bims-nenemi Biomed News
on Neuroinflammation, neurodegeneration and mitochondria
Issue of 2025–03–16
seventeen papers selected by
Marco Tigano, Thomas Jefferson University
  1. Quality control of mitochondrial nucleoids.
  2. Engineering mtDNA deletions by reconstituting end joining in human mitochondria.
  3. Mitochondrial damage in muscle specific PolG mutant mice activates the integrated stress response and disrupts the mitochondrial folate cycle.
  4. Analysis of cytosolic mtDNA release during Staphylococcus aureus infection.
  5. Structural basis for intrinsic strand displacement activity of mitochondrial DNA polymerase.
  6. Mitochondrial genetics, signalling and stress responses.
  7. Cellular dsRNA interactome captured by K1 antibody reveals the regulatory map of exogenous RNA sensing.
  8. Senescent-like microglia limit remyelination through the senescence associated secretory phenotype.
  9. MIA40 suppresses cell death induced by apoptosis-inducing factor 1.
  10. The E3 ubiquitin ligase RNF126 facilitates quality control of unimported mitochondrial membrane proteins.
  11. Electron Microscopy to Visualize and Quantify Mitochondrial Structure and Organellar Interactions in Cultured Cells During Senescence.
  12. Mitochondria are positioned at dendritic branch induction sites, a process requiring rhotekin2 and syndapin I.
  13. VDAC2 and Bak scarcity in liver mitochondria enables targeting hepatocarcinoma while sparing hepatocytes.
  14. Metabolic remodeling in hiPSC-derived myofibers carrying the m.3243A>G mutation.
  15. PKR modulates sterile systemic inflammation-triggered neuroinflammation and brain glucose metabolism disturbances.
  16. A dual-purification system to isolate mitochondrial subpopulations.
  17. Structure of human PINK1 at a mitochondrial TOM-VDAC array.
  1. Trends Cell Biol. 2025 Mar 07. pii: S0962-8924(25)00039-X. [Epub ahead of print]
    Quality control of mitochondrial nucleoids.
    Hao Liu, Haixia Zhuang, Du Feng.
      Mitochondrial nucleoids, organized complexes that house and protect mitochondrial DNA (mtDNA), are normally confined within the mitochondrial double-membrane system. Under cellular stress conditions, particularly oxidative and inflammatory stress, these nucleoids can undergo structural alterations that lead to their aberrant release into the cytoplasm. This mislocalization of nucleoid components, especially mtDNA, can trigger inflammatory responses and cell death pathways, highlighting the critical importance of nucleoid quality control mechanisms. The release of mitochondrial nucleoids occurs through specific membrane channels and transport pathways, fundamentally disrupting cellular homeostasis. Cells have evolved multiple clearance mechanisms to manage cytoplasmic nucleoids, including nuclease-mediated degradation, lysosomal elimination, and cellular excretion. This review examines the molecular mechanisms governing nucleoid quality control and explores the delicate balance between mitochondrial biology and cellular immunity. Our analysis provides insights that could inform therapeutic strategies for mtDNA-associated diseases and inflammatory disorders.
    Keywords:  mitochondria; mitophagy; mtDNA; nucleoid-phagy; nucleoids
    DOI:  https://doi.org/10.1016/j.tcb.2025.02.005
  2. Cell. 2025 Mar 05. pii: S0092-8674(25)00194-1. [Epub ahead of print]
    Engineering mtDNA deletions by reconstituting end joining in human mitochondria.
    Yi Fu, Max Land, Tamar Kavlashvili, Ruobing Cui, Minsoo Kim, Emily DeBitetto, Toby Lieber, Keun Woo Ryu, Elim Choi, Ignas Masilionis, Rahul Saha, Meril Takizawa, Daphne Baker, Marco Tigano, Caleb A Lareau, Ed Reznik, Roshan Sharma, Ronan Chaligne, Craig B Thompson, Dana Pe'er, Agnel Sfeir.
      Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of genomes carrying pathogenic mutations. However, reconstituting mtDNA deletions linked to mitochondrial myopathies remains challenging. Here, we engineered mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases. Using mitochondrial EJ (mito-EJ) and mito-ScaI, we generated a panel of clonal cell lines harboring a ∼3.5 kb mtDNA deletion across the full spectrum of heteroplasmy. Investigating these cells revealed a critical threshold of ∼75% deleted genomes, beyond which oxidative phosphorylation (OXPHOS) protein depletion, metabolic disruption, and impaired growth in galactose-containing media were observed. Single-cell multiomic profiling identified two distinct nuclear gene deregulation responses: one triggered at the deletion threshold and another progressively responding to heteroplasmy. Ultimately, we show that our method enables the modeling of disease-associated mtDNA deletions across cell types and could inform the development of targeted therapies.
    Keywords:  DOGMA-seq; end joining; mitochondrial pathologies; mtDNA; mtDNA deletion
    DOI:  https://doi.org/10.1016/j.cell.2025.02.009
  3. Nat Commun. 2025 Mar 08. 16(1): 2338
    Mitochondrial damage in muscle specific PolG mutant mice activates the integrated stress response and disrupts the mitochondrial folate cycle.
    Simon T Bond, Emily J King, Shannen M Walker, Christine Yang, Yingying Liu, Kevin H Liu, Aowen Zhuang, Aaron W Jurrjens, Haoyun A Fang, Luke E Formosa, Artika P Nath, Sergio Ruiz Carmona, Michael Inouye, Thy Duong, Kevin Huynh, Peter J Meikle, Simon Crawford, Georg Ramm, Sheik Nadeem Elahee Doomun, David P de Souza, Danielle L Rudler, Anna C Calkin, Aleksandra Filipovska, David W Greening, Darren C Henstridge, Brian G Drew.
      During mitochondrial damage, information is relayed between the mitochondria and nucleus to coordinate precise responses to preserve cellular health. One such pathway is the mitochondrial integrated stress response (mtISR), which is known to be activated by mitochondrial DNA (mtDNA) damage. However, the causal molecular signals responsible for activation of the mtISR remain mostly unknown. A gene often associated with mtDNA mutations/deletions is Polg1, which encodes the mitochondrial DNA Polymerase γ (PolG). Here, we describe an inducible, tissue specific model of PolG mutation, which in muscle specific animals leads to rapid development of mitochondrial dysfunction and muscular degeneration in male animals from ~5 months of age. Detailed molecular profiling demonstrated robust activation of the mtISR in muscles from these animals. This was accompanied by striking alterations to enzymes in the mitochondrial folate cycle that was likely driven by a specific depletion in the folate cycle metabolite 5,10 methenyl-THF, strongly implying imbalanced folate intermediates as a previously unrecognised pathology linking the mtISR and mitochondrial disease.
    DOI:  https://doi.org/10.1038/s41467-025-57299-3
  4. Methods Cell Biol. 2025 ;pii: S0091-679X(24)00208-5. [Epub ahead of print]194 93-107
    Analysis of cytosolic mtDNA release during Staphylococcus aureus infection.
    Caterina Licini, Gloria D'Achille, Nada Dhaouadi, Ilaria Nunzi, Fabio Marcheggiani, Matteo Fabbri, Monica Mattioli-Belmonte, Gianluca Morroni, Saverio Marchi.
      Methicillin-resistant Staphylococcus aureus (MRSA) is one of the principal human pathogens, causing severe infections in skin wounds. MRSA infection triggers a cell response mainly by mitochondrial-mediated pathway, resulting in mitochondrial outer membrane permeabilization, extrusion of the mitochondrial inner membrane into the cytoplasm, and then spillage of mitochondrial DNA (mtDNA) into the cytoplasm. The cell recognizes the discharged cytosolic mtDNA (cmtDNA) as "not-itself" because of mtDNA properties and triggers cascade events, such as the activation of inflammasomes. Here, we detail a method to detect and measure the mtDNA release into the cytoplasm in immortalized keratinocytes (HaCaT cells), after the infection with MRSA at different time points after the infection.
    Keywords:  Inflammation; MOMP; Mitochondria; Staphylococcus aureus; mtDNA
    DOI:  https://doi.org/10.1016/bs.mcb.2024.09.003
  5. Nat Commun. 2025 Mar 11. 16(1): 2417
    Structural basis for intrinsic strand displacement activity of mitochondrial DNA polymerase.
    Ashok R Nayak, Viktoriia Sokolova, Sirelin Sillamaa, Karl Herbine, Juhan Sedman, Dmitry Temiakov.
      Members of the Pol A family of DNA polymerases, found across all domains of life, utilize various strategies for DNA strand separation during replication. In higher eukaryotes, mitochondrial DNA polymerase γ relies on the replicative helicase TWINKLE, whereas the yeast ortholog, Mip1, can unwind DNA independently. Using Mip1 as a model, we present a series of high-resolution cryo-EM structures that capture the process of DNA strand displacement. Our data reveal previously unidentified structural elements that facilitate the unwinding of the downstream DNA duplex. Yeast cells harboring Mip1 variants defective in strand displacement exhibit impaired oxidative phosphorylation and loss of mtDNA, corroborating the structural observations. This study provides a molecular basis for the intrinsic strand displacement activity of Mip1 and illuminates the distinct unwinding mechanisms utilized by Pol A family DNA polymerases.
    DOI:  https://doi.org/10.1038/s41467-025-57594-z
  6. Nat Cell Biol. 2025 Mar;27(3): 393-407
    Mitochondrial genetics, signalling and stress responses.
    Yasmine J Liu, Jonathan Sulc, Johan Auwerx.
      Mitochondria are multifaceted organelles with crucial roles in energy generation, cellular signalling and a range of synthesis pathways. The study of mitochondrial biology is complicated by its own small genome, which is matrilineally inherited and not subject to recombination, and present in multiple, possibly different, copies. Recent methodological developments have enabled the analysis of mitochondrial DNA (mtDNA) in large-scale cohorts and highlight the far-reaching impact of mitochondrial genetic variation. Genome-editing techniques have been adapted to target mtDNA, further propelling the functional analysis of mitochondrial genes. Mitochondria are finely tuned signalling hubs, a concept that has been expanded by advances in methodologies for studying the function of mitochondrial proteins and protein complexes. Mitochondrial respiratory complexes are of dual genetic origin, requiring close coordination between mitochondrial and nuclear gene-expression systems (transcription and translation) for proper assembly and function, and recent findings highlight the importance of the mitochondria in this bidirectional signalling.
    DOI:  https://doi.org/10.1038/s41556-025-01625-w
  7. Commun Biol. 2025 Mar 07. 8(1): 389
    Cellular dsRNA interactome captured by K1 antibody reveals the regulatory map of exogenous RNA sensing.
    JinA Lim, Namseok Lee, Seonmin Ju, Jeesoo Kim, Subin Mun, Moonhyeon Jeon, Yong-Ki Lee, Seok-Hoon Lee, Jayoung Ku, Sujin Kim, Sangsu Bae, Jong-Seo Kim, Yoosik Kim.
      RNA-binding proteins (RBPs) provide a critical post-transcriptional regulatory layer in determining RNA fate. Currently, UV crosslinking followed by oligo-dT pull-down is the gold standard in identifying the RBP repertoire of poly-adenylated RNAs, but such method is ineffective in capturing RBPs that recognize double-stranded RNAs (dsRNAs). Here, we utilize anti-dsRNA K1 antibody immunoprecipitation followed by quantitative mass spectrometry to comprehensively identify RBPs bound to cellular dsRNAs without external stimulus. Notably, our dsRNA interactome contains proteins involved in sensing N6-methyladenosine RNAs and stress granule components. We further perform targeted CRISPR-Cas9 knockout functional screening and discover proteins that can regulate the interferon (IFN) response during exogenous RNA sensing. Interestingly, most dsRBPs promote IFN-β secretion in response to dsRNA stimulation and act as antiviral factors during HCoV-OC43 infection. Our dsRNA interactome capture provides an unbiased and comprehensive characterization of putative dsRBPs and will facilitate our understanding of dsRNA sensing in physiological and pathological contexts.
    DOI:  https://doi.org/10.1038/s42003-025-07807-4
  8. Nat Commun. 2025 Mar 07. 16(1): 2283
    Senescent-like microglia limit remyelination through the senescence associated secretory phenotype.
    Phillip S Gross, Violeta Durán-Laforet, Lana T Ho, George S Melchor, Sameera Zia, Zeeba Manavi, William E Barclay, Sung Hyun Lee, Nataliia Shults, Sean Selva, Enrique Alvarez, Jason R Plemel, Meng-Meng Fu, Dorothy P Schafer, Jeffrey K Huang.
      The capacity to regenerate myelin in the central nervous system diminishes with age. This decline is particularly evident in multiple sclerosis (MS), a chronic demyelinating disease. Whether cellular senescence, a hallmark of aging, contributes to remyelination impairment remains unknown. Here, we show that senescent cells accumulate within demyelinated lesions after injury, and treatments with senolytics enhances remyelination in young and middle-aged mice but not aged mice. In young mice, we observe the upregulation of senescence-associated transcripts, primarily in microglia and macrophages, after demyelination, followed by a reduction during remyelination. However, in aged mice, senescence-associated factors persist within lesions, correlating with inefficient remyelination. Proteomic analysis of the senescence-associated secretory phenotype (SASP) reveals elevated levels of CCL11/Eotaxin-1 in lesions of aged mice, which is found to inhibit oligodendrocyte maturation. These results suggest therapeutic targeting of SASP components, such as CCL11, may improve remyelination in aging and MS.
    DOI:  https://doi.org/10.1038/s41467-025-57632-w
  9. EMBO Rep. 2025 Mar 07.
    MIA40 suppresses cell death induced by apoptosis-inducing factor 1.
    Ben Hur Marins Mussulini, Klaudia K Maruszczak, Piotr Draczkowski, Mayra A Borrero-Landazabal, Selvaraj Ayyamperumal, Artur Wnorowski, Michal Wasilewski, Agnieszka Chacinska.
      Mitochondria harbor respiratory complexes that perform oxidative phosphorylation. Complex I is the first enzyme of the respiratory chain that oxidizes NADH. A dysfunction in complex I can result in higher cellular levels of NADH, which in turn strengthens the interaction between apoptosis-inducing factor 1 (AIFM1) and Mitochondrial intermembrane space import and assembly protein 40 (MIA40) in the mitochondrial intermembrane space. We investigated whether MIA40 modulates the activity of AIFM1 upon increased NADH/NAD+ balance. We found that in model cells characterized by an increase in NADH the AIFM1-MIA40 interaction is strengthened and these cells demonstrate resistance to AIFM1-induced cell death. Either silencing of MIA40, rescue of complex I, or depletion of NADH through the expression of yeast NADH-ubiquinone oxidoreductase-2 sensitized NDUFA13-KO cells to AIFM1-induced cell death. These findings indicate that the complex of MIA40 and AIFM1 suppresses AIFM1-induced cell death in a NADH-dependent manner. This study identifies an effector complex involved in regulating the programmed cell death that accommodates the metabolic changes in the cell and provides a molecular explanation for AIFM1-mediated chemoresistance of cancer cells.
    Keywords:  Cancer; Metabolism; Mitochondria; Programmed Cell Death; Protein Import
    DOI:  https://doi.org/10.1038/s44319-025-00406-8
  10. J Biol Chem. 2025 Mar 12. pii: S0021-9258(25)00252-2. [Epub ahead of print] 108403
    The E3 ubiquitin ligase RNF126 facilitates quality control of unimported mitochondrial membrane proteins.
    Di Liu, Xin-Yu Huo, Xiaoli Zhang, Zai-Rong Zhang.
      Pathological stress can lead to failure in the translocation of mitochondrial proteins, resulting in accumulation of unimported proteins within the cytosol and upregulation of proteasome for their quality control. Malfunction or delay in protein clearance causes dysregulation of mitochondrial protein homeostasis, cellular toxicity, and diseases. Ubiquilins (UBQLNs) are known to serve as chaperone which associates with unimported mitochondrial membrane protein precursors, and facilitates their proteasomal degradation. However, how UBQLN-engaged proteins are ubiquitinated and efficiently targeted to the proteasome are poorly understood. Here, using mitochondrial membrane protein ATP5G1 as a model substrate, we report that E3 ubiquitin ligase RNF126 interacts with substrate-engaged UBQLN1, thereby promoting ubiquitination and degradation of unimported proteins during mitochondrial stress. We find that UBQLN1's ubiquitin-associated domain (UBA) recruits RNF126 when its middle domain binds to unimported protein substrate. Recombinant RNF126 forms ternary complex with UBQLN1 and pATP5G1 in vitro and catalyzes ubiquitination of UBQLN1-bound ATP5G1. Without RNF126, proteasomal degradation of ATP5G1 was compromised. These results explain how RNF126 and ubiquilins interplay to ensure specific quality control of unimported mitochondrial membrane proteins under pathophysiological conditions.
    Keywords:  ATP synthase F(0) complex subunit C1; RNF126; Ubiquilin; cytosolic quality control; mitochondrial membrane protein degradation
    DOI:  https://doi.org/10.1016/j.jbc.2025.108403
  11. Methods Mol Biol. 2025 ;2906 229-242
    Electron Microscopy to Visualize and Quantify Mitochondrial Structure and Organellar Interactions in Cultured Cells During Senescence.
    Christina Glytsou.
      Mitochondria are multifunctional organelles that play a crucial role in numerous cellular processes, including oncogene-induced senescence. Recent studies have demonstrated that mitochondria undergo notable morphological and functional changes during senescence, with mitochondria dysregulation being a critical factor contributing to the induction of this state. To elucidate the intricate and dynamic structure of these organelles, high-resolution visualization techniques are imperative. Electron microscopy offers nanometer-scale resolution images, enabling the comprehensive study of organelles' architecture. This chapter provides a detailed guide for preparing fixed samples from cultured cells for electron microscopy imaging. It also describes various quantification methods to accurately assess organellar parameters, including morphometric measurements of mitochondrial shape, cristae structure, and mitochondria-endoplasmic reticulum contact sites. These analyses yield valuable insights into the status of subcellular organelles, advancing our understanding of their involvement in cellular senescence and disease.
    Keywords:  EM sample preparation; Electron microscopy; MERCs; Mitochondria visualization; Mitochondrial structure
    DOI:  https://doi.org/10.1007/978-1-0716-4426-3_13
  12. Nat Commun. 2025 Mar 10. 16(1): 2353
    Mitochondria are positioned at dendritic branch induction sites, a process requiring rhotekin2 and syndapin I.
    Jessica Tröger, Regina Dahlhaus, Anne Bayrhammer, Dennis Koch, Michael M Kessels, Britta Qualmann.
      Proper neuronal development, function and survival critically rely on mitochondrial functions. Yet, how developing neurons ensure spatiotemporal distribution of mitochondria during expansion of their dendritic arbor remained unclear. We demonstrate the existence of effective mitochondrial positioning and tethering mechanisms during dendritic arborization. We identify rhotekin2 as outer mitochondrial membrane-associated protein that tethers mitochondria to dendritic branch induction sites. Rhotekin2-deficient neurons failed to correctly position mitochondria at these sites and also lacked the reduction in mitochondrial dynamics observed at wild-type nascent dendritic branch sites. Rhotekin2 hereby serves as important anchor for the plasma membrane-binding and membrane curvature-inducing F-BAR protein syndapin I (PACSIN1). Consistently, syndapin I loss-of-function phenocopied the rhotekin2 loss-of-function phenotype in mitochondrial positioning at dendritic branch induction sites. The finding that rhotekin2 deficiency impaired dendritic branch induction and that a syndapin binding-deficient rhotekin2 mutant failed to rescue this phenotype highlighted the physiological importance of rhotekin2 functions for neuronal network formation.
    DOI:  https://doi.org/10.1038/s41467-025-57399-0
  13. Nat Commun. 2025 Mar 11. 16(1): 2416
    VDAC2 and Bak scarcity in liver mitochondria enables targeting hepatocarcinoma while sparing hepatocytes.
    Shamim Naghdi, Piyush Mishra, Soumya Sinha Roy, David Weaver, Ludivine Walter, Erika Davies, Anil Noronha Antony, Xuena Lin, Gisela Moehren, Mark A Feitelson, Christopher A Reed, Tullia Lindsten, Craig B Thompson, Hien T Dang, Jan B Hoek, Erik S Knudsen, György Hajnóczky.
      Differences between normal tissues and invading tumors that allow tumor targeting while saving normal tissue are much sought after. Here we show that scarcity of VDAC2, and the consequent lack of Bak recruitment to mitochondria, renders hepatocyte mitochondria resistant to permeabilization by truncated Bid (tBid), a Bcl-2 Homology 3 (BH3)-only, Bcl-2 family protein. Increased VDAC2 and Bak is found in most human liver cancers and mitochondria from tumors and hepatic cancer cell lines exhibit VDAC2- and Bak-dependent tBid sensitivity. Exploring potential therapeutic targeting, we find that combinations of activators of the tBid pathway with inhibitors of the Bcl-2 family proteins that suppress Bak activation enhance VDAC2-dependent death of hepatocarcinoma cells with little effect on normal hepatocytes. Furthermore, in vivo, combination of S63845, a selective Mcl-1 inhibitor, with tumor-nectrosis factor-related, apoptosis-induncing ligand (TRAIL) peptide reduces tumor growth, but only in tumors expressing VDAC2. Thus, we describe mitochondrial molecular fingerprint that discriminates liver from hepatocarcinoma and allows sparing normal tissue while targeting tumors.
    DOI:  https://doi.org/10.1038/s41467-025-56898-4
  14. Stem Cell Reports. 2025 Feb 28. pii: S2213-6711(25)00052-9. [Epub ahead of print] 102448
    Metabolic remodeling in hiPSC-derived myofibers carrying the m.3243A>G mutation.
    Gabriel E Valdebenito, Anitta R Chacko, Chih-Yao Chung, Preethi Sheshadri, Haoyu Chi, Benjamin O'Callaghan, Monika J Madej, Henry Houlden, Hannah Rouse, Valle Morales, Katiuscia Bianchi, Francesco Saverio Tedesco, Robert D S Pitceathly, Michael R Duchen.
      Mutations in mitochondrial DNA cause severe multisystem disease frequently associated with muscle weakness. The m.3243A>G mutation is the major cause of mitochondrial encephalomyopathy lactic acidosis and stroke-like episodes (MELAS). Experimental models that recapitulate the disease phenotype in vitro for disease modeling or drug screening are very limited. We have therefore generated hiPSC-derived muscle fibers with variable heteroplasmic mtDNA mutation load without significantly affecting muscle differentiation potential. The cells exhibit physiological characteristics of muscle fibers and show a well-organized myofibrillar structure. In cells carrying the m.3243A>G mutation, the mitochondrial membrane potential and oxygen consumption were reduced in relation to the mutant load. We have shown through proteomic, phosphoproteomic, and metabolomic analyses that the m.3243A>G mutation variably affects the cell phenotype in relation to the mutant load. This variation is reflected by an increase in the NADH/NAD+ ratio, which in turn influences key nutrient-sensing pathways in the myofibers. This model enables a detailed study of the impact of the mutation on cellular bioenergetics and on muscle physiology with the potential to provide a platform for drug screening.
    Keywords:  iPSC-derived myofibers; mitochondria; mtDNA; mtDNA mutations
    DOI:  https://doi.org/10.1016/j.stemcr.2025.102448
  15. Front Immunol. 2025 ;16 1469737
    PKR modulates sterile systemic inflammation-triggered neuroinflammation and brain glucose metabolism disturbances.
    Wai-Yin Cheng, Xin-Zin Lee, Michael Siu-Lun Lai, Yuen-Shan Ho, Raymond Chuen-Chung Chang.
      Sterile systemic inflammation may contribute to neuroinflammation and accelerate the progression of neurodegenerative diseases. The double-stranded RNA-dependent protein kinase (PKR) is a key signaling molecule that regulates immune responses by regulating macrophage activation, various inflammatory pathways, and inflammasome formation. This study aims to study the role of PKR in regulating sterile systemic inflammation-triggered neuroinflammation and cognitive dysfunctions. Here, the laparotomy mouse model was used to study neuroimmune responses triggered by sterile systemic inflammation. Our study revealed that genetic deletion of PKR in mice potently attenuated the laparotomy-induced peripheral and neural inflammation and cognitive deficits. Furthermore, intracerebroventricular injection of rAAV-DIO-PKR-K296R to inhibit PKR in cholinergic neurons of ChAT-IRES-Cre-eGFP mice rescued the laparotomy-induced changes in key metabolites of brain glucose metabolism, particularly the changes in phosphoenolpyruvate and succinate levels, and cognitive impairment in short-term and spatial working memory. Our results demonstrated the critical role of PKR in regulating neuroinflammation, brain glucose metabolism and cognitive dysfunctions in a peripheral inflammation model. PKR could be a novel pharmacological target for treating systemic inflammation-induced neuroinflammation and cognitive dysfunctions.
    Keywords:  laparotomy; microglia; neuroimmune responses; peripheral inflammation; postoperative cognitive dysfunction; protein kinase R; targeted metabolomics
    DOI:  https://doi.org/10.3389/fimmu.2025.1469737
  16. J Cell Sci. 2025 Mar 13. pii: jcs.263693. [Epub ahead of print]
    A dual-purification system to isolate mitochondrial subpopulations.
    Corey N Cunningham, Jonathan G Van Vranken, Jakeline Larios, Katarina Heyden, Steven P Gygi, Jared Rutter.
      Mitochondria perform diverse functions, such as producing ATP through oxidative phosphorylation, synthesizing macromolecule precursors, maintaining redox balance, and many others. Given this diversity of functions, we and others have hypothesized that cells maintain specialized subpopulations of mitochondria. To begin addressing this hypothesis, we developed a new dual-purification system to isolate subpopulations of mitochondria for chemical and biochemical analyses. We used APEX2 proximity labeling such that mitochondria were biotinylated based on proximity to another organelle. All mitochondria were isolated by an elutable MitoTag-based affinity precipitation system. Biotinylated mitochondria were then purified using immobilized avidin. We used this system to compare the proteomes of endosome- and lipid droplet-associated mitochondria in U-2 OS cells, which demonstrated that these subpopulations were indistinguishable from one another but were distinct from the global mitochondria proteome. Our results suggest that this purification system could aid in describing subpopulations that contribute to intracellular mitochondrial heterogeneity, and that this heterogeneity might be more substantial than previously imagined.
    Keywords:  Biochemistry; Mitochondria; Proximity Labeling; Purification
    DOI:  https://doi.org/10.1242/jcs.263693
  17. Science. 2025 Mar 13. eadu6445
    Structure of human PINK1 at a mitochondrial TOM-VDAC array.
    Sylvie Callegari, Nicholas S Kirk, Zhong Yan Gan, Toby Dite, Simon A Cobbold, Andrew Leis, Laura F Dagley, Alisa Glukhova, David Komander.
      Mutations in the ubiquitin kinase PINK1 cause early onset Parkinson's Disease, but how PINK1 is stabilized at depolarized mitochondrial translocase complexes has remained poorly understood. We determined a 3.1-Å resolution cryo-electron microscopy structure of dimeric human PINK1 stabilized at an endogenous array of mitochondrial TOM and VDAC complexes. Symmetric arrangement of two TOM core complexes around a central VDAC2 dimer is facilitated by TOM5 and TOM20, both of which also bind PINK1 kinase C-lobes. PINK1 enters mitochondria through the proximal TOM40 barrel of the TOM core complex, guided by TOM7 and TOM22. Our structure explains how human PINK1 is stabilized at the TOM complex and regulated by oxidation, uncovers a previously unknown TOM-VDAC assembly, and reveals how a physiological substrate traverses TOM40 during translocation.
    DOI:  https://doi.org/10.1126/science.adu6445
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