bims-nenemi 2025-04-06 papers

bims-nenemi

Biomed News

on Neuroinflammation, neurodegeneration and mitochondria

Issue of 2025–04–06
thirty papers selected by
Marco Tigano, Thomas Jefferson University

The MFN2 Q367H variant reveals a novel pathomechanism connected to mtDNA-mediated inflammation.
Retromer promotes the lysosomal turnover of mtDNA.
NLRP10 Cleaves Oxidized DNA inhibited by OGG1 inhibitors: A Newly Identified Role in DNA Damage Processing and Senescence Regulation.
Atovaquone-induced activation of the PERK/eIF2α signaling axis mitigates metabolic radiosensitisation.
Restoration of Miro1's N-terminal GTPase function alleviates prenatal stress-induced mitochondrial fission via Drp1 modulation.
Characterization of a new mutation of mitochondrial ND6 gene in hepatocellular carcinoma and its effects on respiratory complex I.
The Silent Saboteur: How Mitochondria Shape the Long-Term Fate of the Injured Brain.
DNM1L-mediated fission governs mitophagy & mitochondrial biogenesis during myogenic differentiation.
Cellular Discrepancy of Platinum Complexes in Interfering with Mitochondrial DNA.
HTLV-1 Tax induces PINK1-Parkin-dependent mitophagy to mitigate activation of the cGAS-STING pathway.
Inhibition of PINK1 senses ROS signaling to facilitate neuroblastoma cell pyroptosis.
tRNA synthetase activity is required for stress granule and P-body assembly.
Simvastatin ameliorates senescence-induced mitochondrial dysfunction in vascular smooth muscle cells.
An engineered mitoCBE facilitates efficient mitochondrial DNA editing and modified mitochondrial transfer.
Oncogene-induced senescence mitochondrial metabolism and bioenergetics drive the secretory phenotype: further characterization and comparison with other senescence-inducing stimuli.
Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by spatial and single-cell transcriptomics.
STING immune activation of microglia aggravating neurovascular unit damage in diabetic retinopathy.
Decreased mitochondrial NAD+ in WRN deficient cells links to dysfunctional proliferation.
An inherited mtDNA rearrangement, mimicking a single large-scale deletion, associated with MIDD and a primary cardiological phenotype.
Comparative Study of Mitochondrial DNA Abnormalities in Mesenchymal Stem Cells after Exposure to X-Ray Radiation in Low and Medium Doses.
Intrinsic OASL expression licenses interferon induction during influenza A virus infection.
GI-Y2, a novel gasdermin D inhibitor, attenuates sepsis-induced myocardial dysfunction by inhibiting gasdermin D-mediated pyroptosis in macrophages.
Distinct astrocyte activation patterns associated with neuroinflammation induced by gamma and proton beam irradiation.
Representing Mitochondrial Dynamics with Abstract Algebra.
HELLS controls mitochondrial dynamics and genome stability in liver cancer by collusion with MIEF1.
Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration.
Remodelling of Cellular Protein Homeostasis by Enhanced ER-Mitochondrial Tethering.
Therapeutic potential of DDQ in enhancing mitochondrial health and cognitive function in Late-Onset Alzheimer's disease.
NF-κB signaling directs a program of transient amplifications at innate immune response genes.
Targeting senescent hepatocytes for treatment of metabolic dysfunction-associated steatotic liver disease and multi-organ dysfunction.

Life Sci Alliance. 2025 Jun;pii: e202402921. [Epub ahead of print]8(6):

The MFN2 Q367H variant reveals a novel pathomechanism connected to mtDNA-mediated inflammation.

Mashiat Zaman, Govinda Sharma, Walaa Almutawa, Tyler Gb Soule, Rasha Sabouny, Matt Joel, Armaan Mohan, Cole Chute, Jeffrey T Joseph, Gerald Pfeffer, Timothy E Shutt.

Pathogenic variants in the mitochondrial protein MFN2 are typically associated with a peripheral neuropathy phenotype, but can also cause a variety of additional pathologies including myopathy. Here, we identified an uncharacterized MFN2 variant, Q367H, in a patient diagnosed with late-onset distal myopathy, but without peripheral neuropathy. Supporting the hypothesis that this variant contributes to the patient's pathology, patient fibroblasts and transdifferentiated myoblasts showed changes consistent with impairment of several MFN2 functions. We also observed mtDNA outside of the mitochondrial network that colocalized with early endosomes, and measured activation of both TLR9 and cGAS-STING inflammation pathways that sense mtDNA. Re-expressing the Q367H variant in MFN2 KO cells also induced mtDNA release, demonstrating this phenotype is a direct result of the variant. As elevated inflammation can cause myopathy, our findings linking the Q367H MFN2 variant with elevated TLR9 and cGAS-STING signalling can explain the patient's myopathy. Thus, we characterize a novel MFN2 variant in a patient with an atypical presentation that separates peripheral neuropathy and myopathy phenotypes, and establish a potential pathomechanism connecting MFN2 dysfunction to mtDNA-mediated inflammation.

DOI: https://doi.org/10.26508/lsa.202402921
Sci Adv. 2025 Apr 04. 11(14): eadr6415

Retromer promotes the lysosomal turnover of mtDNA.

Parisa Kakanj, Mari Bonse, Arya Kshirsagar, Aylin Gökmen, Felix Gaedke, Ayesha Sen, Belén Mollá, Elisabeth Vogelsang, Astrid Schauss, Andreas Wodarz, David Pla-Martín.

Mitochondrial DNA (mtDNA) is exposed to multiple insults produced by normal cellular function. Upon mtDNA replication stress, the mitochondrial genome transfers to endosomes for degradation. Using proximity biotinylation, we found that mtDNA stress leads to the rewiring of the mitochondrial proximity proteome, increasing mitochondria's association with lysosomal and vesicle-related proteins. Among these, the retromer complex, particularly VPS35, plays a pivotal role by extracting mitochondrial components. The retromer promotes the formation of mitochondrial-derived vesicles shuttled to lysosomes. The mtDNA, however, directly shuttles to a recycling organelle in a BAX-dependent manner. Moreover, using a Drosophila model carrying a long deletion on the mtDNA (ΔmtDNA), we found that ΔmtDNA activates a specific transcriptome profile to counteract mitochondrial damage. Here, Vps35 expression restores mtDNA homoplasmy and alleviates associated defects. Hence, we demonstrate the existence of a previously unknown quality control mechanism for the mitochondrial matrix and the essential role of lysosomes in mtDNA turnover to relieve mtDNA damage.

DOI: https://doi.org/10.1126/sciadv.adr6415
bioRxiv. 2025 Mar 12. pii: 2025.03.07.642110. [Epub ahead of print]

NLRP10 Cleaves Oxidized DNA inhibited by OGG1 inhibitors: A Newly Identified Role in DNA Damage Processing and Senescence Regulation.

Julia Elise Cabral, Sophia Lin, Haitian Zhou, Anna Wu, Angie Lackner, Minh Anh Pham, Feixuan Chi, Reginald McNulty.

Mitochondrial DNA (mtDNA) release into the cytosol is a critical event in innate immune activation, often acting as a damage-associated molecular pattern (DAMP) that triggers inflammasome assembly. Here, we demonstrate that NLRP3 plays a direct role in cleaving and facilitating the release of D-loop mtDNA into the cytosol. We further show that NLRP3 interacts with NLRP10. NLRP10-mediated ox-DNA cleavage involves a Schiff base intermediate and is inhibited by small molecules known to inhibit glycosylases. These findings support a model where NLRP10 interaction with oxidized DNA may contribute to long-term senescence secretory phenotype and modulate inflammasome activation. Our study highlights a novel mechanism by which NLRP10 can respond to mitochondrial stress signals to influence innate immunity and suggests therapeutic potential for targeting these interactions in inflammatory diseases.

DOI: https://doi.org/10.1101/2025.03.07.642110
Cell Commun Signal. 2025 Apr 02. 23(1): 164

Atovaquone-induced activation of the PERK/eIF2α signaling axis mitigates metabolic radiosensitisation.

Jie Feng, Varun Pathak, Niall M Byrne, Sarah Chambers, Tongchuan Wang, Rayhanul Islam, Reinhold J Medina, Jonathan A Coulter.

   BACKGROUND: Hypoxia, a key feature of most solid tumours, including head and neck cancer, reduces radiotherapy efficacy by promoting radiation resistance through micro-environmental and genomic alterations. Addressing these resistance mechanisms is crucial, as radiotherapy remains central to managing locally advanced disease. Atovaquone, a mitochondrial electron transport chain complex III inhibitor, is reported to reduce tumour hypoxia in preclinical models, however, this response does not consistently enhance radiation sensitivity. This work examines the potential of atovaquone to modify the hypoxic response in models of head and neck squamous cell carcinoma (HNSCC), uncovering an adaptive resistance mechanism driven by integrated stress response (ISR) signaling that limits the radiosensitising potential of this approach.
METHODS: The bioenergetic response of HNSCC cells to atovaquone was assessed using the Seahorse XFe96 Analyzer with the XF Cell Mito Stress Test. Radiation dose modifying effects of atovaquone were tested by clonogenic survival assays, while ROS yields were analysed by flow cytometry. Western blotting and quantitative reverse transcription-PCR were employed to study activation of ISR signaling and the overall influence of atovaquone on the hypoxic response. Finally, the role of the ISR activation in modulating radiosensitivity was investigated using both siRNA and pharmacological inhibition of eIF2α, a central regulator of the ISR.
RESULTS: Herein we report that atovaquone significantly disrupts mitochondrial respiration, triggering phosphorylation of eIF2α, a pivotal regulator of the ISR, and a master regulator of protein synthesis. Notably, atovaquone also increased the autophagic load under hypoxia, while autophagy inhibition significantly enhanced apoptosis, improving radiation sensitivity. Combined eIF2α inhibition and atovaquone promotes cell cycle redistribution and significantly enhances mitochondrial ROS production and compared to atovaquone alone, restoring atovaquone mediated radiosensitisation.
CONCLUSIONS: Our data highlight dual counter opposing impacts of atovaquone, serving as a hypoxic radiosensitiser though oxidative phosphorylation (OXPHOS) inhibition, but also in promoting stress induced ISR signaling, conferring resistance to radiation treatment. Importantly, if ISR activation is impeded, the metabolic radiosensitising properties of atovaquone is restored. These data provide a new insight to a molecular response that could help counteract hypoxia-induced radioresistance.

Keywords:  Autophagy; ER stress; Hypoxia; Radiosensitisation

DOI:  https://doi.org/10.1186/s12964-025-02160-9
Cell Commun Signal. 2025 Apr 02. 23(1): 166

Restoration of Miro1's N-terminal GTPase function alleviates prenatal stress-induced mitochondrial fission via Drp1 modulation.

Gee Euhn Choi, Ji Yong Park, Mo Ran Park, Chang Woo Chae, Young Hyun Jung, Jae Ryong Lim, Jee Hyeon Yoon, Ji Hyeon Cho, Ho Jae Han.

   BACKGROUND: Prenatal stress exposure irreversibly impairs mitochondrial dynamics, including mitochondrial trafficking and morphology in offspring, leading to neurodevelopmental and neuropsychiatric disorders in adulthood. Thus, understanding the molecular mechanism controlling mitochondrial dynamics in differentiating neurons is crucial to prevent the prenatal stress-induced impairments in behavior. We investigated the interplay between mitochondrial transport and fusion/fission in differentiating neurons exposed to prenatal stress, leading to ensuing behavior impairments, and then tried to identify the primary regulator that modulates both phenomena.
METHODS: We used primary hippocampal neurons of mice exposed to prenatal stress and human induced-pluripotent stem cell (hiPSC)-derived neurons, for investigating the impact of glucocorticoid on mitochondrial dynamics during differentiation. For constructing mouse models, we used AAV vectors into mouse pups exposed to prenatal stress to regulate protein expressions in hippocampal regions.
RESULTS: We first observed that prenatal exposure to glucocorticoids induced motility arrest and fragmentation of mitochondria in differentiating neurons derived from mouse fetuses (E18) and human induced pluripotent stem cells (hiPSCs). Further, glucocorticoid exposure during neurogenesis selectively downregulated Miro1 and increased Drp1 phosphorylation (Ser616). MIRO1 overexpression restored mitochondrial motility and increased intramitochondrial calcium influx through ER-mitochondria contact (ERMC) formation. Furthermore, we determined that the N-terminal GTPase domain of Miro1 plays a critical role in ERMC formation, which then decreased Drp1 phosphorylation (Ser616). Similarly, prenatal corticosterone exposure led to impaired neuropsychiatric and cognitive function in the offspring by affecting mitochondrial distribution and synaptogenesis, rescued by Miro1WT, but not N-terminal GTPase active form Miro1P26V, expression.
CONCLUSION: Prenatal glucocorticoid-mediated Miro1 downregulation contributes to dysfunction in mitochondrial dynamics through Drp1 phosphorylation (Ser616) in differentiating neurons.

Keywords:  ER-mitochondria contacts; Miro; Mitochondrial dynamics; Neurodegeneration; Prenatal glucocorticoid

DOI:  https://doi.org/10.1186/s12964-025-02172-5
Sci Rep. 2025 Mar 29. 15(1): 10925

Characterization of a new mutation of mitochondrial ND6 gene in hepatocellular carcinoma and its effects on respiratory complex I.

Veronica Bazzani, Deepali L Kundnani, Mara Equisoain Redin, Francesca Agostini, Kirti Chhatlani, Angelo Corso Faini, Jakub Poziemski, Umberto Baccarani, Pawel Siedlecki, Silvia Deaglio, Francesca Storici, Carlo Vascotto.

  Hepatocellular carcinoma (HCC) is the most common form of liver cancer, which often arises from previous liver pathologies such as HBV, HCV, and alcohol abuse. It is typically associated with an enlarged cirrhotic organ. In this study, we analyzed tumor and distal tissues from a patient who underwent liver resection for HCC with no previous pathologies and whose liver showed normal function without signs of cirrhosis. Genetic analysis of mitochondrial DNA (mtDNA) revealed a novel variant of the gene encoding the NADH dehydrogenase subunit 6 (ND6) protein in the tumor tissue. The deletion of a thymidine generated an early stop codon, resulting in a truncated form of the protein (ΔND6) with 50% of the C-terminal primary sequence missing. ND6 is a subunit of the NADH dehydrogenase complex, also known as Complex I, the largest complex in the electron transport chain. Previous studies have linked mtDNA Complex I mutations to mitochondrial disorders and cancer. Through biochemical analyses, we characterized this new mutation and showed that the expression of ΔND6 negatively affects the stability and functionality of Complex I. Data were confirmed by molecular dynamics simulations suggesting conformational rearrangements, overall revealing a leading role of ND6 in the assembly of Complex I.

Keywords:  Hepatocellular carcinoma; Mitochondria; Mitochondrial DNA; Molecular dynamics simulations.; ND6 gene mutation; Respiratory complex I assembly

DOI:  https://doi.org/10.1038/s41598-025-91746-x
bioRxiv. 2025 Mar 27. pii: 2025.03.19.644244. [Epub ahead of print]

The Silent Saboteur: How Mitochondria Shape the Long-Term Fate of the Injured Brain.

Sahan Bs Kansakar, Sydney P Sterben, Charitha C Anamala, Mitchell D Thielen, Volha Liaudanskaya.

Traumatic brain injury (TBI) is a major risk factor for neurodegenerative diseases, including Alzheimer's disease (AD), yet the mechanistic link remains unclear. Here, we integrated human patient-derived transcriptomics with a 3D in vitro brain injury model to dissect cell-specific mitochondrial dysfunction as a driver of injury-induced neurodegeneration. Comparative transcriptomic analysis at 6 and 48 hours post-injury revealed conserved mitochondrial impairments across excitatory neurons, interneurons, astrocytes, and microglia. Using a novel cell-specific mitochondria tracking system, we demonstrate prolonged neuronal mitochondrial fragmentation, bioenergetic failure, and metabolic instability, coinciding with the emergence of AD markers, including pTau, APP, and Aβ42/40 dysregulation. Glial mitochondria exhibited delayed but distinct metabolic dysfunctions, with astrocytes impaired metabolic support and microglia sustained chronic inflammation. These findings establish neuronal mitochondrial failure as an early trigger of injury-induced neurodegeneration, reinforcing mitochondrial dysfunction as a therapeutic target for preventing TBI-driven AD pathology.

DOI: https://doi.org/10.1101/2025.03.19.644244
Cell Commun Signal. 2025 Apr 01. 23(1): 158

DNM1L-mediated fission governs mitophagy & mitochondrial biogenesis during myogenic differentiation.

Fasih A Rahman, Jasmine M Friedrich Yap, Tyler M Joseph, Amanda M Adam, Sarah M Chapman, Joe Quadrilatero.

   BACKGROUND: Remodeling of the mitochondrial network is implicated in myogenesis. Remodeling processes including mitochondrial fission, mitophagy, and biogenesis are important as they finetune the mitochondrial network to meet the increased energetic demand of myotubes. Evidence suggests that mitochondrial fission governs other mitochondrial remodeling processes; however, this relationship is unclear in the context of myogenesis.
METHODS: We used C2C12 myoblasts to study changes in mitochondrial remodeling processes and their role in regulating myogenesis. To investigate this, we employed genetic manipulation with adenoviruses to modify the levels of key molecules involved in mitochondrial remodeling, including DNM1L, BNIP3, and PPARGC1A.
RESULTS: We demonstrate that overexpression of fission protein DNM1L accelerated mitophagic flux, but reduced myotube size without affecting mitochondrial biogenesis. Conversely, DNM1L knockdown reduced mitophagic flux, impaired myoblast differentiation, and suppressed mitochondrial biogenesis signaling. Additionally, DNM1L knockdown increased mitochondrial apoptotic signaling through CASP9 and CASP3 activation. Attempts to rescue myogenesis through overexpression of the mitophagy receptor BNIP3 or the biogenesis regulator PPARGC1A were unsuccessful in the absence of proper mitochondrial fission. Furthermore, DNM1L overexpression in BNIP3-deficient cells enhanced mitophagic flux, but did not promote myogenesis.
CONCLUSION: These results underscore the complex interdependencies among mitochondrial remodeling processes and highlight the necessity for sequential activation of mitochondrial fission, mitophagy, and biogenesis.

Keywords:  Apoptosis; Mitochondrial biogenesis; Mitochondrial fission; Mitophagy; Myogenesis; Skeletal muscle

DOI:  https://doi.org/10.1186/s12964-025-02142-x
ACS Cent Sci. 2025 Mar 26. 11(3): 393-403

Cellular Discrepancy of Platinum Complexes in Interfering with Mitochondrial DNA.

Suxing Jin, Yafeng He, Chenyao Feng, Jian Yuan, Yan Guo, Zijian Guo, Xiaoyong Wang.

Mitochondria are associated with cellular energy metabolism, proliferation, and mode of death. Damage to mitochondrial DNA (mtDNA) greatly affects mitochondrial function by interfering with energy production and the signaling pathway. Monofunctional trinuclear platinum complex MTPC demonstrates different actions on the mtDNA of cancerous and normal cells. It severely impairs the integrity and function of mitochondria in the human lung cancer A549 cells, such as dissipating mitochondrial membrane potential, decreasing the copy number of mtDNA, interfering in nucleoid proteins and polymerase gamma gene, reducing adenosine triphosphate (ATP), and inducing mitophagy, whereas it barely affects the mtDNA of the human kidney 2 (HK-2) cells. Moreover, MTPC promotes the release of mtDNA into the cytosol and stimulates the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway, thus showing the potential to trigger antitumor immunity. MTPC displays significant cytotoxicity against A549 cells, while it exhibits weak toxicity toward HK-2 cells, therefore displaying great advantage to overcome the lingering nephrotoxicity of platinum anticancer drugs. Discrepant effects of a metal complex on mitochondria of different cells mean that targeting mitochondria has special significance in cancer therapy.

DOI: https://doi.org/10.1021/acscentsci.4c01941
bioRxiv. 2025 Mar 15. pii: 2025.03.15.643451. [Epub ahead of print]

HTLV-1 Tax induces PINK1-Parkin-dependent mitophagy to mitigate activation of the cGAS-STING pathway.

Suchitra Mohanty, Sujit Suklabaidya, Nelli Mnatsakanyan, Steven Jacobson, Edward W Harhaj.

  Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell leukemia/lymphoma (ATLL) and the neuroinflammatory disease, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The HTLV-1 Tax regulatory protein plays a critical role in HTLV-1 persistence and pathogenesis; however, the underlying mechanisms are poorly understood. Here we show that Tax dynamically regulates mitochondrial reactive oxygen species (ROS) and membrane potential to trigger mitochondrial dysfunction. Tax is recruited to damaged mitochondria through its interaction with the IKK regulatory subunit NEMO and directly engages the ubiquitin-dependent PINK1-Parkin pathway to induce mitophagy. Tax also recruits autophagy receptors NDP52 and p62/SQSTM1 to damaged mitochondria to induce mitophagy. Furthermore, Tax requires Parkin to limit the extent of cGAS-STING activation and suppress type I interferon (IFN). HTLV-1-transformed T cell lines and PBMCs from HAM/TSP patients exhibit hallmarks of chronic mitophagy which may contribute to immune evasion and pathogenesis. Collectively, our findings suggest that Tax manipulation of the PINK1-Parkin mitophagy pathway represents a new HTLV-1 immune evasion strategy.

Keywords:  HTLV-1; NDP52; NEMO; Parkin; STING; Tax; cGAS; mitochondria; mitophagy

DOI:  https://doi.org/10.1101/2025.03.15.643451
Autophagy. 2025 Mar 31.

Inhibition of PINK1 senses ROS signaling to facilitate neuroblastoma cell pyroptosis.

Yuyuan Zhu, Min Cao, Yancheng Tang, Yifan Liu, Haiji Wang, Jiaqi Qi, Cainian Huang, Chenghao Yan, Xu Liu, Sijia Jiang, Yufei Luo, Shaogui Wang, Bo Zhou, Haodong Xu, Ying-Ying Lu, Liming Wang.

  Mitochondria serve as the primary source of intracellular reactive oxygen species (ROS), which play a critical role in orchestrating cell death pathways such as pyroptosis in various types of cancers. PINK1-mediated mitophagy effectively removes damaged mitochondria and reduces detrimental ROS levels, thereby promoting cell survival. However, the regulation of pyroptosis by PINK1 and ROS in neuroblastoma remains unclear. In this study, we demonstrate that inhibition or deficiency of PINK1 sensitizes ROS signaling and promotes pyroptosis in neuroblastoma cells via the BAX-caspase-GSDME signaling pathway. Specifically, inhibition of PINK1 by AC220 or knockout of PINK1 impairs mitophagy and enhances ROS production, leading to oxidation and oligomerization of TOMM20, followed by mitochondrial recruitment and activation of BAX. Activated BAX facilitates the release of CYCS (cytochrome c, somatic) from the mitochondria into the cytosol, activating CASP3 (caspase 3). Subsequently, activated CASP3 cleaves and activates GSDME, inducing pyroptosis. Furthermore, inhibition or deficiency of PINK1 potentiates the anti-tumor effects of the clinical ROS-inducing drug ethacrynic acid (EA) to inhibit neuroblastoma progression in vivo. Therefore, our study provides a promising intervention strategy for neuroblastoma through the induction of pyroptosis.

Keywords:  Cell death; GSDME; PINK1; mitochondrial ROS; mitophagy; neuroblastoma

DOI:  https://doi.org/10.1080/15548627.2025.2487037
bioRxiv. 2025 Mar 13. pii: 2025.03.10.642431. [Epub ahead of print]

tRNA synthetase activity is required for stress granule and P-body assembly.

Max Baymiller, Noah S Helton, Benjamin Dodd, Stephanie L Moon.

In response to stress, translation initiation is suppressed and ribosome runoff via translation elongation drives mRNA assembly into ribonucleoprotein (RNP) granules including stress granules and P-bodies. Defects in translation elongation activate the integrated stress response. If and how stalled ribosomes are removed from mRNAs during translation elongation stress to drive RNP granule assembly is not clear. We demonstrate the integrated stress response is induced upon tRNA synthetase inhibition in part via ribosome collision sensing. However, saturating levels of tRNA synthetase inhibitors do not induce stress granules or P-bodies and prevent RNP granule assembly upon exogenous stress. The loss of tRNA synthetase activity causes persistent ribosome stalls that can be released with puromycin but are not rescued by ribosome-associated quality control pathways. Therefore, tRNA synthetase activity is required for ribosomes to run off mRNAs during stress to scaffold cytoplasmic RNP granules. Our findings suggest ribosome stalls can persist in human cells and uniquely uncouple ribonucleoprotein condensate assembly from the integrated stress response.

DOI: https://doi.org/10.1101/2025.03.10.642431
Atherosclerosis. 2025 Mar 21. pii: S0021-9150(25)00074-7. [Epub ahead of print]403 119176

Simvastatin ameliorates senescence-induced mitochondrial dysfunction in vascular smooth muscle cells.

C Rossi, C Macchi, C D'Alonzo, M Venturin, M Ruscica, A Corsini, C Battaglia, S Bellosta.

   BACKGROUND AND AIMS: Senescence and mitochondrial dysfunction are two major indicators of aging. Mitochondria are potential drivers of aging phenotypes and dysfunctional mitochondria are associated with several age-related diseases. There is evidence that senescence induces changes in mitochondrial structure, dynamics, and function. Moreover, senescent vascular smooth muscle cells (VSMCs) are present in atherosclerotic plaques and contribute to their instability. The anti-atherosclerotic effects of simvastatin are well known, but recently other benefits, such as promoting mitochondrial quality and senostatic effects, have been hypothesized. We aimed to analyze simvastatin's senostatic effects in senescent VSMCs.
METHODS: We established and characterized mitochondrial dysfunction in doxorubicin-induced senescent VSMCs (doxorubicin) or VSMCs serially passaged to induce replicative senescence (old).
RESULTS: We observed in both senescent models few typical senescence markers such as altered cell morphology, cell cycle inhibitors, laminB1, an accumulation of dysfunctional mitochondria characterized by reduced mitochondrial membrane potential (MMP) and respiration, accumulation of reactive oxygen species (ROS), and an altered mitochondria morphology. Down-regulation of TFAM and TOM70 expression was observed only in old cells suggesting a reduction of mitochondrial biogenesis. Next, we investigated whether simvastatin could ameliorate age-associated phenotypes in senescent VSMCs. Simvastatin 0.1 μM reduces the senescence-associated secretory phenotype (SASP) and ROS production and improves mitochondrial respiration in doxorubicin and old VSMCs. Interestingly, the effects of simvastatin on mitochondrial respiration and SASP were replicated by using a siRNA for the hydroxy-methyl-glutaryl-coenzyme A (HMG-CoA) reductase, and abolished by adding mevalonic acid, suggesting that these effects are mediated through the inhibition of HMG-CoA reductase.
CONCLUSIONS: Our results suggest that simvastatin controls SASP and exerts potentially beneficial therapeutic effects by ameliorating senescence-induced mitochondrial dysfunction in senescent VSMCs.

Keywords:  Aging; Mitochondrial dysfunction; Senescence; Statins; Vascular smooth muscle cells

DOI:  https://doi.org/10.1016/j.atherosclerosis.2025.119176
Mol Ther. 2025 Apr 03. pii: S1525-0016(25)00260-6. [Epub ahead of print]

An engineered mitoCBE facilitates efficient mitochondrial DNA editing and modified mitochondrial transfer.

Jie Liu, Jun Chen, Shisheng Huang, Junfan Guo, Xiangyang Li, Ying Yan, Ruijing Chen, Guanglei Li, Ming Liu, Jiao Wei, Xingxu Huang, Yunbo Qiao.

Double-stranded DNA (dsDNA) cytosine deaminase DddA orthologs from multiple types of bacteria have been fused with TALE system for mitochondrial DNA (mtDNA) base editing, while the efficiencies remain limited and its nuclear off-targeting activity cannot be ignored yet. Here we identified a DddA ortholog from Burkholderia gladioli (BgDddA) and generated nuclear or mitochondrial DNA cytosine base editors (mitoCBEs), exhibiting higher C•G-to-T•A editing frequencies compared to canonical DdCBE, and fusion with transactivator Rta remarkably improved editing efficiencies by up to 6.4-fold at non-TC targets. Referring to DddA11, we further introduced six substitutions into BgDddA and generated mitoCBE3.2, which efficiently induced disease-associated mtDNA mutations in mouse and human cell lines at both TC and non-TC targets with efficiency reaching up to 99.2%. Using mitoCBE3.2, single clones containing homoplasmic mtDNA mutations or premature stop codons associated with human diseases were generated, and the functions of these mutations have been evaluated upon the treatment of ROS inducers. Importantly, mitochondria harboring these homoplasmic mutations were transplanted into wildtype cells, enabling precise base conversions, without risk of nuclear gene off-targets. Thus, we have engineered an efficient mitoCBE using BgDddA, facilitating mitochondrial disease modeling and potential mutation correction with the aid of mitochondrial transplantation.

DOI: https://doi.org/10.1016/j.ymthe.2025.03.051
Redox Biol. 2025 Mar 22. pii: S2213-2317(25)00119-3. [Epub ahead of print]82 103606

Oncogene-induced senescence mitochondrial metabolism and bioenergetics drive the secretory phenotype: further characterization and comparison with other senescence-inducing stimuli.

Inés Marmisolle, Eliana Chacón, Santiago Mansilla, Santiago Ruiz, Mariana Bresque, Jennyfer Martínez, Ricardo Iván Martínez-Zamudio, Utz Herbig, Jie Liu, Toren Finkel, Carlos Escande, Laura Castro, Celia Quijano.

  Cellular senescence is characterized by proliferation arrest and a senescence-associated secretory phenotype (SASP), that plays a role in aging and the progression of various age-related diseases. Although various metabolic alterations have been reported, no consensus exists regarding mitochondrial bioenergetics. Here we compared mitochondrial metabolism of human fibroblasts after inducing senescence with different stimuli: the oxidant hydrogen peroxide (H2O2), the genotoxic doxorubicin, serial passage, or expression of the H-RASG12V oncogene (RAS). In senescence induced by H2O2, doxorubicin or serial passage a decrease in respiratory control ratio (RCR) and coupling efficiency was noted, in relation to control cells. On the contrary, oncogene-induced senescent cells had an overall increase in respiration rates, RCR, spare respiratory capacity and coupling efficiency. In oncogene-induced senescence (OIS) the increase in respiration rates was accompanied by an increase in fatty acid catabolism, AMPK activation, and a persistent DNA damage response (DDR), that were not present in senescent cells induced by either H2O2 or doxorubicin. Inhibition of AMPK reduced mitochondrial oxygen consumption and secretion of proinflammatory cytokines in OIS. Assessment of enzymes involved in acetyl-CoA metabolism in OIS showed a 3- to 7.5-fold increase in pyruvate dehydrogenase complex (PDH), a 40% inhibition of mitochondrial aconitase, increased phosphorylation and activation of ATP-citrate lyase (ACLY), and inhibition of acetyl-CoA carboxylase (ACC). There was also a significant increase in expression and nuclear levels of the deacetylase sirtuin 6 (SIRT6). These changes can influence the sub-cellular distribution of acetyl-CoA and modulate protein acetylation reactions in the cytoplasm and nuclei. In fact, ACLY inhibition reduced histone 3 acetylation (H3K9Ac) in OIS and secretion of SASP components. In summary, our data show marked heterogeneity in mitochondrial energy metabolism of senescent cells, depending on the inducing stimulus, reveal new metabolic features of oncogene-induced senescent cells and identify AMPK and ACLY as potential targets for SASP modulation.

Keywords:  Bioenergetics; Fatty acid oxidation; Mitochondria; RAS oncogene; Senescence; TCA cycle

DOI:  https://doi.org/10.1016/j.redox.2025.103606
Sci Adv. 2025 Apr 04. 11(14): eadq1575

Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by spatial and single-cell transcriptomics.

Tasneem Qaqorh, Yusuke Takahashi, Kohei Sameshima, Kentaro Otani, Issei Yazawa, Yuya Nishida, Kohei Tonai, Yoshitaka Fujihara, Mizuki Honda, Shinya Oki, Yasuyuki Ohkawa, David R Thorburn, Ann E Frazier, Atsuhito Takeda, Yoshihiko Ikeda, Heima Sakaguchi, Takuya Watanabe, Norihide Fukushima, Yasumasa Tsukamoto, Naomasa Makita, Osamu Yamaguchi, Kei Murayama, Akira Ohtake, Yasushi Okazaki, Takanari Kimura, Hisakazu Kato, Hijiri Inoue, Ken Matsuoka, Seiji Takashima, Yasunori Shintani.

Oxidative phosphorylation defects result in now intractable mitochondrial diseases (MD) with cardiac involvement markedly affecting prognosis. The mechanisms underlying the transition from compensation to dysfunction in response to metabolic deficiency remain unclear. Here, we used spatially resolved transcriptomics and single-nucleus RNA sequencing (snRNA-seq) on the heart of a patient with mitochondrial cardiomyopathy (MCM), combined with an MCM mouse model with cardiac-specific Ndufs6 knockdown (FS6KD). Cardiomyocytes demonstrated the most heterogeneous expression landscape among cell types caused by metabolic perturbation, and pseudotime trajectory analysis revealed dynamic cellular states transitioning from compensation to severe compromise. This progression coincided with the transient up-regulation of a transcription factor, ATF3. Genetic ablation of Atf3 in FS6KD corroborated its pivotal role, effectively delaying cardiomyopathy progression in a female-specific manner. Our findings highlight a fate-determining role of ATF3 in female MCM progression and that the latest transcriptomic analysis will help decipher the mechanisms underlying MD progression.

DOI: https://doi.org/10.1126/sciadv.adq1575
Free Radic Biol Med. 2025 Mar 28. pii: S0891-5849(25)00192-3. [Epub ahead of print]

STING immune activation of microglia aggravating neurovascular unit damage in diabetic retinopathy.

Hong-Ying Li, Jingfan Wang, Tianhao Xiao, Qinyuan Gu, Yuanyuan Fan, Pengfei Ge, Jingyi Xu, Cheng Wang, Ping Xie, Zizhong Hu.

  Diabetic retinopathy (DR) is the leading cause of blindness and is pathologically characterized by neuroinflammation and neovascularization. Retinal homeostasis is critically maintained by the retinal neurovascular unit (NVU), which can be disrupted by abnormal activation of microglia in DR. However, the underlying mechanism remains unclear. Here, we provide the first evidence of upregulated stimulator of interferon genes (STING) in microglia within fibrovascular membranes (FVMs) and retinas from oxygen-induced retinopathy (OIR) and streptozotocin (STZ)-induced diabetic mice. Furthermore, we identified STING upregulation in BV2 cells stimulated with high glucose (HG) or hypoxia, accompanied by mitochondrial dysfunction and cytoplasmic leakage of damaged mitochondrial DNA (mtDNA). Pharmacologic or genetic inhibition of STING in microglia prevented their activation and polarization. Next, we demonstrated that STING-deficient BV2 cells reversed the proangiogenic behavior of endothelial cells and protected retinal ganglion cells (RGCs) from oxidative stress. Finally, intravitreal injection of AAV-STING alleviated retinal neurovascular pathologies in both OIR and STZ mice. This study demonstrated that the release of mtDNA mediates STING immune activation of microglia, which further exacerbates NVU damage in DR. In contrast, immunosuppressing STING in microglia could serve as a potential therapeutic strategy.

Keywords:  Diabetic retinopathy; Neuroinflammation; Neurovascular unit; Oxidative stress; STING

DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.03.042
Aging (Albany NY). 2025 Apr 02. null

Decreased mitochondrial NAD+ in WRN deficient cells links to dysfunctional proliferation.

Sofie Lautrup, Shi-Qi Zhang, Shinichiro Funayama, Lisa Lirussi, Tina Visnovska, Hoi-Hung Cheung, Marc Niere, Yuyao Tian, Hilde Loge Nilsen, Geir Selbæk, Janna Saarela, Yoshiro Maezawa, Koutaro Yokote, Per Nilsson, Wai-Yee Chan, Hisaya Kato, Mathias Ziegler, Vilhelm A Bohr, Evandro F Fang.

  Werner syndrome (WS), caused by mutations in the RecQ helicase WERNER (WRN) gene, is a classical accelerated aging disease with patients suffering from several metabolic dysfunctions without a cure. While, as we previously reported, depleted NAD+ causes accumulation of damaged mitochondria, leading to compromised metabolism, how mitochondrial NAD+ changes in WS and the impact on WS pathologies were unknown. We show that loss of WRN increases senescence in mesenchymal stem cells (MSCs) likely related to dysregulation of metabolic and aging pathways. In line with this, NAD+ augmentation, via supplementation with nicotinamide riboside, reduces senescence and improves mitochondrial metabolic profiles in MSCs with WRN knockout (WRN-/-) and in primary fibroblasts derived from WS patients compared to controls. Moreover, WRN deficiency results in decreased mitochondrial NAD+ (measured indirectly via mitochondrially-expressed PARP activity), and altered expression of key salvage pathway enzymes, including NMNAT1 and NAMPT; ChIP-seq data analysis unveils a potential co-regulatory axis between WRN and the NMNATs, likely important for chromatin stability and DNA metabolism. However, restoration of mitochondrial or cellular NAD+ is not sufficient to reinstall cellular proliferation in immortalized cells with siRNA-mediated knockdown of WRN, highlighting an indispensable role of WRN in proliferation even in an NAD+ affluent environment. Further cell and animal studies are needed to deepen our understanding of the underlying mechanisms, facilitating related drug development.

Keywords:  NAD+; Werner syndrome; mitochondria; premature aging; proliferation

DOI:  https://doi.org/10.18632/aging.206236
Mitochondrion. 2025 Mar 29. pii: S1567-7249(25)00034-0. [Epub ahead of print]83 102037

An inherited mtDNA rearrangement, mimicking a single large-scale deletion, associated with MIDD and a primary cardiological phenotype.

Piervito Lopriore, Andrea Legati, Christiane Michaela Neuhofer, Annalisa Lo Gerfo, Robert Kopajtich, Marco Barresi, Giulia Cecchi, Martin Pavlov, Rossella Izzo, Vincenzo Montano, Maria Adelaide Caligo, Riccardo Berutti, Michelangelo Mancuso, Holger Prokisch, Daniele Ghezzi.

   AIM: To identify the genetic cause in a previously unsolved pedigree, with mother and two daughters suffering of dilated cardiomyopathy with prevailing arrhythmic burden associated with diabetes mellitus and sensorineural hearing loss, without clear evidence of progressive external ophthalmoplegia.
METHODS: Several genetic tests were performed over the years including single-gene sequencing, mitochondrial DNA (mtDNA) sequencing, NGS panel for mitochondrial diseases and cardiomyopathies, clinical exome sequencing and whole exome sequencing. Specific amplifications and long-read NGS were used to evaluate mtDNA structural alterations.
RESULTS: By means of whole exome sequencing we found a novel heteroplasmic 12 kb-long single deletion in the mtDNA in all affected family members, confirmed by long-range PCR. However, a deeper investigation by long-read NGS revealed indeed the presence of rearranged mtDNA species, formed by a wild-type plus a deleted molecule. This mtDNA duplication turned out to be inherited in our pedigree and present in all tested specimens.
CONCLUSION: While mtDNA single large-scale deletions are generally considered sporadic, few old reports described maternally inherited mtDNA duplication We suggest that mtDNA large rearrangements should be considered as possible disease causes in familial cases with unusual mitochondrial phenotypes. Long-read sequencing is useful for the detection of these variants, particularly mtDNA duplications.

Keywords:  MIDD (Maternally Inherited Diabetes and Deafness); Mitochondrial DNA; Single large-scale deletion; Structural rearrangement; mtDNA; mtDNA duplication

DOI:  https://doi.org/10.1016/j.mito.2025.102037
Bull Exp Biol Med. 2025 Feb;178(4): 541-546

Comparative Study of Mitochondrial DNA Abnormalities in Mesenchymal Stem Cells after Exposure to X-Ray Radiation in Low and Medium Doses.

M V Dushenko, S A Abdullaev, M A Ignatov, A N Osipov.

  The effects of low- and medium-dose X-rays on mitochondrial function in mesenchymal stem (stromal) cells (MSCs) were compared. Irradiation at a dose of 80 mGy did not lead to mitochondrial disorders in MSCs by all analyzed parameters, while 24 h after irradiation at a dose of 2000 mGy, damage to mitochondrial and nuclear DNA was recorded, as well as the initiation of replicative synthesis of mitochondrial DNA involving damaged molecules, which led to an increase in the level of heteroplasmy. The increased level of mitochondrial DNA heteroplasmy after irradiation at a dose of 2000 mGy was accompanied by a decrease in the expression of genes involved in the process of oxidative phosphorylation and regulating mitochondrial dynamics.

Keywords:  X-ray radiation; biogenesis of mitochondrial DNA; damage to mitochondrial and nuclear DNA; gene expression; mutant copies of mitochondrial DNA

DOI:  https://doi.org/10.1007/s10517-025-06370-6
bioRxiv. 2025 Mar 17. pii: 2025.03.14.643375. [Epub ahead of print]

Intrinsic OASL expression licenses interferon induction during influenza A virus infection.

Joel Rivera-Cardona, Tarun Mahajan, Neeharika R Kakuturu, Qi Wen Teo, Joseph Lederer, Elizabeth A Thayer, Elizabeth F Rowland, Kyle Heimburger, Jiayi Sun, Cera A McDonald, Clayton K Mickelson, Ryan A Langlois, Nicholas C Wu, Olgica Milenkovic, Sergei Maslov, Christopher B Brooke.

Effective control of viral infection requires rapid induction of the innate immune response, especially the type I and type III interferon (IFN) systems. Despite the critical role of IFN induction in host defense, numerous studies have established that most cells fail to produce IFNs in response to viral stimuli. The specific factors that govern cellular heterogeneity in IFN induction potential during infection are not understood. To identify specific host factors that license some cells but not others to mount an IFN response to viral infection, we developed an approach for analyzing temporal scRNA-seq data of influenza A virus (IAV)-infected cells. This approach identified the expression of several interferon stimulated genes (ISGs) within pre-infection cells as correlates of IFN induction potential of those cells, post-infection. Validation experiments confirmed that intrinsic expression of the ISG OASL is essential for robust IFNL induction during IAV infection. Altogether, our findings reveal an important role for IFN-independent, intrinsic expression of ISGs in promoting IFN induction and provide new insights into the mechanisms that regulate cell-to-cell heterogeneity in innate immune activation.

DOI: https://doi.org/10.1101/2025.03.14.643375
Br J Pharmacol. 2025 Mar 31.

GI-Y2, a novel gasdermin D inhibitor, attenuates sepsis-induced myocardial dysfunction by inhibiting gasdermin D-mediated pyroptosis in macrophages.

Yiling Mei, Xudong Chen, Si Shi, Wante Lin, Zhenfeng Cheng, Xiaoxi Fan, Wenqi Wu, Jibo Han, Weijian Huang, Bozhi Ye, Shanshan Dai.

   BACKGROUND AND PURPOSE: Myocardial dysfunction is a significant complication associated with sepsis. However, there are currently no specific and effective treatments available. Inhibiting gasdermin D (GSDMD)-mediated pyroptosis has shown promise in mitigating sepsis-induced myocardial dysfunction. The GSDMD inhibitor Y2 (GI-Y2) has been demonstrated to directly bind to GSDMD. Nonetheless, it remains uncertain whether GI-Y2 offers a cardioprotective effect in the context of sepsis-induced myocardial dysfunction.
EXPERIMENTAL APPROACH: A mouse model of sepsis was created using lipopolysaccharide (LPS), caecal ligation and puncture. Following treatment with GI-Y2 or macrophage membrane-encapsulated GI-Y2 nanoparticles (GI-Y2@MM-NPs), myocardial dysfunction and pyroptosis levels in heart tissues were assessed. Transcriptome sequencing revealed the molecular mechanism of GI-Y2 in treating septic cardiomyopathy.
KEY RESULTS: We observed that GI-Y2 alleviated myocardial dysfunction and attenuated cardiac inflammation in mice induced by LPS, caecal ligation and puncture. GI-Y2 reduced macrophage pyroptosis and attenuated macrophage-mediated cardiomyocyte injury induced by LPS/nigericin. Concurrently, we confirmed the protective effect of GI-Y2 against LPS-induced cardiac dysfunction was abolished in the absence of GSDMD. Additionally, GI-Y2 attenuated the mitochondrial damage induced by LPS by inhibiting GSDMD in the mitochondria. Furthermore, we developed GI-Y2@MM-NPs to enhance the targeting capability of GI-Y2 towards macrophages in heart tissues and demonstrated its protective effect in vivo.
CONCLUSION AND IMPLICATIONS: These findings indicate that GI-Y2 alleviates septic myocardial injury and dysfunction by specifically targeting GSDMD, thereby inhibiting GSDMD-mediated pyroptosis and mitochondrial damage. Both GI-Y2 and GI-Y2@MM-NPs may serve as promising therapeutic options for addressing septic myocardial dysfunction.

Keywords:  GI‐Y2; GSDMD; Pyroptosis; inhibitor; septic cardiomyopathy

DOI:  https://doi.org/10.1111/bph.70040
Sci Rep. 2025 Apr 03. 15(1): 11481

Distinct astrocyte activation patterns associated with neuroinflammation induced by gamma and proton beam irradiation.

Liben Yan, Tianyi Er, Shaoqian Sun, Yulin Deng, Zhirong Wan, Jing Zhao, Ailu Wang, Beiqin Liu, Qiaojuan Wang, Li Sui, Hong Ma.

  The aim of this study was to investigate the impact of radiation exposure on astrocyte response and assess their potential roles and mechanisms in surrounding neural cells. Healthy male rats were irradiated different radiation types to induce the neural inflammation. U87-MG cells were exposed respectively to gamma rays (2 Gy and 10 Gy) and proton irradiation (0.1 Gy and 0.5 Gy). Cell viability, mRNA expression, mitochondrial membrane potential, glucose uptake and cytokine levels were analyzed respectively to evaluate the neuroinflammation or neural damage. Gamma rays and proton beam irradiation induced distinct patterns of inflammatory factor expression in the hippocampal region of rats. Moreover, we observed changes in cell morphology and a dose-dependent inhibition of cell proliferation across all radiation types. Significant upregulation of caspase-8 and caspase-3 enzymatic activities in U87-MG cells was observed after exposure to gamma rays. Astrocytes showed increased expression of GFAP, C3, and PTX3 after exposure to gamma rays, and downregulation while exposure to proton. Additionally, proton beam irradiation potentially increased glutamine synthesis in astrocytes. Furthermore, we investigated the influence of irradiated astrocytes on neurons via mitochondrial integrity, neurotransmitter levels, and glucose metabolism. Additionally, the expression of miR92a-3p, which can significantly downregulate GFAP and IL-6 expression, was downregulated by gamma rays, while upregulated by proton irradiation. The findings highlight the differential impact of gamma rays and proton radiation on inflammatory responses in vivo, with gamma rays inducing a pro-inflammatory effect and proton radiation exerting anti-inflammatory properties. Overall, this study provides valuable insights for radiotherapy management.

Keywords:  Astrocytes; Neuroinflammation; Radiotherapy; microRNA

DOI:  https://doi.org/10.1038/s41598-025-94812-6
bioRxiv. 2025 Mar 28. pii: 2025.03.17.643721. [Epub ahead of print]

Representing Mitochondrial Dynamics with Abstract Algebra.

Raphael Mostov, Greyson R Lewis, Gabriel Sturm, Wallace F Marshall.

This paper addresses the increasing need for comprehensive mathematical descriptions of cell organization by examining the algebraic structure of mitochondrial network dynamics. Mitochondria are cellular structures involved in metabolism that take the form of a network of membrane-based tubes that undergo continuous re-arrangement by a set of morphological processes, including fission and fusion, carried out by protein-based machinery. Because of their network structure, mitochondria can be represented as graphs, and the morphological operations that take place in the cell, referred to as mitochondrial dynamics, can be represented by changes to the graphs. Prior studies have classified mitochondrial graphs based on graph-theoretic features, but an alternative approach is to focus not on the graphs themselves but on the set of morphological operations inducing mitochondrial dynamics, since this may provide a simpler representation. Moreover, the operations are what determine the graphs that will be generated in a biological system. Here we show that mitochondrial dynamics on a single connected mitochondrion constitute a groupoid that includes the automorphism group of each mitochondria graph. For multi-component mitochondria we define a graph structure that encapsulates the structure of mitochondrial dynamics. Using these formalisms we define a distance metric for similarity between mitochondrial structures based on an edit distance. In the course of defining these structures we provide a mathematical motivation for new experimental questions regarding mitochondrial fusion and the impacts of cell division on mitochondrial morphology. This work points to a general strategy for formulating a cell structure state-space, based not on the shapes of cellular structures, but on relations between the dynamic operations that produce them.

DOI: https://doi.org/10.1101/2025.03.17.643721
Cell Death Dis. 2025 Apr 02. 16(1): 239

HELLS controls mitochondrial dynamics and genome stability in liver cancer by collusion with MIEF1.

Sung Kyung Choi, Jihye Park, Sang Yun Ha, Myoung Jun Kim, Seor I Ahn, Jeongah Kim, Woong Sun, Yeong Min Park, Suk Woo Nam, Jeung-Whan Han, Keunsoo Kang, Jueng Soo You.

Dysregulated chromatin remodelers have emerged as critical disease targets. However, owing to the pleiotropic functions of chromatin remodelers, the underlying mechanisms of their effects on cancer have been difficult to elucidate. Here, we investigated the helicase lymphoid-specific (HELLS) oncogenic mechanism by identifying a new direct transcriptional target. Using loss or gain experiments, we identified Mitochondrial elongation factor 1 (MIEF1) as a critical target of the HELLS molecular network in liver cancer. Liver cancer patients with a poor prognosis exhibited upregulated expression of MIEF1, and MIEF1 knockdown led to the loss of tumor capabilities, indicating MIEF1 as an oncogene in liver cancer. Suppressing the HELLS-MIEF1 axis caused mitochondrial hyperfusion, energy deprivation, and further resulting senescence. HELLS knockdown globally increased histone 3 lysine 9 trimethylation (H3K9me3), especially in genomic hotspots with upregulation of SUV39H1 and further augmented DNA methylation. This stabilized genome and hyperfused mitochondria led to reduced levels of reactive oxygen species (ROS) and DNA damage. Finally, tumor cells became famished and calm. We further validated the functions of the HELLS-MIEF1 axis by MIEF1 overexpression and mitochondrial fusion drug. Our study has important implications for medical science by highlighting the crosstalk between epigenetics and metabolism through nuclear chromatin remodeler HELLS and mitochondrial protein MIEF1.

DOI: https://doi.org/10.1038/s41419-025-07589-x
Cell Rep. 2025 Apr 03. pii: S2211-1247(25)00273-6. [Epub ahead of print]44(4): 115502

Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration.

Holly Merta, Kaitlynn Gov, Tadamoto Isogai, Blessy Paul, Achinta Sannigrahi, Arun Radhakrishnan, Gaudenz Danuser, W Mike Henne.

  The endoplasmic reticulum (ER) is structurally and functionally diverse, yet how its functions are organized within morphological subdomains is incompletely understood. Utilizing TurboID-based proximity labeling and CRISPR knockin technologies, we map the proteomic landscape of the human ER network. Sub-organelle proteomics reveals enrichments of proteins into ER tubules, sheets, and the nuclear envelope. We uncover an ER-enriched actin-binding protein, calmin/CLMN, and define it as an ER-actin tether that localizes to focal adhesions adjacent to ER tubules. Mechanistically, we find that CLMN depletion perturbs adhesion disassembly, actin dynamics, and cell movement. CLMN-depleted cells display decreased polarization of ER-plasma membrane contacts and calcium signaling factor STIM1 and altered calcium signaling near ER-actin interfaces, suggesting that CLMN influences calcium signaling to facilitate F-actin/adhesion dynamics. Collectively, we map the sub-organelle proteome landscape of the ER, identify CLMN as an ER-actin tether, and describe a non-canonical mechanism by which ER tubules engage actin to regulate cell migration.

Keywords:  CLMN; CP: Cell biology; ER; TurboID; adhesion; calmin; endoplasmic reticulum; migration

DOI:  https://doi.org/10.1016/j.celrep.2025.115502
Contact (Thousand Oaks). 2025 Jan-Dec;8:8 25152564251329704

Remodelling of Cellular Protein Homeostasis by Enhanced ER-Mitochondrial Tethering.

Elisa Tonelli, Justyna Malecka, Elettra Barberis, Camilla Romano, Emanuela Pessolano, Maria Talmon, Armando A Genazzani, Claudio Casali, Marco Biggiogera, Marcello Manfredi, Laura Tapella, Dmitry Lim, Giulia Dematteis.

  Alterations of endoplasmic reticulum (ER)-mitochondrial interaction have been associated with different pathological conditions, including neurodegenerative diseases, characterized by dysregulation of protein homeostasis. However, little is known about how enhanced ER-mitochondrial tethering affects cellular proteostatic machinery. Here, we transiently overexpressed synthetic ER-mitochondrial linkers (EMLs), stabilizing the ER-mitochondrial distance at ≤5 nm (denominated as 5 nm-EML) and ∼10 nm (10 nm-EML), in HeLa cells. No alterations were found in cell growth, although metabolic activity and total ATP were significantly reduced. In EML-expressing cells, global protein synthesis was significantly reduced, accompanied by a reduction of total PERK and eIF2α protein levels, but increased p-eIF2α. Unfolded protein response (UPR) markers ATF4 and ATF6 were upregulated, suggesting that enhanced ER-mitochondrial tethering deranges protein synthesis and induces a low-grade ER stress/UPR. To further investigate ER-mitochondrial tethering-induced protein dyshomeostasis, we performed shotgun mass spectrometry proteomics followed by bioinformatic analysis. Analysis of highly changed proteins and the most significantly overrepresented gene ontology (GO) terms revealed that ≤5 nm tethering preferentially affected the expression of proteins involved in RNA processing and splicing and proteasomal protein degradation, while ∼10 nm tethering preferentially affected protein translation. Both EMLs affected expression of proteins involved in mitochondrial bioenergetics and metabolism, defense against oxidative stress, ER protein homeostasis, signaling and secretion. Finally, lipidomic analysis suggests that 5 nm-EML and 10 nm-EML differentially affect lipid homeostasis. Altogether, our results suggest that enhanced ER-mitochondrial tethering leads to a profound remodeling of cellular protein homeostasis, which may play a key role in pathogenesis of Alzheimer's and other neurodegenerative diseases.

Keywords:  MAMs; MERCS; mitochondria-ER contact sites; proteostasis

DOI:  https://doi.org/10.1177/25152564251329704
Mitochondrion. 2025 Mar 28. pii: S1567-7249(25)00033-9. [Epub ahead of print]83 102036

Therapeutic potential of DDQ in enhancing mitochondrial health and cognitive function in Late-Onset Alzheimer's disease.

Sudhir Kshirsagar, Rainier Vladlen Alvir, Jangampalli Adi Pradeepkiran, Arubala P Reddy, P Hemachandra Reddy.

  Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline, mitochondrial dysfunction, and neuroinflammation. This study evaluates the therapeutic potential of DDQ, a small molecule in the humanized Abeta knockin (hAbKI) mice that represents late-onset AD. Our findings demonstrate that DDQ treatment significantly improves cognitive performance as assessed through behavioral tests, including the rotarod, open field, Y-maze, and Morris water maze, compared to untreated hAbKI mice. At the molecular level, DDQ promoted mitochondrial biogenesis, as evidenced by enhanced expression of key proteins like PGC1α, NRF1, and TFAM. Additionally, DDQ treatment facilitated mitophagy, as indicated by elevated levels of PINK1 and Parkin, and reduced neuroinflammation, reflected by decreased Iba1 and GFAP levels. Transmission electron microscopy analysis revealed a marked improvement in mitochondrial morphology, with increased mitochondrial length and reduced mitochondrial numbers in DDQ-treated mice. Furthermore, DDQ treatment led to an increase in mitophagic vacuoles, suggesting that it effectively removes dysfunctional mitochondria. Taken together, for the first time, our study results support the potential of DDQ as a promising neuroprotective agent for late-onset AD, addressing mitochondrial dysfunction, neuroinflammation, and cognitive decline. Our study focused on developing small molecules that modulate mitophagy, mitochondrial dynamics and neuroinflammatory pathways for aging, AD and other neurodegenerative disorders.

Keywords:  Alzheimer’s disease; Behavioral tests; Cognitive function; DDQ; Mitochondrial biogenesis; Mitochondrial dysfunction; Mitophagy; Neurodegenerative disorders; Neuroinflammation; Neuroprotection; Transmission electron microscopy; hAbKI mouse model

DOI:  https://doi.org/10.1016/j.mito.2025.102036
bioRxiv. 2025 Mar 13. pii: 2025.03.11.641929. [Epub ahead of print]

NF-κB signaling directs a program of transient amplifications at innate immune response genes.

Michael P Ludwig, Jason R Wilson, Matthew D Galbraith, Nirajan Bhandari, Lauren N Dunn, Joshua C Black, Kelly D Sullivan.

The cellular response to pathogens involves an intricate response directed by key innate immune signaling pathways which is characterized by cell-to-cell heterogeneity. How this heterogeneity is established and regulated remains unclear. We describe a program of transient site-specific gains (TSSG) producing extrachromosomal DNA (ecDNA) of immune-related genes in response to innate immune signaling. Activation of NF-κB drives TSSG of the interferon receptor gene cluster through inducible recruitment of the transcription factor RelA and the pre-replication complex member MCM2 to an epigenetically regulated TSSG control element. Targeted recruitment of RelA or p300 are sufficient to induce TSSG formation. RelA and MCM2 specify a program of TSSG for at least six and as many as 179 regions enriched in innate immune response genes. Identification of this program reveals regulated production of ecDNA as a mechanism of heterogeneity in the host response.

DOI: https://doi.org/10.1101/2025.03.11.641929
Nat Commun. 2025 Mar 28. 16(1): 3038

Targeting senescent hepatocytes for treatment of metabolic dysfunction-associated steatotic liver disease and multi-organ dysfunction.

Kuo Du, David S Umbaugh, Wang Liuyang, Ji Hye Jun, Rajesh K Dutta, Seh Hoon Oh, Niansheng Ren, Qiaojuan Zhang, Dennis C Ko, Ana Ferreira, Jon Hill, Guannan Gao, Steven S Pullen, Vaibhav Jain, Simon Gregory, Manal F Abdelmalek, Anna Mae Diehl.

Senescent hepatocytes accumulate in metabolic dysfunction-associated steatotic liver disease (MASLD) and are linked to worse clinical outcomes. However, their heterogeneity and lack of specific markers have made them difficult to target therapeutically. Here, we define a senescent hepatocyte gene signature (SHGS) using in vitro and in vivo models and show that it tracks with MASLD progression/regression across mouse models and large human cohorts. Single-nucleus RNA-sequencing and functional studies reveal that SHGS+ hepatocytes originate from p21+ cells, lose key liver functions and release factors that drive disease progression. One such factor, GDF15, increases in circulation alongside SHGS+ burden and disease progression. Through chemical screening, we identify senolytics that selectively eliminate SHGS+ hepatocytes and improve MASLD in male mice. Notably, SHGS enrichment also correlates with dysfunction in other organs. These findings establish SHGS+ hepatocytes as key drivers of MASLD and highlight a potential therapeutic strategy for targeting senescent cells in liver disease and beyond.

DOI: https://doi.org/10.1038/s41467-025-57616-w