mitochondrial membrane potential, increased sensitivity to complex III blockade, and decreased mitochondrial calcium uptake during neuronal activity. The altered mitochondrial network culminated in elevated resting calcium levels that increased dendritic branching but reduced spine density. We conclude that Fis1 regulates morphological and functional mitochondrial characteristics that influence dendritic tree arborization and connectivity.
    DOI:  https://doi.org/10.1101/2025.01.07.631801
  12. Sci Adv. 2025 Jan 24. 11(4): eadu5787
    Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.
    Felix Kraus, Yuchen He, Sharan Swarup, Katherine A Overmyer, Yizhi Jiang, Johann Brenner, Cristina Capitanio, Anna Bieber, Annie Jen, Nicole M Nightingale, Benton J Anderson, Chan Lee, Joao A Paulo, Ian R Smith, Jürgen M Plitzko, Steven P Gygi, Brenda A Schulman, Florian Wilfling, Joshua J Coon, J Wade Harper.
      Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multiomic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lysophosphatidylcholine species and multilamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.
    DOI:  https://doi.org/10.1126/sciadv.adu5787
  13. Metabolites. 2025 Jan 16. pii: 59. [Epub ahead of print]15(1):
    Exerkines and Sarcopenia: Unveiling the Mechanism Behind Exercise-Induced Mitochondrial Homeostasis.
    Jiayin Wang, Dandan Jia, Zhiwang Zhang, Dan Wang.
      Background/Objectives: Sarcopenia, characterized by the progressive loss of muscle mass and strength, is linked to physical disability, metabolic dysfunction, and an increased risk of mortality. Exercise therapy is currently acknowledged as a viable approach for addressing sarcopenia. Nevertheless, the molecular mechanisms behind exercise training or physical activity remain poorly understood. The disruption of mitochondrial homeostasis is implicated in the pathogenesis of sarcopenia. Exercise training effectively delays the onset of sarcopenia by significantly maintaining mitochondrial homeostasis, including promoting mitophagy, improving mitochondrial biogenesis, balancing mitochondrial dynamics, and maintaining mitochondrial redox. Exerkines (e.g., adipokines, myokines, hepatokines, and osteokines), signaling molecules released in response to exercise training, may potentially contribute to skeletal muscle metabolism through ameliorating mitochondrial homeostasis, reducing inflammation, and regulating protein synthesis as a defense against sarcopenia. Methods: In this review, we provide a detailed summary of exercise-induced exerkines and confer their benefit, with particular focus on their impact on mitochondrial homeostasis in the context of sarcopenia. Results: Exercise induces substantial adaptations in skeletal muscle, including increased muscle mass, improved muscle regeneration and hypertrophy, elevated hormone release, and enhanced mitochondrial function. An expanding body of research highlights that exerkines have the potential to regulate processes such as mitophagy, mitochondrial biogenesis, dynamics, autophagy, and redox balance. These mechanisms contribute to the maintenance of mitochondrial homeostasis, thereby supporting skeletal muscle metabolism and mitochondrial health. Conclusions: Through a comprehensive investigation of the molecular mechanisms within mitochondria, the context reveals new insights into the potential of exerkines as key exercise-protective sensors for combating sarcopenia.
    Keywords:  exercise; exerkines; mitochondrial homeostasis; sarcopenia
    DOI:  https://doi.org/10.3390/metabo15010059
  14. Sci China Life Sci. 2025 Jan 21.
    Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm.
    Lintao Luo, Mengge Wang, Yunhui Liu, Jianbo Li, Fengxiao Bu, Huijun Yuan, Renkuan Tang, Chao Liu, Guanglin He.
      Human mitochondrial DNA (mtDNA) harbors essential mutations linked to aging, neurodegenerative diseases, and complex muscle disorders. Due to its uniparental and haploid inheritance, mtDNA captures matrilineal evolutionary trajectories, playing a crucial role in population and medical genetics. However, critical questions about the genomic diversity patterns, inheritance models, and evolutionary and medical functions of mtDNA remain unresolved or underexplored, particularly in the transition from traditional genotyping to large-scale genomic analyses. This review summarizes recent advancements in data-driven genomic research and technological innovations that address these questions and clarify the biological impact of nuclear-mitochondrial segments (NUMTs) and mtDNA variants on human health, disease, and evolution. We propose a streamlined pipeline to comprehensively identify mtDNA and NUMT genomic diversity using advanced sequencing and computational technologies. Haplotype-resolved mtDNA sequencing and assembly can distinguish authentic mtDNA variants from NUMTs, reduce diagnostic inaccuracies, and provide clearer insights into heteroplasmy patterns and the authenticity of paternal inheritance. This review emphasizes the need for integrative multi-omics approaches and emerging long-read sequencing technologies to gain new insights into mutation mechanisms, the influence of heteroplasmy and paternal inheritance on mtDNA diversity and disease susceptibility, and the detailed functions of NUMTs.
    Keywords:  NUMT; evolutionary medicine; genomic database; heteroplasmy; mitochondrial DNA
    DOI:  https://doi.org/10.1007/s11427-024-2736-7
  15. Genome Biol. 2025 Jan 21. 26(1): 13
    MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays.
    Alan F Rubin, Jeremy Stone, Aisha Haley Bianchi, Benjamin J Capodanno, Estelle Y Da, Mafalda Dias, Daniel Esposito, Jonathan Frazer, Yunfan Fu, Sally B Grindstaff, Matthew R Harrington, Iris Li, Abbye E McEwen, Joseph K Min, Nick Moore, Olivia G Moscatelli, Jesslyn Ong, Polina V Polunina, Joshua E Rollins, Nathan J Rollins, Ashley E Snyder, Amy Tam, Matthew J Wakefield, Shenyi Sunny Ye, Lea M Starita, Vanessa L Bryant, Debora S Marks, Douglas M Fowler.
      Multiplexed assays of variant effect (MAVEs) are a critical tool for researchers and clinicians to understand genetic variants. Here we describe the 2024 update to MaveDB ( https://www.mavedb.org/ ) with four key improvements to the MAVE community's database of record: more available data including over 7 million variant effect measurements, an improved data model supporting assays such as saturation genome editing, new built-in exploration and visualization tools, and powerful APIs for data federation and streamlined submission and access. Together these changes support MaveDB's role as a hub for the analysis and dissemination of MAVEs now and into the future.
    Keywords:  DMS; Deep mutational scanning; Functional genomics; MAVEs; Multiplexed assays of variant effect; Variant classification
    DOI:  https://doi.org/10.1186/s13059-025-03476-y
  16. Kidney Int. 2025 Feb;pii: S0085-2538(24)00811-1. [Epub ahead of print]107(2): 225-227
    The mitochondrial choline transporter, SLC25A48, regulates urine and blood choline levels in humans.
    Soumya Maity, Kumar Sharma.
      Choline is an essential nutrient for the biosynthesis of phospholipids and neurotransmitters and controls several physiological functions in mammals. It is metabolized in the organelles within cells, including mitochondria. However, its subcellular distribution and mode of mitochondrial transport remain poorly understood. Patil et al. identified SLC25A48 as a mitochondrial choline transporter, and its loss-of-function mutations were associated with elevated urine and plasma choline levels in humans.
    DOI:  https://doi.org/10.1016/j.kint.2024.11.014
  17. J Struct Biol. 2025 Jan 20. pii: S1047-8477(25)00005-X. [Epub ahead of print] 108170
    GCTransNet: 3D mitochondrial instance segmentation based on Global Context Vision Transformers.
    Chaoyi Chen, Yidan Yan, Jingpeng Wu, Wen-Biao Gan.
      Mitochondria are double membrane-bound organelles essential for generating energy in eukaryotic cells. Mitochondria can be readily visualized in 3D using Volume Electron Microscopy (vEM), and accurate image segmentation is vital for quantitative analysis of mitochondrial morphology and function. To address the challenge of segmenting small mitochondrial compartments in vEM images, we propose an automated mitochondrial segmentation method called GCTransNet. This method employs grayscale migration technology to preprocess images, effectively reducing intensity distribution differences across EM images. By utilizing 3D Global Context Vision Transformers (GC-ViT) combined with global context self-attention modules and local self-attention modules, GCTransNet precisely models long-range and short-range spatial interactions. The long-range interactions enable the model to capture the global structural relationships within the mitochondrial segmentation network, while the short-range interactions refine local details and boundaries. In our approach, the encoder of the 3D U-Net network, a classical multi-scale learning architecture that retains high-resolution features through skip connections and combines multi-scale features for precise segmentation, is replaced by a 3D GC-ViT. The GC-ViT leverages shifted window-based self-attention, capturing long-range dependencies and offering improved segmentation accuracy compared to traditional U-Net encoders. In the MitoEM mitochondrial segmentation challenge, GCTransNet achieved state-of-the-art results, demonstrating its superiority in automated mitochondrial segmentation. The code and its documentation are publicly available at https://github.com/GanLab123/GCTransNet.
    Keywords:  3D instance segmentation; Electron microscopy image; Mitochondrial morphology; Vision Transformer
    DOI:  https://doi.org/10.1016/j.jsb.2025.108170
  18. Curr Biol. 2025 Jan 20. pii: S0960-9822(24)01646-4. [Epub ahead of print]35(2): R76-R79
    Mitochondria mechanosensing: The powerhouse fueling cellular force signaling.
    Jorge Oliver-De La Cruz, Pere Roca-Cusachs.
      Mechanical forces influence mitochondrial dynamics through previously unexplored mechanisms. A new study demonstrates that actomyosin tension inhibits mitochondrial fission by phosphorylating a key component of the fission complex and that this event regulates the nuclear accumulation of critical transcription factors.
    DOI:  https://doi.org/10.1016/j.cub.2024.12.006
  19. Nat Cancer. 2025 Jan 17.
    Selective deficiency of mitochondrial respiratory complex I subunits Ndufs4/6 causes tumor immunogenicity.
    Jiaxin Liang, Tevis Vitale, Xixi Zhang, Thomas D Jackson, Deyang Yu, Mark Jedrychowski, Steve P Gygi, Hans R Widlund, Kai W Wucherpfennig, Pere Puigserver.
      Cancer cells frequently rewire their metabolism to support proliferation and evade immune surveillance, but little is known about metabolic targets that could increase immune surveillance. Here we show a specific means of mitochondrial respiratory complex I (CI) inhibition that improves tumor immunogenicity and sensitivity to immune checkpoint blockade (ICB). Targeted genetic deletion of either Ndufs4 or Ndufs6, but not other CI subunits, induces an immune-dependent growth attenuation in melanoma and breast cancer models. We show that deletion of Ndufs4 induces expression of the major histocompatibility complex (MHC) class I co-activator Nlrc5 and antigen presentation machinery components, most notably H2-K1. This induction of MHC-related genes is driven by a pyruvate dehydrogenase-dependent accumulation of mitochondrial acetyl-CoA, which leads to an increase in histone H3K27 acetylation within the Nlrc5 and H2-K1 promoters. Taken together, this work shows that selective CI inhibition restricts tumor growth and that specific targeting of Ndufs4 or Ndufs6 increases T cell surveillance and ICB responsiveness.
    DOI:  https://doi.org/10.1038/s43018-024-00895-x
  20. Funct Integr Genomics. 2025 Jan 23. 25(1): 26
    Mitochondria and its epigenetic dynamics: Insight into synaptic regulation and synaptopathies.
    Shiwangi Gupta, Abhinoy Kishore, Vikas Rishi, Aanchal Aggarwal.
      Mitochondria, the cellular powerhouses, are pivotal to neuronal function and health, particularly through their role in regulating synaptic structure and function. Spine reprogramming, which underlies synapse development, depends heavily on mitochondrial dynamics-such as biogenesis, fission, fusion, and mitophagy as well as functions including ATP production, calcium (Ca2+) regulation, and retrograde signaling. Mitochondria supply the energy necessary for assisting synapse development and plasticity, while also regulating intracellular Ca2+ homeostasis to prevent excitotoxicity and support synaptic neurotransmission. Additionally, the dynamic processes of mitochondria ensure mitochondrial quality and adaptability, which are essential for maintaining effective synaptic activity. Emerging evidence highlights the significant role of epigenetic modifications in regulating mitochondrial dynamics and function. Epigenetic changes influence gene expression, which in turn affects mitochondrial activity, ensuring coordinated responses necessary for synapse development. Furthermore, metabolic changes within mitochondria can impact the epigenetic machinery, thereby modulating gene expression patterns that support synaptic integrity. Altered epigenetic regulation affecting mitochondrial dynamics and functions is linked to several neurological disorders, including Amyotrophic Lateral Sclerosis, Huntington's, Alzheimer's, and Parkinson's diseases, emphasizing its crucial function. The review delves into the molecular machinery involved in mitochondrial dynamics, ATP and Ca2+ regulation, highlighting the role of key proteins that facilitate the processes. Additionally, it also shed light on the emerging epigenetic factors influencing these regulations. It provides a thorough summary on the current understanding of the role of mitochondria in synapse development and emphasizes the importance of both molecular and epigenetic mechanisms in maintaining synaptic integrity.
    DOI:  https://doi.org/10.1007/s10142-025-01530-3
  21. Am J Hum Genet. 2025 Jan 15. pii: S0002-9297(24)00463-4. [Epub ahead of print]
    Discovery of a DNA methylation profile in individuals with Sifrim-Hitz-Weiss syndrome.
    Karim Karimi, Yael Lichtenstein, Jack Reilly, Haley McConkey, Raissa Relator, Michael A Levy, Jennifer Kerkhof, Arjan Bouman, Joseph D Symonds, Jamal Ghoumid, Thomas Smol, Katie Clarkson, Katy Drazba, Raymond J Louie, Valancy Miranda, Cathleen McCann, Jamie Motta, Emily Lancaster, Suzanne Sallevelt, Richard Sidlow, Jennifer Morrison, Mark Hannibal, Jessica O'Shea, Victor Marin, Chitra Prasad, Chirag Patel, Salmo Raskin, Seco Moro Maria-Noelia, Aranzazú Diaz de Bustamante, Daphna Marom, Tali Barkan, Boris Keren, Celine Poirsier, Lior Cohen, Estelle Colin, Kathleen Gorman, Emily Gallant, Leonie A Menke, Irene Valenzuela Palafoll, Natalie Hauser, Ingrid M Wentzensen, Julia Rankin, Peter D Turnpenny, Philippe M Campeau, Tugce B Balci, Matthew L Tedder, Bekim Sadikovic, Karin Weiss.
      Pathogenic heterozygous variants in CHD4 cause Sifrim-Hitz-Weiss syndrome, a neurodevelopmental disorder associated with brain anomalies, heart defects, macrocephaly, hypogonadism, and additional features with variable expressivity. Most individuals have non-recurrent missense variants, complicating variant interpretation. A few were reported with truncating variants, and their role in disease is unclear. DNA methylation episignatures have emerged as highly accurate diagnostic biomarkers in a growing number of rare diseases. We aimed to study evidence for the existence of a CHD4-related DNA methylation episignature. We collected blood DNA samples and/or clinical information from 39 individuals with CHD4 variants, including missense and truncating variants. Genomic DNA methylation analysis was performed on 28 samples. We identified a sensitive and specific DNA methylation episignature in samples with pathogenic missense variants within the ATPase/helicase domain. The same episignature was observed in a family with variable expressivity, a de novo variant near the PHD domain, variants of uncertain significance within the ATPase/helicase domain, and a sample with compound heterozygous variants. DNA methylation data revealed higher percentages of shared probes with BAFopathies, CHD8, and the terminal ADNP variants encoding a protein known to form the ChAHP complex with CHD4. Truncating variants, as well as a sample with a recurrent pathogenic missense variant, exhibited DNA methylation profiles distinct from the ATPase/helicase domain episignature. These DNA methylation differences, together with the distinct clinical features observed in those individuals, provide preliminary evidence for clinical and molecular sub-types in the CHD4-related disorder.
    Keywords:  ADNP; CHD4; autism; chromatin remodeler; compound heterozygous; methylation; neurodevelopmental; truncating; variable expressivity
    DOI:  https://doi.org/10.1016/j.ajhg.2024.12.020
  22. bioRxiv. 2025 Jan 10. pii: 2025.01.10.632366. [Epub ahead of print]
    A zebrafish model of nicotinamide adenine dinucleotide (NAD+) deficiency-derived congenital disorders.
    Visakuo Tsurho, Carla Gilliland, Jessica Ensing, Elizabeth Vansickle, Nathan J Lanning, Paul R Mark, Stephanie Grainger.
      Congenital NAD deficiency disorder (CNDD) is a multisystem condition in which cardiac, renal, vertebral, and limb anomalies are most common, but anomalies in all organ systems have been identified. Patients with this condition have biallelic pathogenic variants involving genes in the nicotinamide adenine dinucleotide (NAD+) synthesis pathway leading to decreased systemic NAD+ levels. CNDD anomalies mimic the clinical features described in vertebral-anal-cardiac-tracheoesophageal fistula-renal-limb (VACTERL) association raising the possibility that CNDD and VACTERL association possess similar underlying causes. However, the mechanism by which NAD+ deficiency causes CNDD developmental anomalies has not been determined, nor has NAD+ deficiency been definitively linked to VACTERL association. Therefore, additional animal models amenable to detailed observation of embryonic development are needed to address the causes and progression of congenital anomalies in both CNDD and VACTERL association. Here, we describe a zebrafish model of NAD+ disruption to begin to model CNDD and VACTERL association phenotypes, assessing developmental anomalies in real-time. Treatment of zebrafish embryos with 2-amino-1,3,4-thiadiazole (ATDA), a teratogen known to disrupt NAD+ metabolism, resulted in neural tube, craniofacial, cardiac, and tail defects. These defects were rescued by the administration of nicotinamide (NAM) in a dose-dependent manner. Our work establishes zebrafish as a useful model for investigating the mechanistic causes and developmental dynamics of CNDD and VACTERL association. Further, as VACTERL association has been linked to teratogens, our zebrafish model provides a platform to assess these agents.
    Keywords:  2-Amino-1,3,4-thiadiazole (ATDA); birth defects; congenital NAD deficiency disorder (CNDD); nicotinamide (NAM); nicotinamide adenine dinucleotide (NAD+); vertebral-anal-cardiac-tracheoesophageal fistula-renal-limb (VACTERL) association; zebrafish
    DOI:  https://doi.org/10.1101/2025.01.10.632366
  23. Sci Transl Med. 2025 Jan 22. 17(782): eadr4049
    Hypoxia as a medicine.
    Robert S Rogers, Vamsi K Mootha.
      Oxygen is essential for human life, yet a growing body of preclinical research is demonstrating that chronic continuous hypoxia can be beneficial in models of mitochondrial disease, autoimmunity, ischemia, and aging. This research is revealing exciting new and unexpected facets of oxygen biology, but translating these findings to patients poses major challenges, because hypoxia can be dangerous. Overcoming these barriers will require integrating insights from basic science, high-altitude physiology, clinical medicine, and sports technology. Here, we explore the foundations of this nascent field and outline a path to determine how chronic continuous hypoxia can be safely, effectively, and practically delivered to patients.
    DOI:  https://doi.org/10.1126/scitranslmed.adr4049
  24. Neuromuscul Disord. 2024 Dec 21. pii: S0960-8966(24)01767-X. [Epub ahead of print]47 105271
    Novel c.221+1dup pathogenic variant in AGK gene linked to Sengers syndrome.
    Mercedes Galloway, Lizbeth Mellin, Violeta Alvarez Retamales, Charles W Heilig.
      Sengers Syndrome (SS) is a rare autosomal recessive mitochondrial disorder caused by mutations in the acylglycerol kinase (AGK) gene on chromosome 7, also known as cardiomyopathic mitochondrial DNA depletion syndrome (MTDPS10). This disorder disrupts mitochondrial DNA function and energy metabolism, presenting with symptoms such as congenital cataracts, hypertrophic cardiomyopathy, skeletal myopathy, exercise intolerance, and lactic acidosis. Previous research has shown SS affects oxidative phosphorylation and mitochondrial respiration, implicating the TIM22 complex and carrier import. We report a 32-year-old Palestinian female with a novel homozygous pathogenic variant, c.221+1dup, in the AGK gene. Her clinical presentation included chronic lactic acidosis, congenital cataracts, exercise intolerance, mild hypertrophic cardiomyopathy, and persistent muscle fatigue. Genetic testing was essential for confirming the diagnosis of Sengers Syndrome, revealing this previously undocumented variant. Family history indicated a hereditary pattern with a brother exhibiting similar symptoms. Typically diagnosed in infancy, SS's diverse and rare clinical manifestations can sometimes delay diagnosis. This case emphasizes the importance of considering SS in differential diagnoses when patients present with ocular lesions, lactic acidosis, muscle weakness, and cardiomyopathy. The novel AGK gene variant, with its rarity, highlights the need for heightened clinical suspicion and genetic evaluation, while suggesting further investigation into its pathogenic role and potential founder effects to enhance understanding of the genetic diversity of Sengers Syndrome.
    Keywords:  AGK gene; Acylglycerol kinase; Congenital cataracts; Hypertrophic cardiomyopathy; Lactic acidosis; Sengers Syndrome
    DOI:  https://doi.org/10.1016/j.nmd.2024.105271
  25. Sci Adv. 2025 Jan 24. 11(4): eadu4369
    Mitochondria complex III-generated superoxide is essential for IL-10 secretion in macrophages.
    Joshua S Stoolman, Rogan A Grant, Leah K Billingham, Taylor A Poor, Samuel E Weinberg, Madeline C Harding, Ziyan Lu, Jason Miska, Marten Szibor, Gr Scott Budinger, Navdeep S Chandel.
      Mitochondrial electron transport chain (ETC) function modulates macrophage biology; however, mechanisms underlying mitochondria ETC control of macrophage immune responses are not fully understood. Here, we report that mutant mice with mitochondria ETC complex III (CIII)-deficient macrophages exhibit increased susceptibility to influenza A virus (IAV) and LPS-induced endotoxic shock. Cultured bone marrow-derived macrophages (BMDMs) isolated from these mitochondria CIII-deficient mice released less IL-10 than controls following TLR3 or TLR4 stimulation. Unexpectedly, restoring mitochondrial respiration without generating superoxide using alternative oxidase (AOX) was not sufficient to reverse LPS-induced endotoxic shock susceptibility or restore IL-10 release. However, activation of protein kinase A (PKA) rescued IL-10 release in mitochondria CIII-deficient BMDMs following LPS stimulation. In addition, mitochondria CIII deficiency did not affect BMDM responses to interleukin-4 (IL-4) stimulation. Thus, our results highlight the essential role of mitochondria CIII-generated superoxide in the release of anti-inflammatory IL-10 in response to TLR stimulation.
    DOI:  https://doi.org/10.1126/sciadv.adu4369
  26. Nat Cardiovasc Res. 2025 Jan 22.
    Mitochondrial NAD+ transporter SLC25A51 linked to human aortic disease.
    Gabriel K Adzika, Ricardo A Velázquez Aponte, Joseph A Baur.
      
    DOI:  https://doi.org/10.1038/s44161-024-00599-6
  27. DNA Repair (Amst). 2025 Jan 17. pii: S1568-7864(25)00008-4. [Epub ahead of print]146 103812
    Long-range PCR as a tool for evaluating mitochondrial DNA damage: Principles, benefits, and limitations of the technique.
    Artem P Gureev, Veronika V Nesterova, Irina S Sadovnikova.
      Mitochondrial DNA (mtDNA) is often more susceptible to damage compared to nuclear DNA. This is due to its localization in the mitochondrial matrix, where a large portion of reactive oxygen species are produced. Mitochondria do not have histones and mtDNA is only slightly protected by histone-like proteins and is believed to have less efficient repair mechanisms. In this review, we discuss the long-range PCR method, which allows for the effective detection of mtDNA damage. The method is based on the assumption that various types of DNA lesions can interfere the progress of DNA polymerase, resulting in reduced amplification efficiency. It can be used to estimate the number of additional (above background) lesions in mtDNA. The review outlines the evolution of the methodology, its variations, applications in a wide range of model organisms, the advantages of the method and its limitations, as well as ways to overcome these limitations. Over the past two decades, the use of long-range PCR has allowed the study of mtDNA repair mechanisms, the characteristics of mitochondrial genome damage in various neurodegenerative diseases, aging, ischemic and oncological processes, as well as in anticancer therapy. The assessment of mtDNA damage has also been proposed for use in environmental biomonitoring. This review provides a critical evaluation of the various variations of this method, summarizes the accumulated data, and discusses the role of mtDNA damage in different organs at the organismal level.
    Keywords:  DNA polymerase; DNA repair; long-range PCR; mitochondrial DNA
    DOI:  https://doi.org/10.1016/j.dnarep.2025.103812
  28. Sci Adv. 2025 Jan 24. 11(4): eadr2282
    The oxygen level in air directs airway epithelial cell differentiation by controlling mitochondrial citrate export.
    Bo Ram Kim, Adam J Rauckhorst, Michael S Chimenti, Tayyab Rehman, Henry L Keen, Philip H Karp, Eric B Taylor, Michael J Welsh.
      Oxygen controls most metazoan metabolism, yet in mammals, tissue O2 levels vary widely. While extensive research has explored cellular responses to hypoxia, understanding how cells respond to physiologically high O2 levels remains uncertain. To address this problem, we investigated respiratory epithelia as their contact with air exposes them to some of the highest O2 levels in the body. We asked how the O2 level in air controls differentiation of airway basal stem cells into the ciliated epithelial cells essential for clearing airborne pathogens from the lung. Through a metabolomics screen and 13C tracing on primary cultures of human airway basal cells, we found that the O2 level in air directs ciliated cell differentiation by increasing mitochondrial citrate export. Unexpectedly, disrupting mitochondrial citrate export elicited hypoxia transcriptional responses independently of HIF1α stabilization and at O2 levels that would be hyperoxic for most tissues. These findings identify mitochondrial citrate export as a cellular mechanism for responding to physiologically high O2 levels.
    DOI:  https://doi.org/10.1126/sciadv.adr2282
  29. Nat Cardiovasc Res. 2025 Jan 22.
    Discovering and targeting mitochondrial loss in NOTCH1-related aortic aneurysm.
      
    DOI:  https://doi.org/10.1038/s44161-025-00607-3
  30. Neurotherapeutics. 2025 Jan 17. pii: S1878-7479(25)00003-0. [Epub ahead of print] e00525
    Mitochondrial dysfunction in Alzheimer's disease: Guiding the path to targeted therapies.
    Kyle C McGill Percy, Zhunren Liu, Xin Qi.
      Alzheimer's disease (AD) is characterized by progressive neurodegeneration, marked by the accumulation of amyloid-β (Aβ) plaques and tau tangles. Emerging evidence suggests that mitochondrial dysfunction plays a pivotal role in AD pathogenesis, driven by impairments in mitochondrial quality control (MQC) mechanisms. MQC is crucial for maintaining mitochondrial integrity through processes such as proteostasis, mitochondrial dynamics, mitophagy, and precise communication with other subcellular organelles. In AD, disruptions in these processes lead to bioenergetic failure, gene dysregulation, the accumulation of damaged mitochondria, neuroinflammation, and lipid homeostasis impairment, further exacerbating neurodegeneration. This review elucidates the molecular pathways involved in MQC and their pathological relevance in AD, highlighting recent discoveries related to mitochondrial mechanisms underlying neurodegeneration. Furthermore, we explore potential therapeutic strategies targeting mitochondrial dysfunction, including gene therapy and pharmacological interventions, offering new avenues for slowing AD progression. The complex interplay between mitochondrial health and neurodegeneration underscores the need for innovative approaches to restore mitochondrial function and mitigate the onset and progression of AD.
    Keywords:  Alzheimer's disease; Amyloid beta; Gene therapy; Mitochondrial quality control; Pharmacotherapy; Tauopathy
    DOI:  https://doi.org/10.1016/j.neurot.2025.e00525
  31. Nat Commun. 2025 Jan 18. 16(1): 817
    Numerous rRNA molecules form the apicomplexan mitoribosome via repurposed protein and RNA elements.
    Shikha Shikha, Victor Tobiasson, Mariana Ferreira Silva, Jana Ovciarikova, Dario Beraldi, Alexander Mühleip, Lilach Sheiner.
      Mitochondrial ribosomes (mitoribosomes) are essential, and their function of synthesising mitochondrial proteins is universal. The core of almost all mitoribosomes is formed from a small number of long and self-folding rRNA molecules. In contrast, the mitoribosome of the apicomplexan parasite Toxoplasma gondii assembles from over 50 extremely short rRNA molecules. Here, we use cryo-EM to discover the features that enable this unusual mitoribosome to perform its function. We reveal that poly-A tails added to rRNA molecules are integrated into the ribosome, and we demonstrate their essentiality for mitoribosome formation and for parasite survival. This is a distinct function for poly-A tails, which are otherwise known primarily as stabilisers of messenger RNAs. Furthermore, while ribosomes typically consist of unique rRNA sequences, here nine sequences are used twice, each copy integrated in a different mitoribosome domain, revealing one of the mechanisms enabling the extreme mitochondrial genome reduction characteristic to Apicomplexa and to a large group of related microbial eukaryotes. Finally, several transcription factor-like proteins are repurposed to compensate for reduced or lost critical ribosomal domains, including members of the ApiAP2 family thus far considered to be DNA-binding transcription factors.
    DOI:  https://doi.org/10.1038/s41467-025-56057-9
  32. bioRxiv. 2025 Jan 06. pii: 2025.01.06.631511. [Epub ahead of print]
    Tissue-specific modulation of NADH consumption as an anti-aging intervention in Drosophila.
    Shweta Yadav, Xingxiu Pan, Shengxi Li, Paige LaRae Martin, Ngoc Hoang, Kejin Chen, Aditi Karhadkar, Jatin Malhotra, Austin L Zuckerman, Subrata Munan, Markus K Klose, Lin Wang, Valentin Cracan, Andrey A Parkhitko.
      Aging is characterized by extensive metabolic dysregulation. Redox coenzyme nicotinamide adenine dinucleotide (NAD) can exist in oxidized (NAD+) or reduced (NADH) states, which together form a key NADH/NAD+ redox pair. Total levels of NAD decline with age in a tissue-specific manner, thereby playing a significant role in the aging process. Supplementation with NAD precursors boosts total cellular NAD levels and provides some therapeutic benefits in human clinical trials. However, supplementation studies cannot determine tissue-specific effects of an altered NADH/NAD+ ratio. Here, we created transgenic Drosophila expressing a genetically encoded xenotopic tool LbNOX to directly manipulate the cellular NADH/NAD+ ratio. We found that LbNOX expression in Drosophila impacts both NAD(H) and NADP(H) metabolites in a sex-specific manner. LbNOX rescues neuronal cell death induced by the expression of mutated alpha-B crystallin in the Drosophila eye, a widely used system to study reductive stress. Utilizing LbNOX, we demonstrate that targeting redox NAD metabolism in different tissues may have drastically different outcomes, as the expression of LbNOX solely in the muscle is much more effective for rescuing paraquat-induced oxidative stress compared to whole-body expression. Excitingly, we demonstrate that perturbing NAD(P) metabolism in non-neuronal tissues is sufficient to rejuvenate sleep profiles in aged flies to a youthful state. In summary, we used xenotopic tool LbNOX to identify tissues and metabolic processes which benefited the most from the modulation of the NAD metabolism thereby highlighting important aspects of rebalancing the NAD and NADP pools, all of which can be translated into novel designs of NAD-related human clinical trials.
    Keywords:  B-mediated reductive stress; Drosophila; LbNOX; NAD+; NADH; NADP+; NADPH; aging; mitochondria; mutated α-crystallin; xenotopic tool
    DOI:  https://doi.org/10.1101/2025.01.06.631511
  33. Prog Mol Biol Transl Sci. 2025 ;pii: S1877-1173(24)00168-6. [Epub ahead of print]210 163-203
    Current progress in CRISPR-Cas systems for rare diseases.
    Juveriya Israr, Ajay Kumar.
      The groundbreaking CRISPR-Cas gene editing method permits exact genetic code alteration. The "CRISPR" DNA protects bacteria from viruses. CRISPR-Cas utilizes a guide RNA to steer the Cas enzyme to the genome's gene editing target. After attaching to a sequence, Cas enzymes cleave DNA to insert, delete, or modify genes. The influence of CRISPR-Cas technology on molecular biology and genetics is profound. It allows for gene function research, animal disease models, and patient genetic therapy. Gene editing has transformed biotechnology, agriculture, and customized medicine. CRISPR-Cas could revolutionize genetics and medicine. CRISPR-Cas may accurately correct genetic flaws that underlie rare diseases, improving their therapy. Gene mutations make CRISPR-Cas gene editing a viable cure for uncommon diseases. We can use CRISPR-Cas to correct genetic abnormalities at the molecular level. This strategy offers hope for remedies and disease understanding. CRISPR-Cas genome editing may enable more targeted and effective treatments for rare medical illnesses with few therapy options. By developing base- and prime-editing CRISPR technology, CRISPR-Cas allows for accurate and efficient genome editing and advanced DNA modification. This advanced method provides precise DNA alterations without double-strand breakage. These advances have improved gene editing safety and precision, reducing unfavorable effects. Lipid nanoparticles, which use viral vectors, improve therapeutic cell and tissue targeting. In rare disorders, gene therapy may be possible with CRISPR-Cas clinical trials. CRISPR-Cas research is improving gene editing, delivery, and rare disease treatment.
    Keywords:  CRISPER-Cas systems; Clinical trials; Genome editing; Precision medicine; Rare diseases; Therapeutic applications
    DOI:  https://doi.org/10.1016/bs.pmbts.2024.07.019
  34. Sci Adv. 2025 Jan 24. 11(4): eadq9301
    Mitochondrial fatty acid oxidation regulates monocytic type I interferon signaling via histone acetylation.
    Jing Wu, Komudi Singh, Vivian Shing, Anand Gupta, Brett C Arenberg, Rebecca D Huffstutler, Duck-Yeon Lee, Michael N Sack.
      Although lipid-derived acetyl-coenzyme A (CoA) is a major carbon source for histone acetylation, the contribution of fatty acid β-oxidation (FAO) to this process remains poorly characterized. To investigate this, we generated mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1, distal FAO enzyme) knockout macrophages. 13C-carbon tracing confirmed reduced FA-derived carbon incorporation into histone H3, and RNA sequencing identified diminished interferon-stimulated gene expression in the absence of ACAT1. Chromatin accessibility at the Stat1 locus was diminished in ACAT1-/- cells. Chromatin immunoprecipitation analysis demonstrated reduced acetyl-H3 binding to Stat1 promoter/enhancer regions, and increasing histone acetylation rescued Stat1 expression. Interferon-β release was blunted in ACAT1-/- and recovered by ACAT1 reconstitution. Furthermore, ACAT1-dependent histone acetylation required an intact acetylcarnitine shuttle. Last, obese subjects' monocytes exhibited increased ACAT1 and histone acetylation levels. Thus, our study identifies an intriguing link between FAO-mediated epigenetic control of type I interferon signaling and uncovers a potential mechanistic nexus between obesity and type I interferon signaling.
    DOI:  https://doi.org/10.1126/sciadv.adq9301
  35. Nat Biotechnol. 2025 Jan;43(1): 5
    Ionis wins FDA nod for triglyceride-lowering rare disease drug.
      
    DOI:  https://doi.org/10.1038/s41587-024-02546-z
  36. Eur J Neurol. 2025 Jan;32(1): e70014
    Mitochondrial DNA (mtDNA) as fluid biomarker in neurodegenerative disorders: A systematic review.
    Barbara Risi, Alberto Imarisio, Giada Cuconato, Alessandro Padovani, Enza Maria Valente, Massimiliano Filosto.
       BACKGROUND: Several studies evaluated peripheral and cerebrospinal fluid (CSF) mtDNA as a putative biomarker in neurodegenerative diseases, often yielding inconsistent findings. We systematically reviewed the current evidence assessing blood and CSF mtDNA levels and variant burden in Parkinson's disease (PD), Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS). Multiple sclerosis (MS) was also included as a paradigm of chronic neuroinflammation-driven neurodegeneration.
    METHODS: Medline, Embase, Scopus and Web of Science were searched for articles published from inception until October 2023. Studies focused on mtDNA haplogroups or hereditary pathogenic variants were excluded. Critical appraisal was performed using the Quality Assessment for Diagnostic Accuracy Studies criteria.
    RESULTS: Fifty-nine original studies met our a priori-defined inclusion criteria. The majority of CSF-focused studies showed (i) decreased mtDNA levels in PD and AD; (ii) increased levels in MS compared to controls. No studies evaluated CSF mtDNA in ALS. Results focused on blood cell-free and intracellular mtDNA were contradictory, even within studies evaluating the same disease. This poor reproducibility is likely due to the lack of consideration of the many factors known to affect mtDNA levels. mtDNA damage and methylation levels were increased and reduced in patients compared to controls, respectively. A few studies investigated the correlation between mtDNA and disease severity, with conflicting results.
    CONCLUSIONS: Additional well-designed studies are needed to evaluate CSF and blood mtDNA profiles as putative biomarkers in neurodegenerative diseases. The identification of "mitochondrial subtypes" of disease may enable novel precision medicine strategies to counteract neurodegeneration.
    Keywords:  Alzheimer's disease; Parkinson's disease; amyotrophic lateral sclerosis; biomarker; blood; cerebrospinal fluid; mitochondrial DNA; neurodegeneration
    DOI:  https://doi.org/10.1111/ene.70014
  37. Brain Behav. 2025 Jan;15(1): e70283
    Bidirectional Mendelian Randomization Analysis of the Association Between Mitochondrial Proteins and Neurodegenerative Diseases.
    Fangyuan Wang, Zhou Jing, Qingyi Wang, Minghe Li, Bingqi Lu, Ao Huo, Chenglin Zhao, Huanyu Zhou, Wulong Liang, Weihua Hu, Xudong Fu.
       BACKGROUND: Neurodegenerative diseases involve progressive neuronal dysfunction and cognitive decline, posing substantial global challenges. Although the precise causes remain unclear, several studies highlight the role of protein metabolism abnormalities in disease development. This study investigates the causal links between variations in mitochondrial protein genes and neurodegenerative diseases, aiming to elucidate their potential contributions to disease progression and identify novel therapeutic strategies.
    METHODS: Herein, we utilized data from genome-wide association studies (GWAS) on mitochondrial proteins and neurodegenerative diseases. Bidirectional Mendelian randomization (MR), employing instrumental variables (IVs), was used to assess causal relationships. The primary method for estimating causal effects was the inverse variance-weighted (IVW) method, supplemented by additional MR approaches.
    RESULTS: Bidirectional MR revealed significant associations between mitochondrial protein gene variants and neurodegenerative diseases. Specifically, associations were found with Alzheimer's disease (AD) (three proteins), Parkinson's disease (PD) (four proteins), amyotrophic lateral sclerosis (ALS) (six proteins), multiple sclerosis (two proteins), and dementia with Lewy bodies (four proteins). Conversely, analyses indicated significant associations of neurodegenerative diseases with mitochondrial protein gene variants, notably with AD, dementia with Lewy bodies, and multiple sclerosis, affecting multiple mitochondrial protein levels. Bidirectional causality was observed between dementia with Lewy bodies and C21orf33.
    CONCLUSIONS: Using MR, we identified significant links between mitochondrial protein gene mutations and the risk of neurodegenerative diseases. These results highlight reciprocal relationships where certain neurodegenerative diseases influence mitochondrial protein expression levels. These findings underscore the pivotal role of mitochondrial proteins in neurodegenerative diseases, offering critical insights into disease mechanisms and potential therapeutic avenues.
    Keywords:  mendelian randomization analysis; mitochondrial proteins; neurodegenerative diseases
    DOI:  https://doi.org/10.1002/brb3.70283
  38. Biochim Biophys Acta Mol Basis Dis. 2025 Jan 19. pii: S0925-4439(25)00027-4. [Epub ahead of print] 167682
    Mitochondrial regulation of obesity by POMC neurons.
    Xing-Dan Luo, Si Tang, Xiang-Yun Luo, Luosang Quzhen, Ruo-Han Xia, Xian-Wang Wang.
      Pro-opiomelanocortin (POMC) neurons, nestled in the hypothalamus, play a pivotal role in the intricate coordination of energy homeostasis and metabolic pathways. These neurons' mitochondria, often hailed as the cell's powerhouses, are crucial for maintaining cellular energy equilibrium and metabolic functionality. Recent research has illuminated the complex interplay between mitochondrial dynamics and POMC neuronal activity, underscoring their critical involvement in the pathogenesis of a spectrum of metabolic disorders, notably obesity and diabetes. This comprehensive review delves into the molecular mechanisms that underlie how mitochondrial function within POMC neurons modulates metabolic regulation. We dissect the impact of mitochondrial dynamics, encompassing fusion, fission, mitophagy, and biogenesis, on the regulation of POMC neuronal activity. Furthermore, we scrutinize the role of mitochondrial dysfunction in POMC neurons in the etiology of obesity, identifying key therapeutic targets within these pathways. We offer an in-depth perspective on the indispensable role of POMC neuronal mitochondria in metabolic regulation and chart future research directions to bridge the existing knowledge gaps in this field.
    Keywords:  Metabolic regulation; Mitochondrion; Obesity; POMC
    DOI:  https://doi.org/10.1016/j.bbadis.2025.167682
  39. BioData Min. 2025 Jan 17. 18(1): 6
    Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients.
    Undiagnosed Diseases Network
       BACKGROUND: The mechanistic pathways that give rise to the extreme symptoms exhibited by rare disease patients are complex, heterogeneous, and difficult to discern. Understanding these mechanisms is critical for developing treatments that address the underlying causes of diseases rather than merely the presenting symptoms. Moreover, the same dysfunctional series of interrelated symptoms implicated in rare recessive diseases may also lead to milder and potentially preventable symptoms in carriers in the general population. Seizures are a common and extreme phenotype that can result from diverse and often elusive pathways in patients with ultrarare or undiagnosed disorders.
    METHODS: In this pilot study, we present an approach to understand the underlying pathways leading to seizures in patients from the Undiagnosed Diseases Network (UDN) by analyzing aggregated genotype and phenotype data from the UK Biobank (UKB). Specifically, we look for enriched phenotypes across UKB participants who harbor rare variants in the same gene known or suspected to be causally implicated in a UDN patient's recessively manifesting disorder. Analyzing these milder but related associated phenotypes in UKB participants can provide insight into the disease-causing mechanisms at play in rare disease UDN patients.
    RESULTS: We present six vignettes of undiagnosed patients experiencing seizures as part of their recessive genetic condition. For each patient, we analyze a gene of interest: MPO, P2RX7, SQSTM1, COL27A1, PIGQ, or CACNA2D2, and find relevant symptoms associated with UKB participants. We discuss the potential mechanisms by which the digestive, skeletal, circulatory, and immune system abnormalities found in the UKB patients may contribute to the severe presentations exhibited by UDN patients. We find that in our set of rare disease patients, seizures may result from diverse, multi-step pathways that involve multiple body systems.
    CONCLUSIONS: Analyses of large-scale population cohorts such as the UKB can be a critical tool to further our understanding of rare diseases in general. Continued research in this area could lead to more precise diagnostics and personalized treatment strategies for patients with rare and undiagnosed conditions.
    Keywords:  Compound heterozygous; Rare diseases; Recessive conditions; Seizures; Variant carriers
    DOI:  https://doi.org/10.1186/s13040-024-00418-5
  40. Nat Commun. 2025 Jan 20. 16(1): 865
    Accelerated enzyme engineering by machine-learning guided cell-free expression.
    Grant M Landwehr, Jonathan W Bogart, Carol Magalhaes, Eric G Hammarlund, Ashty S Karim, Michael C Jewett.
      Enzyme engineering is limited by the challenge of rapidly generating and using large datasets of sequence-function relationships for predictive design. To address this challenge, we develop a machine learning (ML)-guided platform that integrates cell-free DNA assembly, cell-free gene expression, and functional assays to rapidly map fitness landscapes across protein sequence space and optimize enzymes for multiple, distinct chemical reactions. We apply this platform to engineer amide synthetases by evaluating substrate preference for 1217 enzyme variants in 10,953 unique reactions. We use these data to build augmented ridge regression ML models for predicting amide synthetase variants capable of making 9 small molecule pharmaceuticals. Over these nine compounds, ML-predicted enzyme variants demonstrate 1.6- to 42-fold improved activity relative to the parent. Our ML-guided, cell-free framework promises to accelerate enzyme engineering by enabling iterative exploration of protein sequence space to build specialized biocatalysts in parallel.
    DOI:  https://doi.org/10.1038/s41467-024-55399-0
  41. FASEB J. 2025 Jan 31. 39(2): e70277
    mTOR Ser1261 is an AMPK-dependent phosphosite in mouse and human skeletal muscle not required for mTORC2 activity.
    Jingwen Li, Agnete B Madsen, Jonas R Knudsen, Carlos Henriquez-Olguin, Kaspar W Persson, Zhencheng Li, Steffen H Raun, Tianjiao Li, Bente Kiens, Jørgen F P Wojtaszewski, Erik A Richter, Leonardo Nogara, Bert Blaauw, Riki Ogasawara, Thomas E Jensen.
      The kinases AMPK, and mTOR as part of either mTORC1 or mTORC2, are major orchestrators of cellular growth and metabolism. Phosphorylation of mTOR Ser1261 is reportedly stimulated by both insulin and AMPK activation and a regulator of both mTORC1 and mTORC2 activity. Intrigued by the possibilities that Ser1261 might be a convergence point between insulin and AMPK signaling in skeletal muscle, we investigated the regulation and function of this site using a combination of human exercise, transgenic mouse, and cell culture models. Ser1261 phosphorylation on mTOR did not respond to insulin in any of our tested models, but instead responded acutely to contractile activity in human and mouse muscle in an AMPK activity-dependent manner. Contraction-stimulated mTOR Ser1261 phosphorylation in mice was decreased by Raptor muscle knockout (mKO) and increased by Raptor muscle overexpression, yet was not affected by Rictor mKO, suggesting most of Ser1261 phosphorylation occurs within mTORC1 in skeletal muscle. In accordance, HEK293 cells mTOR Ser1261Ala mutation strongly impaired phosphorylation of mTORC1 substrates but not mTORC2 substrates. However, neither mTORC1 nor mTORC2-dependent phosphorylations were affected in muscle-specific kinase-dead AMPK mice with no detectable mTOR Ser1261 phosphorylation in skeletal muscle. Thus, mTOR Ser1261 is an exercise but not insulin-responsive AMPK-dependent phosphosite in human and murine skeletal muscle, playing an unclear role in mTORC1 regulation but clearly not required for mTORC2 activity.
    Keywords:  AMPK; exercise; mTORC1; mTORC2; skeletal muscle
    DOI:  https://doi.org/10.1096/fj.202402064R
  42. STAR Protoc. 2025 Jan 23. pii: S2666-1667(25)00001-2. [Epub ahead of print]6(1): 103595
    Protocol for real-time assessment of energy metabolism in dissociated mouse retinal photoreceptors using a SeahorseXFe24 analyzer.
    Maria Yera, Joshua J Wang, Sarah X Zhang.
      Defects in retinal metabolism have been linked to the onset and progression of various retinal diseases. Herein, we provide a protocol for measuring bioenergetics in dissociated mouse retinal photoreceptors. We outline detailed instructions for obtaining morphologically intact and viable photoreceptor cells from adult mice and preparing the cells for metabolic analysis using a SeahorseXFe24 analyzer. This protocol allows a real-time assessment of mitochondrial respiration and glycolysis in retinal photoreceptors in response to genetic modifications or pathological insults in mouse models.
    Keywords:  Cell Biology; Metabolism; Neuroscience
    DOI:  https://doi.org/10.1016/j.xpro.2025.103595
  43. Curr Environ Health Rep. 2025 Jan 20. 12(1): 6
    Caenorhabditis Elegans as a Model for Environmental Epigenetics.
    Adam Filipowicz, Patrick Allard.
       PURPOSE OF REVIEW: The burgeoning field of environmental epigenetics has revealed the malleability of the epigenome and uncovered numerous instances of its sensitivity to environmental influences; however, pinpointing specific mechanisms that tie together environmental triggers, epigenetic pathways, and organismal responses has proven difficult. This article describes how Caenorhabditis elegans can fill this gap, serving as a useful model for the discovery of molecular epigenetic mechanisms that are conserved in humans.
    RECENT FINDINGS: Recent results show that environmental stressors such as methylmercury, arsenite, starvation, heat, bacterial infection, and mitochondrial inhibitors can all have profound effects on the epigenome, with some insults showing epigenetic and organismal effects for multiple generations. In some cases, the pathways connecting the stressor to epigenetic pathways and organismal responses have been elucidated. For example, a small RNA from the bacterial pathogen Pseudomonas aeruginosa induces transgenerational learned avoidance by activating the RNA interference PIWI-interacting RNA pathways across generations to downregulate, via Cer1 retrotransposon particles and histone methylation, maco-1, a gene that functions in sensory neurons to regulate chemotaxis. Mitochondrial inhibitors seem to have a profound effect on both the DNA methylation mark 6mA and histone methylation, and may act within mitochondrial DNA (mtDNA) to regulate mitochondrial stress response genes. Transgenerational transcriptional responses to alcohol have also been worked out at the single-nucleus resolution in C. elegans, demonstrating its utility when combined with modern sequencing technologies. These recent studies highlight how C. elegans can serve as a bridge between biochemical in vitro experiments and the more associative findings of epidemiological studies in humans to unveil possible mechanisms of environmental influence on the epigenome. The nematode is particularly well-suited to transgenerational experiments thanks to its rapid generation time and ability to self-fertilize. These studies have revealed connections between the various epigenetic mechanisms, and so studies in C. elegans that take advantage of recent advancements in sequencing technologies, including single-cell techniques, to gain unprecedented resolution of the whole epigenome across development and generations will be critical.
    Keywords:  Developmental origins of health and disease; Environmental toxicology; Epigenetics; Histone post-translational modifications; Non-coding RNAs; Transgenerational inheritance
    DOI:  https://doi.org/10.1007/s40572-025-00472-z
  44. Cell Death Dis. 2025 Jan 17. 16(1): 24
    Programmed neurite degeneration in human central nervous system neurons driven by changes in NAD+ metabolism.
    Markus Brüll, Selina Multrus, Michael Schäfer, Ivana Celardo, Christiaan Karreman, Marcel Leist.
      Neurite degeneration (ND) precedes cell death in many neurodegenerative diseases. However, it remains unclear how this compartmentalized cell death process is orchestrated in the central nervous system (CNS). The establishment of a CNS axotomy model (using modified 3D LUHMES cultures) allowed us to study metabolic control of ND in human midbrain-derived neurons without the use of toxicants or other direct disturbance of cellular metabolism. Axotomy lead to a loss of the NAD+ synthesis enzyme NMNAT2 within 2 h and a depletion of NAD+ within 4-6 h. This process appeared specific, as isolated neurites maintained ATP levels and a coupled mitochondrial respiration for at least 6 h. In the peripheral nervous system (PNS) many studies observed that NAD+ metabolism, in particular by the NADase SARM1, plays a major role in the ND occurring after axotomy. Since neither ferroptosis nor necroptosis, nor caspase-dependent apoptosis seemed to be involved in neurite loss, we investigated SARM1 as potential executioner (or controller). Knock-down or expression of a dominant-negative isoform of SARM1 indeed drastically delayed ND. Various modifications of NAD+ metabolism known to modulate SARM1 activity showed the corresponding effects on ND. Moreover, supplementation with NAD+ attenuated ND. As a third approach to investigate the role of altered NAD+ metabolism, we made use of the WLD(s) protein, which has been found in a mutant mouse to inhibit Wallerian degeneration of axons. This protein, which has a stable NMNAT activity, and thus can buffer the loss of NMNAT2, protected the neurites by stabilizing neurite NAD+ levels. Thus CNS-type ND was tightly linked to neurite metabolism in multiple experimental setups. Based on this knowledge, several new strategies for treating neurodegenerative diseases can be envisaged.
    DOI:  https://doi.org/10.1038/s41419-024-07326-w
  45. Ophthalmic Genet. 2025 Jan 20. 1-9
    Family and genetic counseling in Leber hereditary optic neuropathy.
    David A Mackey, Sandra E Staffieri, M Isabel G Lopez Sanchez, Lisa S Kearns.
       AIM: Leber hereditary optic neuropathy (LHON) predominantly manifests during adolescence or young adulthood, resulting in sudden and profound vision loss in individuals who previously had normal vision. This abrupt change significantly impacts daily life, necessitating emotional support, counseling and low-vision rehabilitative services to help affected individuals cope with the shock and adapt to their residual vision. The psychosocial burden of dealing with vision loss extends beyond the individuals directly affected by LHON, affecting matrilineal relatives who face the dual challenges of grieving for their loved one's vision loss and managing their own uncertainty about potential vision loss and its familial implications.
    METHOD: We reviewed key information that needs to be obtained prior to genetic counseling for LHON. We reviewed key counseling issues within LHON-affected families and the issues pending several subgroups of family members with distinct and varying genetic counseling needs.
    RESULTS: Family subgroups requiring specific counseling issues include the individuals affected by LHON, their mother, siblings, father, partner, and children. Genetic counseling plays an integral part of clinical care in families affected by LHON, providing tailored support and information to each subgroup.
    CONCLUSION: To provide accurate information to families and guide them toward potential supports, treatments and preventive measures, health professionals need to be aware of the factors influencing visual recovery and individual risk of vision loss.
    Keywords:  Leber hereditary optic neuropathy; genetic counselling; mitochondrial mutations
    DOI:  https://doi.org/10.1080/13816810.2025.2451175
  46. Sci China Life Sci. 2025 Jan 14.
    Tangled but ordered human mitochondrial tRNA maturation.
    Shi-Ying Yao, Xiao-Long Zhou.
      
    DOI:  https://doi.org/10.1007/s11427-024-2782-1
  47. ACS Nano. 2025 Jan 24.
    Nanoenzyme-Anchored Mitofactories Boost Mitochondrial Transplantation to Restore Locomotor Function after Paralysis Following Spinal Cord Injury.
    Runxiu Wei, Yiman Chen, Qiang Yang, Tongge Wang, Yanyun He, Na Yin, Liya Yang, Yifei Gao, Ling Guo, Min Feng.
      Mitochondrial transplantation is a significant therapeutic approach for addressing mitochondrial dysfunction in patients with spinal cord injury (SCI), yet it is limited by rapid mitochondrial deactivation and low transfer efficiency. Here, high-quality mitochondria microfactories (HQ-Mitofactories) were constructed by anchoring Prussian blue nanoenzymes onto mesenchymal stem cells for effective mitochondrial transplantation to treat paralysis from SCI. Notably, the results demonstrated that HQ-Mitofactories could continuously produce vitality-boosting mitochondria with highly interconnected and elongated network structures under oxidative stress by scavenging excessive ROS. Furthermore, HQ-Mitofactories enabled efficient transfer of therapeutic mitochondria to injured neurons primarily via gap junctions, resulting in the restoration of mitochondrial homeostasis and thereby suppressing intracellular ROS burst and facilitating neuronal repair. After i.v. administration, HQ-Mitofactories migrated to the injured spinal cords of SCI mice and subsequently promoted neuronal regeneration and remyelination. Consequently, HQ-Mitofactory-treated mice successfully recovered locomotor function within 4 weeks, with 40% of the mice fully restoring walking after hindlimb paralysis. Conversely, untreated SCI exhibited completely abolished hindlimb movements. In light of real-time generation of vitality-boosting mitochondria even under oxidative stress and enabling targeted mitochondrial transfer, HQ-Mitofactories have promising therapeutic potential in the context of mitochondrial transplantation to reduce SCI-related paralysis, and more broadly impact the field of neuroregenerative medicine.
    Keywords:  gap junctions; locomotor function; mitochondrial activity; mitochondrial transplantation; oxidative stress damage; spinal cord injury
    DOI:  https://doi.org/10.1021/acsnano.4c12557
  48. Nat Med. 2025 Jan 17.
    Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses.
    Solve-RD DITF-GENTURIS
      Genetic diagnosis of rare diseases requires accurate identification and interpretation of genomic variants. Clinical and molecular scientists from 37 expert centers across Europe created the Solve-Rare Diseases Consortium (Solve-RD) resource, encompassing clinical, pedigree and genomic rare-disease data (94.5% exomes, 5.5% genomes), and performed systematic reanalysis for 6,447 individuals (3,592 male, 2,855 female) with previously undiagnosed rare diseases from 6,004 families. We established a collaborative, two-level expert review infrastructure that allowed a genetic diagnosis in 506 (8.4%) families. Of 552 disease-causing variants identified, 464 (84.1%) were single-nucleotide variants or short insertions/deletions. These variants were either located in recently published novel disease genes (n = 67), recently reclassified in ClinVar (n = 187) or reclassified by consensus expert decision within Solve-RD (n = 210). Bespoke bioinformatics analyses identified the remaining 15.9% of causative variants (n = 88). Ad hoc expert review, parallel to the systematic reanalysis, diagnosed 249 (4.1%) additional families for an overall diagnostic yield of 12.6%. The infrastructure and collaborative networks set up by Solve-RD can serve as a blueprint for future further scalable international efforts. The resource is open to the global rare-disease community, allowing phenotype, variant and gene queries, as well as genome-wide discoveries.
    DOI:  https://doi.org/10.1038/s41591-024-03420-w
  49. Front Bioeng Biotechnol. 2024 ;12 1500343
    Optogenetic control of mitochondrial aggregation and function.
    Luhao Zhang, Xuechun Liu, Min Zhu, Yuanfa Yao, Zhichao Liu, Xianming Zhang, Xin Deng, Yi Wang, Liting Duan, Xiaogang Guo, Junfen Fu, Yingke Xu.
      The balance of mitochondrial fission and fusion plays an important role in maintaining the stability of cellular homeostasis. Abnormal mitochondrial fission and fragmentation have been shown to be associated with oxidative stress, which causes a variety of human diseases from neurodegeneration disease to cancer. Therefore, the induction of mitochondrial aggregation and fusion may provide an alternative approach to alleviate these conditions. Here, an optogenetic-based mitochondrial aggregation system (Opto-MitoA) developed, which is based on the CRY2clust/CIBN light-sensitive module. Upon blue light illumination, CRY2clust relocates from the cytosol to mitochondria where it induces mitochondrial aggregation by CRY2clust homo-oligomerization and CRY2clust-CIBN hetero-dimerization. Our functional experiments demonstrate that Opto-MitoA-induced mitochondrial aggregation potently alleviates niclosamide-caused cell dysfunction in ATP production. This study establishes a novel optogenetic-based strategy to regulate mitochondrial dynamics in cells, which may provide a potential therapy for treating mitochondrial-related diseases.
    Keywords:  ATP; aggregation; imaging; mitochondria; optogenetics
    DOI:  https://doi.org/10.3389/fbioe.2024.1500343
  50. bioRxiv. 2025 Jan 08. pii: 2025.01.07.631808. [Epub ahead of print]
    Landscape of human protein-coding somatic mutations across tissues and individuals.
    Huixin Xu, Rob Bierman, Dayna Akey, Cooper Koers, Troy Comi, Claire McWhite, Joshua M Akey.
      Although somatic mutations are fundamentally important to human biology, disease, and aging, many outstanding questions remain about their rates, spectrum, and determinants in apparently healthy tissues. Here, we performed high-coverage exome sequencing on 265 samples from 14 GTEx donors sampled for a median of 17.5 tissues per donor (spanning 46 total tissues). Using a novel probabilistic method tailored to the unique structure of our data, we identified 8,470 somatic variants. We leverage our compendium of somatic mutations to quantify the burden of deleterious somatic variants among tissues and individuals, identify molecular features such as chromatin accessibility that exhibit significantly elevated somatic mutation rates, provide novel biological insights into mutational mechanisms, and infer developmental trajectories based on patterns of multi-tissue somatic mosaicism. Our data provides a high-resolution portrait of somatic mutations across genes, tissues, and individuals.
    DOI:  https://doi.org/10.1101/2025.01.07.631808
  51. QJM. 2025 Jan 23. pii: hcaf020. [Epub ahead of print]
    Hypertrophic Inferior Olivary Nucleus Degeneration and Peri-dentate Hyperintensities in POLG mutation.
    Alvee Saluja, Samrin Haq, Pratik Karak, Sayani Mahal.
      
    Keywords:  Hypertrophic Olivary Degeneration; Inferior Olivary Nucleus; Middle cerebellar Peduncle hyperintensity; POLG; Peri-dentate white matter hyperintensity; mitochondrial disorders
    DOI:  https://doi.org/10.1093/qjmed/hcaf020
  52. Mol Cell Biochem. 2025 Jan 22.
    Synaptic-mitochondrial transport: mechanisms in neural adaptation and degeneration.
    Yang Ding, Huan Yang, Jie Gao, Can Tang, Yu-Yuan Peng, Xin-Mei Ma, Sen Li, Hai-Yan Wang, Xiu-Min Lu, Yong-Tang Wang.
      Synaptic plasticity is the basis for the proper functioning of the central nervous system. Synapses are the contact points between neurons and are crucial for information transmission, the structure and function of synapses change adaptively based on the different activities of neurons, thus affecting processes such as learning, memory, and neural development and repair. Synaptic activity requires a large amount of energy provided by mitochondria. Mitochondrial transport proteins regulate the positioning and movement of mitochondria to maintain normal energy metabolism. Recent studies have shown a close relationship between mitochondrial transport proteins and synaptic plasticity, providing a new direction for the study of adaptive changes in the central nervous system and new targets for the treatment of neurodegenerative diseases.
    Keywords:  Mitochondrial transport proteins; Neurodegenerative diseases; Synaptic energy; Synaptic mitochondria; Synaptic plasticity
    DOI:  https://doi.org/10.1007/s11010-025-05209-y
  53. Small. 2025 Jan 19. e2407353
    Use of Quantum Dots as Nanotheranostic Agents: Emerging Applications in Rare Genetic Diseases.
    Neethu K M, Shyamal Karmakar, Baishakhi Sahoo, Navniet Mishrra, Parikshit Moitra.
      Rare genetic diseases (RGDs) affect a small percentage of the global population but collectively have a substantial impact due to their diverse manifestations. Although the precise reasons behind these diseases remain unclear, roughly 80% of cases are genetically linked. Recent efforts focus on understanding pathology and developing new diagnostic and therapeutic approaches for RGDs. However, there persists a gap between fundamental research and clinical therapeutic approaches, where advancements in nanotechnology offer promising improvements. In this context, nanosized light-emitting quantum dots (QDs), ranging from 2-10 nm, are promising materials for diverse applications. Their size-tunable light emission, high quantum yield, and photostability allow for precise tracking of cargo. Additionally, QDs can be functionalized with therapeutic agents, antibodies, or peptides to target specific cellular pathways, enhancing treatment efficacy while minimizing side effects. By combining diagnostic and therapeutic capabilities in a single platform, QDs thus offer a versatile and powerful approach to tackle rare genetic disorders. Despite several reviews on various therapeutic applications of QDs, their utilization in the specific domain of RGDs is not well documented. This review highlight QDs' potential in diagnosing and treating certain RGDs and addresses the challenges limiting their application.
    Keywords:  bioimaging; diagnosis; quantum dot; rare genetic disease; therapy
    DOI:  https://doi.org/10.1002/smll.202407353
  54. J Transl Med. 2025 Jan 20. 23(1): 86
    A genomic strategy for precision medicine in rare diseases: integrating customized algorithms into clinical practice.
    Cristina Méndez-Vidal, Nereida Bravo-Gil, Javier Pérez-Florido, Irene Marcos-Luque, Raquel M Fernández, José Luis Fernández-Rueda, María González-Del Pozo, Marta Martín-Sánchez, Elena Fernández-Suárez, Marcela Mena, Rosario Carmona, Joaquín Dopazo, Salud Borrego, Guillermo Antiñolo.
       BACKGROUND: Despite the use of Next-Generation Sequencing (NGS) as the gold standard for the diagnosis of rare diseases, its clinical implementation has been challenging, limiting the cost-effectiveness of NGS and the understanding, control and safety essential for decision-making in clinical applications. Here, we describe a personalized NGS-based strategy integrating precision medicine into a public healthcare system and its implementation in the routine diagnosis process during a five-year pilot program.
    METHODS: Our approach involved customized probe designs, the generation of virtual panels and the development of a personalized medicine module (PMM) for variant prioritization. This strategy was applied to 6500 individuals including 6267 index patients and 233 NGS-based carrier screenings.
    RESULTS: Causative variants were identified in 2061 index patients (average 32.9%, ranging from 12 to 62% by condition). Also, 131 autosomal-recessive cases could be partially genetically diagnosed. These results led to over 5000 additional studies including carrier, prenatal and preimplantational tests or pharmacological and gene therapy treatments.
    CONCLUSION: This strategy has shown promising improvements in the diagnostic rate, facilitating timely diagnosis and gradually expanding our services portfolio for rare diseases. The steps taken towards the integration of clinical and genomic data are opening new possibilities for conducting both retrospective and prospective healthcare studies. Overall, this study represents a major milestone in the ongoing efforts to improve our understanding and clinical management of rare diseases, a crucial area of medical research and care.
    Keywords:  Genetic diagnosis; Genomic medicine; Next generation sequencing; Precision medicine; Rare diseases; Research implementation
    DOI:  https://doi.org/10.1186/s12967-025-06069-2
  55. Adv Sci (Weinh). 2025 Jan 24. e2414141
    The Lactate-Primed KAT8‒PCK2 Axis Exacerbates Hepatic Ferroptosis During Ischemia/Reperfusion Injury by Reprogramming OXSM-Dependent Mitochondrial Fatty Acid Synthesis.
    Jingsheng Yuan, Mingyang Yang, Zhenru Wu, Jun Wu, Kejie Zheng, JiaGuo Wang, Qiwen Zeng, Menglin Chen, Tao Lv, Yujun Shi, Jiayin Yang, Jian Yang.
      Recipients often suffer from hyperlactatemia during liver transplantation (LT), but whether hyperlactatemia exacerbates hepatic ischemia-reperfusion injury (IRI) after donor liver implantation remains unclear. Here, the role of hyperlactatemia in hepatic IRI is explored. In this work, hyperlactatemia is found to exacerbate ferroptosis during hepatic IRI. Lactate-primed lysine acetyltransferase 8 (KAT8) is determined to directly lactylate mitochondrial phosphoenolpyruvate carboxykinase 2 (PCK2) at Lys100 and augments PCK2 kinase activity. By using gene-edited mice, evidence indicating that PCK2 exacerbates hepatic ferroptosis during IRI is generated. Mechanistically, PCK2 lactylate at Lys100 acts as a critical inducer of ferroptosis during IRI by competitively inhibiting the Parkin-mediated polyubiquitination of 3-oxoacyl-ACP synthase (OXSM), thereby leading to metabolic remodeling of mitochondrial fatty acid synthesis (mtFAS) and the potentiation of oxidative phosphorylation and the tricarboxylic acid cycle. More importantly, targeting PCK2 is demonstrated to markedly ameliorate hyperlactatemia-mediated ferroptosis during hepatic IRI. Collectively, the findings support the use of therapeutics targeting PCK2 to suppress hepatic ferroptosis and IRI in patients with hyperlactatemia during LT.
    Keywords:  ferroptosis; hepatic ischemia‒reperfusion injury; lactate; lactylation; metabolic reprogramming; mitochondrial fatty acid synthesis; phosphoenolpyruvate carboxykinase 2
    DOI:  https://doi.org/10.1002/advs.202414141
  56. Biochim Biophys Acta Mol Cell Res. 2025 Jan 19. pii: S0167-4889(25)00011-4. [Epub ahead of print]1872(3): 119906
    Mitochondrial quality control: Biochemical mechanism of cardiovascular disease.
    Francesca Inferrera, Ylenia Marino, Tiziana Genovese, Salvatore Cuzzocrea, Roberta Fusco, Rosanna Di Paola.
      Mitochondria play a key role in the regulation of energy homeostasis and ATP production in cardiac cells. Mitochondrial dysfunction can trigger several pathological events that contribute to the development and progression of cardiovascular diseases. These mechanisms include the induction of oxidative stress, dysregulation of intracellular calcium cycling, activation of the apoptotic pathway, and alteration of lipid metabolism. This review focuses on the role of mitochondria in intracellular signaling associated with cardiovascular diseases, emphasizing the contributions of reactive oxygen species production and mitochondrial dynamics. Indeed, mitochondrial dysfunction has been implicated in every aspect of cardiovascular disease and is currently being evaluated as a potential target for therapeutic interventions. To treat cardiovascular diseases and improve overall heart health, it is important to better understand these biochemical systems. These findings allow the achievement of targeted therapies and preventive measures. Therefore, this review investigates different studies that demonstrate how changes in mitochondrial dynamics like fusion, fission, and mitophagy contribute to the development or worsening of disorders related to heart diseases by summarizing current research on their role.
    Keywords:  Cardiovascular diseases; Intracellular signaling; Mitochondrial dysfunction; Oxidative stress; Therapeutic interventions
    DOI:  https://doi.org/10.1016/j.bbamcr.2025.119906
  57. Nature. 2025 Jan 22.
    Multimodal cell mapping with optimal transport.
      
    Keywords:  Cell biology; Computational biology and bioinformatics; Machine learning
    DOI:  https://doi.org/10.1038/d41586-025-00107-1
  58. Nature. 2025 Jan 22.
    Mitochondrial swap from cancer to immune cells thwarts anti-tumour defences.
    Jonathan R Brestoff.
      
    Keywords:  Cancer; Immunology; Medical research
    DOI:  https://doi.org/10.1038/d41586-025-00077-4
  59. Antioxid Redox Signal. 2025 Jan 23.
    Exploring the Molecular Interplay Between Oxygen Transport, Cellular Oxygen Sensing, and Mitochondrial Respiration.
    Sirsendu Jana, Abdu I Alayash.
      Significance: The mitochondria play a key role in maintaining oxygen homeostasis under normal oxygen tension (normoxia) and during oxygen deprivation (hypoxia). This is a critical balancing act between the oxygen content of the blood, the tissue oxygen sensing mechanisms, and the mitochondria, which ultimately consume most oxygen for energy production. Recent Advances: We describe the well-defined role of the mitochondria in oxygen metabolism with a special focus on the impact on blood physiology and pathophysiology. Critical Issues: Fundamental questions remain regarding the impact of mitochondrial responses to changes in overall blood oxygen content under normoxic and hypoxic states and in the case of impaired oxygen sensing in various cardiovascular and pulmonary complications including blood disorders involving hemolysis and hemoglobin toxicity, ischemia reperfusion, and even in COVID-19 disease. Future Directions: Understanding the nature of the crosstalk among normal homeostatic pathways, oxygen carrying by hemoglobin, utilization of oxygen by the mitochondrial respiratory chain machinery, and oxygen sensing by hypoxia-inducible factor proteins, may provide a target for future therapeutic interventions. Antioxid. Redox Signal. 00, 000-000.
    Keywords:  blood; hemoglobin; hypoxia; mitochondria; oxygen homeostasis
    DOI:  https://doi.org/10.1089/ars.2023.0428
  60. Commun Biol. 2025 Jan 22. 8(1): 109
    Illuminating understudied kinases: a generalizable biosensor development method applied to protein kinase N.
    Julius Bogomolovas, Ju Chen.
      Protein kinases play crucial roles in regulating cellular processes, making real-time visualization of their activity essential for understanding signaling dynamics. While genetically encoded fluorescent biosensors have emerged as powerful tools for studying kinase activity, their development for many kinases remains challenging due to the lack of suitable substrate peptides. Here, we present a novel approach for identifying peptide substrates and demonstrate its effectiveness by developing a biosensor for Protein Kinase N (PKN) activity. Our method identified a new PKN substrate peptide that we optimized for use in a fluorescent biosensor design. The resulting biosensor shows specificity for PKN family kinases and can detect both overexpressed and endogenous PKN activity in live cells. Importantly, our biosensor revealed sustained basal PKN2 activity at the plasma membrane, identifying it as a PKN2 activity hotspot. This work not only provides a valuable tool for studying PKN signaling but also demonstrates a promising strategy for developing biosensors for other understudied kinases, potentially expanding our ability to monitor kinase activity across the human kinome.
    DOI:  https://doi.org/10.1038/s42003-025-07510-4
  61. bioRxiv. 2025 Jan 14. pii: 2025.01.14.633047. [Epub ahead of print]
    KAT6A acetylation drives metabolic adaptation to mediate cellular growth and mitochondrial metabolism through AMPK interaction.
    Mariko Aoyagi Keller, Andreas Ivessa, Tong Liu, Hong Li, Peter J Romanienko, Michinari Nakamura.
      Diets influence metabolism and disease susceptibility, with lysine acetyltransferases (KATs) serving as key regulators through acetyl-CoA. We have previously demonstrated that a ketogenic diet alleviates cardiac pathology, though the underlying mechanisms remain largely unknown. Here we show that KAT6A acetylation is crucial for mitochondrial function and cell growth. Proteomic analysis revealed that KAT6A is acetylated at lysine (K)816 in the hearts of mice fed a ketogenic diet under hypertension, which enhances its interaction with AMPK regulatory subunits. RNA-sequencing analysis demonstrated that the KAT6A acetylation-mimetic mutant stimulates AMPK signaling in cardiomyocytes. Moreover, the acetylation-mimetic mutant mitigated phenylephrine-induced mitochondrial dysfunction and cardiomyocyte hypertrophy via AMPK activation. However, KAT6A-K816R acetylation-resistant knock-in mice unexpectedly exhibited smaller hearts with enhanced AMPK activity, conferring protection against neurohumoral stress-induced cardiac hypertrophy and remodeling. These findings indicate that KAT6A regulates metabolism and cellular growth by interacting with and modulating AMPK activity through K816-acetylation in a cell type-specific manner.
    DOI:  https://doi.org/10.1101/2025.01.14.633047
  62. ACS Nano. 2025 Jan 21.
    Emerging Delivery Systems for Enabling Precision Nucleic Acid Therapeutics.
    Xiaochun Bian, Liping Zhou, Zhiwei Luo, Guotao Liu, Zhongci Hang, Haohao Li, Fengyong Li, Yongqiang Wen.
      Nucleic acid therapeutics represent a highly promising treatment approach in modern medicine, treating diseases at the genetic level. However, these therapeutics face numerous challenges in practical applications, particularly regarding their stability, effectiveness, cellular uptake efficiency, and limitations in delivering them specifically to target tissues. To overcome these obstacles, researchers have developed various innovative delivery systems, including viral vectors, lipid nanoparticles, polymer nanoparticles, inorganic nanoparticles, protein carriers, exosomes, antibody oligonucleotide conjugates, and DNA nanostructure-based delivery systems. These systems enhance the therapeutic efficacy of nucleic acid drugs by improving their stability, targeting specificity, and half-life in vivo. In this review, we systematically discuss different types of nucleic acid drugs, analyze the major barriers encountered in their delivery, and summarize the current research progress in emerging delivery systems. We also highlight the latest advancements in the application of these systems for treating genetic diseases, infectious diseases, cancer, brain diseases, and wound healing. This review aims to provide a comprehensive overview of nucleic acid drug delivery systems' current status and future directions by integrating the latest advancements in nanotechnology, biomaterials science, and gene editing technologies, emphasizing their transformative potential in precision medicine.
    Keywords:  Clinical applications; Delivery systems; Drug delivery barriers; Gene therapy; Nucleic acid drugs; Nucleic acid therapeutics; Precision medicine; Targeted delivery
    DOI:  https://doi.org/10.1021/acsnano.4c11858
  63. Nat Cardiovasc Res. 2025 Jan 22.
    Mitochondrial NAD+ deficiency in vascular smooth muscle impairs collagen III turnover to trigger thoracic and abdominal aortic aneurysm.
    Jingjing Zhang, Yuyi Tang, Shan Zhang, Zhuxin Xie, Wenrui Ma, Shaowen Liu, Yixuan Fang, Shufen Zheng, Ce Huang, Guoquan Yan, Mieradilijiang Abudupataer, Yue Xin, Jingqiao Zhu, Wenjing Han, Weizhong Wang, Fenglin Shen, Hao Lai, Yang Liu, Dan Ye, Fa-Xing Yu, Yanhui Xu, Cuiping Pan, Chunsheng Wang, Kai Zhu, Weijia Zhang.
      Thoracic and abdominal aortic aneurysm poses a substantial mortality risk in adults, yet many of its underlying factors remain unidentified. Here, we identify mitochondrial nicotinamide adenine dinucleotide (NAD)⁺ deficiency as a causal factor for the development of aortic aneurysm. Multiomics analysis of 150 surgical aortic specimens indicated impaired NAD+ salvage and mitochondrial transport in human thoracic aortic aneurysm, with expression of the NAD+ transporter SLC25A51 inversely correlating with disease severity and postoperative progression. Genome-wide gene-based association analysis further linked low SLC25A51 expression to risk of aortic aneurysm and dissection. In mouse models, smooth muscle-specific knockout of Nampt, Nmnat1, Nmnat3, Slc25a51, Nadk2 and Aldh18a1, genes involved in NAD+ salvage and transport, induced aortic aneurysm, with Slc25a51 deletion producing the most severe effects. Using these models, we suggest a mechanism that may explain the disease pathogenesis: the production of type III procollagen during aortic medial matrix turnover imposes a high demand for proline, an essential amino acid component of collagen. Deficiency in the mitochondrial NAD⁺ pool, regulated by NAD⁺ salvage and transport, hinders proline biosynthesis in mitochondria, contributing to thoracic and abdominal aortic aneurysm.
    DOI:  https://doi.org/10.1038/s44161-024-00606-w
  64. Cell Mol Life Sci. 2025 Jan 21. 82(1): 53
    TMAO accelerates cellular aging by disrupting endoplasmic reticulum integrity and mitochondrial unfolded protein response.
    Fahimeh Varzideh, Emanuele Farroni, Urna Kaunsakar, Mahaba Eiwaz, Stanislovas S Jankauskas, Gaetano Santulli.
      
    DOI:  https://doi.org/10.1007/s00018-024-05546-z
  65. Sci Adv. 2025 Jan 24. 11(4): eads2664
    Cryo-EM structure and regulation of human NAD kinase.
    Prakash P Praharaj, Yang Li, Charline Mary, Mona H Soflaee, Kevin Ryu, Dohun Kim, Diem H Tran, Trishna Dey, Harrison J Tom, Halie Rion, Muriel Gelin, Andrew Lemoff, Lauren G Zacharias, João S Patricio, Thomas P Mathews, Zhe Chen, Corinne Lionne, Gerta Hoxhaj, Gilles Labesse.
      Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a crucial reducing cofactor for reductive biosynthesis and protection from oxidative stress. To fulfill their heightened anabolic and reductive power demands, cancer cells must boost their NADPH production. Progrowth and mitogenic protein kinases promote the activity of cytosolic NAD kinase (NADK), which produces NADP+, a limiting NADPH precursor. However, the molecular architecture and mechanistic regulation of human NADK remain undescribed. Here, we report the cryo-electron microscopy structure of human NADK, both in its apo-form and in complex with its substrate NAD+ (nicotinamide adenine dinucleotide), revealing a tetrameric organization with distinct structural features. We discover that the amino (N)- and carboxyl (C)-terminal tails of NADK have opposing effects on its enzymatic activity and cellular NADP(H) levels. Specifically, the C-terminal region is critical for NADK activity, whereas the N-terminal region exhibits an inhibitory role. This study highlights molecular insights into the regulation of a vital enzyme governing NADP(H) production.
    DOI:  https://doi.org/10.1126/sciadv.ads2664
  66. Biol Psychiatry Glob Open Sci. 2025 Mar;5(2): 100422
    Increased Rate of Unique Mitochondrial DNA Deletion Breakpoints in Young Adults With Early-Life Stress.
    Teresa E Daniels, Brooke E Hjelm, William W Lewis-de Los Angeles, Eric Smith, Audrey A Omidsalar, Brandi L Rollins, Anna Sherman, Stephanie Parade, Marquis P Vawter, Audrey R Tyrka.
       Background: Mounting evidence suggests that mitochondria respond to psychosocial stress. Recent studies suggest mitochondrial DNA (mtDNA) deletions may be increased in some psychiatric disorders, but no studies have examined early-life stress (ELS) and mtDNA deletions. In this study, we assessed mtDNA deletions in peripheral blood mononuclear cells of medically healthy young adults with and without ELS.
    Methods: Participants (n = 181; 69% female), ages 18 to 40 years, were recruited from the community. Participants with ELS (n = 108) had moderate to severe childhood maltreatment; 83 also had parental loss, and 59 had psychiatric disorders. Participants in the control group (n = 73) had no maltreatment, parental loss, or psychiatric disorders. Standardized interviews and self-report measures assessed demographic variables, stress, and mental health. mtDNA from peripheral blood mononuclear cells was amplified via long-range polymerase chain reaction; mtDNA deletions were quantified via Seq-Well, next-generation sequencing, and the Splice-Break pipeline. Linear regression models were used to assess relationships of mtDNA deletion metrics with ELS, adult stressors, psychiatric disorders, and demographics.
    Results: Participants with ELS had significantly greater rates of unique mtDNA deletion breakpoints per 10,000 coverage than participants without ELS (p < .001), correcting for age, sex, and sequencing depth. Cumulative mtDNA deletion read percentage was not significantly different between groups. Psychiatric disorders and adult stressors were associated with greater unique mtDNA deletion breakpoints (ps < .05) but did not account for associations of ELS with mtDNA deletions.
    Conclusions: The increased number of unique mtDNA deletion breakpoints in participants with ELS suggests that mitochondrial genomes undergo observable alterations in the context of early stress. Future studies will examine mtDNA deletions with metabolic health measures.
    Keywords:  Allostatic load; Childhood adversity; Early-life stress; Mitochondria; mtDNA; mtDNA deletions
    DOI:  https://doi.org/10.1016/j.bpsgos.2024.100422
  67. Dis Model Mech. 2025 Jan 20. pii: dmm.052063. [Epub ahead of print]
    KNTC1 introduces segmental heterogeneity to mitochondria.
    Atsushi Tsukamura, Hirotaka Ariyama, Natsuki Hayashi, Satoko Miyatake, Satoko Okado, Sara Sultana, Ichiro Terakado, Takefumi Yamamoto, Shoji Yamanaka, Satoshi Fujii, Haruka Hamanoue, Ryoko Asano, Taichi Mizushima, Naomichi Matsumoto, Yoshihiro Maruo, Masaki Mori.
      Mitochondria contribute to cellular metabolism by providing a specialised milieu for energising cells by incorporating and processing the metabolites. However, heterogeneity in the mitochondria within is only partially elucidated. Mitochondria dynamically alter their morphology and functions during the life of animals, in which cells proliferate and grow. We here show that Kntc1, a highly evolutionarily conserved protein, translocates from the Golgi apparatus to linear mitochondrial segments (LMS) upon glutamine deprivation and plays an essential role in maintaining LMS. The LMS with Kntc1 localisation exhibits an increase in the membrane potential, suggesting the role of Kntc1 in functioning as a reservoir for the energy-generating potential. Suppression of Kntc1 leads to glutamine consumption and lactate production, thus impacting cellular metabolism, eventually leading to anchorage-independent growth of cells. Indeed, the KNTC1 variant was identified in a patient with ovarian cancer, suggesting that segmental regulation of the mitochondrial function is essential for maintaining tissue integrity.
    Keywords:  Bent mitochondrial segment (BMS); Glutamine metabolism; KNTC1; Linear mitochondrial segment (LMS); Mitochondrial structural heterogeneity
    DOI:  https://doi.org/10.1242/dmm.052063
  68. Commun Biol. 2025 Jan 21. 8(1): 105
    Dysfunctional BCAA degradation triggers neuronal damage through disrupted AMPK-mitochondrial axis due to enhanced PP2Ac interaction.
    Shih-Cheng Wu, Yan-Jhen Chen, Shih-Han Su, Pai-Hsiang Fang, Rei-Wen Liu, Hui-Ying Tsai, Yen-Jui Chang, Hsing-Han Li, Jian-Chiuan Li, Chun-Hong Chen.
      Metabolic and neurological disorders commonly display dysfunctional branched-chain amino acid (BCAA) metabolism, though it is poorly understood how this leads to neurological damage. We investigated this by generating Drosophila mutants lacking BCAA-catabolic activity, resulting in elevated BCAA levels and neurological dysfunction, mimicking disease-relevant symptoms. Our findings reveal a reduction in neuronal AMP-activated protein kinase (AMPK) activity, which disrupts autophagy in mutant brain tissues, linking BCAA imbalance to brain dysfunction. Mechanistically, we show that excess BCAA-induced mitochondrial reactive oxygen species (ROS) triggered the binding of protein phosphatase 2 A catalytic subunit (PP2Ac) to AMPK, suppressing AMPK activity. This initiated a dysregulated feedback loop of AMPK-mitochondrial interactions, exacerbating mitochondrial dysfunction and oxidative neuronal damage. Our study identifies BCAA imbalance as a critical driver of neuronal damage through AMPK suppression and autophagy dysfunction, offering insights into metabolic-neuronal interactions in neurological diseases and potential therapeutic targets for BCAA-related neurological conditions.
    DOI:  https://doi.org/10.1038/s42003-025-07457-6
  69. Front Immunol. 2024 ;15 1516145
    Drp1-associated genes implicated in sepsis survival.
    Marissa D Pokharel, Anlin Feng, Ying Liang, Wenli Ma, Saurabh Aggarwal, Hoshang Unwalla, Stephen M Black, Ting Wang.
      Sepsis is a severe and life-threatening medical syndrome that can lead to organ failure and death. Despite advances in medical treatment, current therapies are often inadequate, with high septic mortality rates. Therefore, there is a critical need for reliable prognostic markers to be used in clinical settings to improve the management and outcomes of patients with sepsis. Recent studies have suggested that mitochondrial dynamics, including the processes of mitochondrial fission and fusion, are closely related to the severity of sepsis and the status of inflammation. By monitoring transcriptomic signals related to mitochondrial dynamics, new and reliable biomarkers can be engineered to more accurately predict sepsis survival risk. Such biomarkers would be invaluable in clinical settings, aiding healthcare providers in the early identification of high-risk patients and improving treatment strategies. To achieve this goal, we utilized the major mitochondrial fission regulatory protein dynamin-related protein 1 (Drp1, gene code DNM1L) and identified Drp1-associated genes that are enriched with sepsis survival genes. A 12-gene signature (GS) was established as a differentially expressed gene (DEG)-based GS. Next, we compared genes of proteins that interact with Drp1 to sepsis survival genes and identified 7 common genes, establishing a GS we term as protein-protein interaction (PPI)-based GS. To evaluate if these GSs can predict sepsis survival, we used publicly available human blood transcriptomic datasets from sepsis patients. We confirmed that both GSs can successfully predict sepsis survival in both discovery and validation cohorts with high sensitivity and specificity, with the PPI-based GS showing enhanced prognostic performance. Together, this study successfully engineers a new and validated blood-borne biomarker (PPI-based 7-gene GS) for sepsis survival risk prediction. This biomarker holds the potential for improving the early identification of high-risk sepsis patients and optimizing personalized treatment strategies to reduce sepsis mortality.
    Keywords:  DRP1; fission; inflammation; mitochondria; sepsis survival
    DOI:  https://doi.org/10.3389/fimmu.2024.1516145
  70. Genome Med. 2025 Jan 20. 17(1): 7
    Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery.
    Arda Halu, Sarvesh Chelvanambi, Julius L Decano, Joan T Matamalas, Mary Whelan, Takaharu Asano, Namitra Kalicharran, Sasha A Singh, Joseph Loscalzo, Masanori Aikawa.
       BACKGROUND: Large-scale pharmacogenomic resources, such as the Connectivity Map (CMap), have greatly assisted computational drug discovery. However, despite their widespread use, CMap-based methods have thus far been agnostic to the biological activity of drugs as well as to the genomic effects of drugs in multiple disease contexts. Here, we present a network-based statistical approach, Pathopticon, that uses CMap to build cell type-specific gene-drug perturbation networks and integrates these networks with cheminformatic data and diverse disease phenotypes to prioritize drugs in a cell type-dependent manner.
    METHODS: We build cell type-specific gene-drug perturbation networks from CMap data using a statistical procedure we call Quantile-based Instance Z-score Consensus (QUIZ-C). Using these networks and a large-scale disease-gene network consisting of 569 disease signatures from the Enrichr database, we calculate Pathophenotypic Congruity Scores (PACOS) between input gene signatures and drug perturbation signatures and combine these scores with cheminformatic data from ChEMBL to prioritize drugs. We benchmark our approach by calculating area under the receiver operating characteristic curves (AUROC) for 73 gene sets from the Molecular Signatures Database (MSigDB) using target gene expression profiles from the Comparative Toxicogenomics Database (CTD). We validate the drugs predicted in our proofs-of-concept using real-time polymerase chain reaction (qPCR) experiments.
    RESULTS: Cell type-specific gene-drug perturbation networks built using QUIZ-C are topologically distinct, reflecting the biological uniqueness of the cell lines in CMap, and are enriched in known drug targets. Pathopticon demonstrates a better prediction performance than solely cheminformatic measures as well as state-of-the-art network and deep learning-based methods. Top predictions made by Pathopticon have high chemical structural diversity, suggesting their potential for building compound libraries. In proof-of-concept applications on vascular diseases, we demonstrate that Pathopticon helps guide in vitro experiments by identifying pathways that are potentially regulated by the predicted therapeutic candidates.
    CONCLUSIONS: Our network-based analytical framework integrating pharmacogenomics and cheminformatics (available at https://github.com/r-duh/Pathopticon ) provides a feasible blueprint for a cell type-specific drug discovery and repositioning platform with broad implications for the efficiency and success of drug development.
    Keywords:  CMap; Cell type-specific; Cheminformatics; Connectivity mapping; Drug discovery; Endotypes; Inflammation; Network pharmacology; Pharmacogenomics; Vascular disease
    DOI:  https://doi.org/10.1186/s13073-025-01431-x
  71. Brain Res Bull. 2025 Jan 15. pii: S0361-9230(25)00024-3. [Epub ahead of print] 111212
    Translating Time: Challenges, Progress, and Future Directions.
    Christine J Charvet, Alexandra A de Sousa, Tatianna Vassilopoulos.
      Mice are the dominant model system to study human health and disease. Yet, there is a pressing need to use diverse model systems to address long-standing issues in biomedical sciences. Mice do not spontaneously recapitulate many of the diseases we seek to study. Accordingly, the relevance of studying mice to understand human disease is limited. We discuss examples associated with limitations of the mouse model, and how the inclusion of a richer array of model systems can help address long standing issues in biomedical sciences. We also discuss a tool called Translating Time, an online resource (www.translatingtime.org) that equates corresponding ages across model systems and humans. The translating time resource can be used to bridge the gap across species and make predictions when data are sparse or unavailable as is the case for human fetal development. Moreover, the Translating Time tool can map findings across species, make inferences about the evolution of shared neuropathologies, and inform the optimal model system for studying human biology in health and in disease. Resources such as these can be utilized to integrate information across diverse model systems to improve the study of human biology in health and disease.
    Keywords:  Translating Time; chimpanzee; evolution; human; mouse
    DOI:  https://doi.org/10.1016/j.brainresbull.2025.111212
  72. Front Pharmacol. 2024 ;15 1543291
    Editorial: Revealing the unconventional mechanisms of mitochondria-targeting drugs in heart-related diseases.
    Kaidi Ren, Yang Yang.
      
    Keywords:  drug; heart; heart disease; mitochondria; mitochondria al pathway
    DOI:  https://doi.org/10.3389/fphar.2024.1543291
  73. NPJ Parkinsons Dis. 2025 Jan 20. 11(1): 21
    Long-read sequencing revealed complex biallelic pentanucleotide repeat expansions in RFC1-related Parkinson's disease.
    Peng Liu, Fan Zhang, Xinhui Chen, Xiaosheng Zheng, Miao Chen, Zhiru Lin, Shuqi Chen, Lebo Wang, Xinchen Wang, Nan Jin, Chenxin Ying, Fei Xie, Bo Wang, Sheng Wu, Zhidong Cen, Wei Luo.
      Biallelic intronic pentanucleotide repeat expansions, mainly (AAGGG)exp and/or (ACAGG)exp in RFC1, are detected in cerebellar ataxia, neuropathy and vestibular areflexia syndrome, late-onset ataxia, and in a wide disease spectrum including Charcot-Marie-Tooth disease, multiple system atrophy, and Parkinson's disease (PD). However, the genotype-phenotype correlation and underlying mechanism are mostly unknown. We screened RFC1-repeat expansions in 1445 patients with parkinsonism. Comprehensive genetic and clinical, and pathological assessments were performed. We report two early-onset patients with PD carrying complex biallelic pentanucleotide repeat expansions in RFC1. Long-read sequencing revealed a novel repeat configuration of (AGGGG)exp(AAGGG)14 and a possible somatic variant of (AAGGG)exp(AATGG)exp(AAGGG)exp in the (AAGGG)exp alleles in two RFC1-related PD patients. RNA foci were detected in the (AGGGG)exp-expressed HEK293T cell line as well as (AAGGG)exp and (ACAGG)exp, supporting (AGGGG)exp as a novel pathogenic repeat motif. This work revealed complex genotypes with novel repeat configuration of (AGGGG)exp and possible somatic (AATGG)exp insertion in RFC1-related PD.
    DOI:  https://doi.org/10.1038/s41531-025-00868-6
  74. Acad Biol. 2024 ;2(4):
    Unlocking biological complexity: the role of machine learning in integrative multi-omics.
    Ravindra Kumar, Rajrani Ruhel, Andre J van Wijnen.
      The increasing complexity of biological systems demands advanced analytical approaches to decode the underlying mechanisms of health and disease. Integrative multi-omics approaches use multi-layered datasets such as genomic, transcriptomic, proteomic, and metabolomic data to understand biological processes much more comprehensively compared to the single-omics analysis and to provide a comprehensive view of cellular and molecular processes. However, these integrative approaches have their own computational and analytical challenges due to the large volume and nature of multi-omics data. Machine learning has emerged as a powerful tool to help and resolve these challenges. It offers sophisticated algorithms that can identify and discover hidden patterns and provide insights into complex biological networks. By integrating machine learning in multi-omics, we can enhance our understanding of drug discovery, disease, pathway, and network analysis. Machine learning and ensemble methods allow researchers to model nonlinear relationships and manage high-dimensional data, improving the precision of predictions. This approach paves the way for personalized medicine by identifying unique molecular signatures for individual patients, which can provide valuable insights into treatment planning and support more effective treatment. As machine learning continues to evolve, its role in multi-omics analysis will be pivotal in advancing our ability to interpret biological complexity and translate findings into clinical applications.
    Keywords:  data integration; machine learning; multi-omics
    DOI:  https://doi.org/10.20935/acadbiol7428
  75. STAR Protoc. 2025 Jan 17. pii: S2666-1667(24)00743-3. [Epub ahead of print]6(1): 103578
    Protocol for generating protein profiles and distance-based network analysis of murine tissue slices.
    Luisa Schmidt, Philipp Antczak, Marcus Krüger.
      We introduce a protocol for spatial proteomics using thin cryotome sections of mouse skeletal muscle tissue. We describe steps for preparing muscle sections and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses to generate spatial protein profiles along the longitudinal skeletal muscle axis. We detail procedures for scanning longitudinal protein profiles and replacing missing data using a sliding window approach. This protocol has potential for applications in spatial proteomics to other tissues with asymmetric patterns such as the brain and heart tissue. For complete details on the use and execution of this protocol, please refer to Schmidt et al.1.
    Keywords:  Bioinformatics; Cell Biology; Protein Biochemistry
    DOI:  https://doi.org/10.1016/j.xpro.2024.103578
  76. Cureus. 2024 Dec;16(12): e76332
    Carnitine Palmitoyltransferase II (CPT2) Deficiency in a Patient With Recurrent Rhabdomyolysis: A Case Report.
    Kevin A Lease, David Wang.
      Carnitine palmitoyltransferase II (CPT2) deficiency is a rare genetic disorder that prevents the body from using long-chain fatty acids (LCFAs) for energy. We report a case of a 40-year-old male with a recent episode of rhabdomyolysis triggered by an illness. His liver function tests (LFTs) and creatine kinase (CK) levels were markedly elevated. His rhabdomyolysis improved in the hospital with supportive treatment. At follow-up appointments, it was found that he had labs consistent with CPT2 deficiency. Genetic testing confirmed a homozygous mutation in the CPT2 gene. This report highlights the importance of considering CPT2 deficiency as a cause of recurrent rhabdomyolysis, especially when triggered by non-traumatic causes.
    Keywords:  beta-oxidation; cpt2 deficiency; medium-chain triglycerides; non-traumatic rhabdomyolysis; rare genetic diseases
    DOI:  https://doi.org/10.7759/cureus.76332
  77. Free Radic Biol Med. 2025 Jan 15. pii: S0891-5849(25)00028-0. [Epub ahead of print]229 58-67
    MnSOD non-acetylation mimic knock-in mice exhibit dilated cardiomyopathy.
    Joseph R Schell, Sung-Jen Wei, Jun Zhang, Rolando Trevino, Wan Hsi Chen, Leonardo Aguilar, Wei Qian, Cole W Corbett, Haiyan Jiang, Felix F Dong, E Sandra Chocron, Alia Nazarullah, Jenny Chang, Margaret E Flanagan, Vaida Glatt, Sergey Dikalov, Erin Munkácsy, Nobuo Horikoshi, David Gius.
      Manganese superoxide dismutase (MnSOD/SOD2) is an essential mitochondrial enzyme that detoxifies superoxide radicals generated during oxidative respiration. MnSOD/SOD2 lysine 68 acetylation (K68-Ac) is an important post-translational modification (PTM) that regulates enzymatic activity, responding to nutrient status or oxidative stress, and elevated levels have been associated with human illness. To determine the in vivo role of MnSOD-K68 in the heart, we used a whole-body non-acetylation mimic mutant (MnSODK68R) knock-in mouse. These mice exhibited several cardiovascular phenotypes, including lower blood pressure, decreased ejection fraction, and importantly, dilated cardiomyopathy, as evidenced by echocardiography at four months of age. In addition, both mouse embryo fibroblasts (MEFs) and cardiovascular tissue from MnSODK68R/K68R mice exhibited an increase in cellular senescence. Finally, MnSODK68R/K68R mouse hearts also showed an increase in lipid peroxidation. We conclude that constitutively active MnSOD detoxification activity, lacking the normal switch between non-acetylated and acetylated forms, dysregulates mitochondrial physiology during development, leading to dilated cardiomyopathy.
    Keywords:  Acetylation; Cardiomyopathy; Cell senescence; Echocardiography; Manganese superoxide dismutase; Mitochondria; MnSOD; SIRT3; SOD2; Sirtuin
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.01.028
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