bims-nenemi 2025-06-29 papers

bims-nenemi

Biomed News

on Neuroinflammation, neurodegeneration and mitochondria

Issue of 2025–06–29
twenty papers selected by
Marco Tigano, Thomas Jefferson University

Mitochondrial DNA: leakage, recognition, and associated human diseases.
The mitochondrial methylation potential gates mitoribosome assembly.
Microglia promote inflammatory cell death upon neuronal mitochondrial impairment during neurodegeneration.
Mislocalization of nucleic acids is a convergent and targetable mechanism in Alzheimer's disease and frontotemporal dementia.
Replication competition drives the selective mtDNA inheritance in Drosophila ovary.
Structural basis of BAX pore formation.
Discussing the future of mitochondrial biochemistry.
Acute high-altitude hypoxia induced NLRP3 inflammasome activation in pulmonary artery smooth muscle cells by BMAL1 targeting mitochondrial VDAC1-mediated MtDNA leakage.
AIM2 activation mediated by RIPK1/3-dependent mitochondrial DNA release drives Aβ1-40-Induced retinal pigment epithelium injury.
Flow Cytometric Quantification of Mitochondrial Properties: A High-Throughput Approach for Single Organelle Analysis.
Age-dependent accumulation of mitochondrial tRNA mutations in mouse kidneys linked to mitochondrial kidney diseases.
Interaction with AK2A links AIFM1 to cellular energy metabolism.
Inhibition of the ATP synthase c subunit ameliorates HDM/LPS-induced inflammatory responses in asthmatic bronchial epithelial cells by blocking the mPTP-mtDNA-cGAS-STING axis.
A substrate-interacting region of Parkin directs ubiquitination of the mitochondrial GTPase Miro1.
Exosome-Mediated Mitochondrial Delivery of Antisense Oligonucleotides.
Changes in mitochondrial thymidine metabolism and mtDNA copy number during induced pluripotency.
Microprotein SMIM26 drives oxidative metabolism via serine-responsive mitochondrial translation.
Specificity and mechanism of the double-stranded RNA-specific J2 monoclonal antibody.
PHB1 and PHB2 positively regulate IFN-β production by targeting MAVS in ducks.
Immunometabolism in heart failure.

J Biochem. 2025 Jun 20. pii: mvaf037. [Epub ahead of print]

Mitochondrial DNA: leakage, recognition, and associated human diseases.

Hyota Takamatsu.

  Mitochondria are intracellular organelles originating from intracellular symbiotic bacteria that play essential roles in life activities such as energy production, metabolism, Ca2+ storage, signal transduction, and cell death. Mitochondria also function as hubs for host defense against harmful stimuli such as infection and inflammation control. However, when cells are exposed to stress, mitochondrial homeostasis is disrupted, and mitochondrial DNA (mtDNA) can leak into the cytoplasm or extracellular space. Leaked mtDNA activates innate immune sensors, causing severe inflammation and contributing to the pathogenesis of human diseases. In this review, we summarize the mechanisms by which mtDNA leaks from the mitochondria and subsequently induces inflammation. We also review the relationship between mtDNA leakage and human diseases.

Keywords:  human diseases; innate immune response; mitochondria quality control; mitochondrial DNA; mtDNA leakage

DOI:  https://doi.org/10.1093/jb/mvaf037
Nat Commun. 2025 Jun 25. 16(1): 5388

The mitochondrial methylation potential gates mitoribosome assembly.

Ruth I C Glasgow, Vivek Singh, Lucía Peña-Pérez, Alissa Wilhalm, Marco F Moedas, David Moore, Florian A Rosenberger, Xinping Li, Ilian Atanassov, Mira Saba, Miriam Cipullo, Joanna Rorbach, Anna Wedell, Christoph Freyer, Alexey Amunts, Anna Wredenberg.

S-adenosylmethionine (SAM) is the principal methyl donor in cells and is essential for mitochondrial gene expression, influencing RNA modifications, translation, and ribosome biogenesis. Using direct long-read RNA sequencing in mouse tissues and embryonic fibroblasts, we show that processing of the mitochondrial ribosomal gene cluster fails in the absence of mitochondrial SAM, leading to an accumulation of unprocessed precursors. Proteomic analysis of ribosome fractions revealed these precursors associated with processing and assembly factors, indicating stalled biogenesis. Structural analysis by cryo-electron microscopy demonstrated that SAM-dependent methylation is required for peptidyl transferase centre formation during mitoribosome assembly. Our findings identify a critical role for SAM in coordinating mitoribosomal RNA processing and large subunit maturation, linking cellular methylation potential to mitochondrial translation capacity.

DOI: https://doi.org/10.1038/s41467-025-60977-x
Nat Struct Mol Biol. 2025 Jun 25.

Microglia promote inflammatory cell death upon neuronal mitochondrial impairment during neurodegeneration.

Guangyan Miao, Tina M Fortier, Haibo Liu, Dorothy P Schafer, Katherine A Fitzgerald, Junhao Mao, Eric H Baehrecke.

The failure to clear dysfunctional mitochondria, cell death and inflammation have been linked in neurodegenerative disease, but their relationship and role in these conditions is not fully understood. Loss of Vps13d prevents clearance of mitochondria, and mutations in human VPS13D have been associated with neurological movement disorders. To investigate the relationship between mitochondrial health, inflammation and neurodegeneration, we created a conditional Vps13d-knockout mouse. Loss of Vps13d in excitatory neurons resulted in behavioral changes and neurodegeneration. Vacuolar protein sorting 13D (VPS13D) deficiency also caused mitochondrial ultrastructural defects and dysfunction in neurons followed by gasdermin E processing, cyclic GMP-AMP synthase (cGAS)-stimulator of interferon response cGAMP interactor (STING) signaling, microglial activation and cell death. Gasdermin E localization with mitochondria in Vps13d-mutant neurons was required for elevated extracellular mitochondrial DNA that promoted activation of microglia. Depletion of microglia suppressed cell death and behavioral phenotypes but not mitochondrial changes in the neuron-specific Vps13d-knockout model, indicating that microglia promote cell death in this model of neurodegenerative disease.

DOI: https://doi.org/10.1038/s41594-025-01602-9
Cell Rep. 2025 Jun 24. pii: S2211-1247(25)00638-2. [Epub ahead of print]44(7): 115867

Mislocalization of nucleic acids is a convergent and targetable mechanism in Alzheimer's disease and frontotemporal dementia.

Christy Hung, Miriam Llorian, Koustav Pal, Frederick J Livesey, Jyoti Choudhary, Theodoros I Roumeliotis, Rickie Patani.

  Nucleocytoplasmic transport defects are observed in Alzheimer's disease (AD) and frontotemporal dementia (FTD). Here, we assess mRNA nucleocytoplasmic localization by performing transcriptome-wide profiling on nuclear and cytoplasmic fractions of human iPSC-derived cortical neurons from healthy individuals compared to those with familial AD or FTD. We find that AD- and FTD-causing mutations induce significant changes in mRNA nucleocytoplasmic distribution. We additionally observe the redistribution of mitochondria-related transcripts across AD and FTD neurons. The significantly increased mitochondrial RNA (mtRNA) in the cytosol of AD and FTD mutant neurons raised the possibility of leakage, which motivated us to investigate mtDNA leakage. We reveal abnormal cytoplasmic accumulation of mtDNA in AD and FTD cortical neurons together with evidence of mitochondrial aberrance. Importantly, mislocalisation of nucleic acids, mitochondrial dysfunction and cGAS-STING activation can be ameliorated through VCP D2 ATPase inhibition.

Keywords:  Alzheimer's disease; CP: Molecular biology; CP: Neuroscience; VCP inhibition; cGAS-STING; frontotemporal dementia; mRNA; mitochondrial DNA; mitochondrial RNA; mitochondrial dysfunction; neurodegeneration; nucleocytoplasmic redistribution

DOI:  https://doi.org/10.1016/j.celrep.2025.115867
bioRxiv. 2025 May 03. pii: 2025.04.29.650984. [Epub ahead of print]

Replication competition drives the selective mtDNA inheritance in Drosophila ovary.

Cheng Zhang, Zhe Chen, Hansong Ma, Hong Xu.

Purifying selection that limits the transmission of harmful mitochondrial DNA (mtDNA) mutations has been observed in both human and animal models. Yet the precise mechanism underlying this process remains undefined. Here, we present a highly specific and efficient in situ imaging method capable of visualizing mtDNA variants that differ by only a few nucleotides at single-molecule resolution in Drosophila ovaries. Using this method, we revealed that selection primarily occurs within a narrow developmental window during germline cysts differentiation. At this stage, the proportion of the deleterious mtDNA variant decreases without a reduction in its absolute copy number. Instead, the healthier mtDNA variant replicates more frequently, thereby outcompeting the co-existing deleterious variant. These findings provide direct evidence that mtDNA selection is driven by replication competition rather than active elimination processes, shedding light on a fundamental yet previously unresolved mechanism governing mitochondrial genome transmission.

DOI: https://doi.org/10.1101/2025.04.29.650984
Science. 2025 Jun 26. 388(6754): eadv4314

Structural basis of BAX pore formation.

Ying Zhang, Lu Tian, Gaoxingyu Huang, Xiaofei Ge, Fang Kong, Pengqi Wang, Yige Xu, Yigong Shi.

During apoptosis, cytosolic BAX monomers are translocated to the mitochondria to permeabilize the outer membrane. Here, we identified a dimer of BAX dimers as the basic repeating unit of its various oligomeric forms: arcs, lines, and rings. Cryo-electron microscopy structure of the BAX repeating unit at 3.2-angstrom resolution revealed the interactions within and between dimers. End-to-end stacking of the repeating units through the protruding α9 pairs yielded lines, arcs, polygons, and rings. We structurally characterized the tetragon, pentagon, hexagon, and heptagon, which comprise 16, 20, 24, and 28 BAX protomers, respectively. Missense mutations at the BAX inter-protomer interface damage pore formation and cripple its proapoptotic function. The assembly principle of the various BAX oligomers reported here provides the structural basis of membrane permeabilization by BAX.

DOI: https://doi.org/10.1126/science.adv4314
Trends Biochem Sci. 2025 Jun 20. pii: S0968-0004(25)00130-6. [Epub ahead of print]

Discussing the future of mitochondrial biochemistry.

Antoni Barrientos, Flavia Fontanesi, Pierre Rustin, Agnieszka Chacinska.

DOI: https://doi.org/10.1016/j.tibs.2025.05.010
Apoptosis. 2025 Jun 22.

Acute high-altitude hypoxia induced NLRP3 inflammasome activation in pulmonary artery smooth muscle cells by BMAL1 targeting mitochondrial VDAC1-mediated MtDNA leakage.

Si-Yuan He, Ying-Rui Bu, Jin Xu, Yu-Meng Wang, Tian-Xi Feng, Pei-Jie Li, Yi-Xiao Zhao, Yi-Ling Ge, Man-Jiang Xie.

  Hypoxia-induced inflammatory injury is an important pathological mechanism underlying the progression of acute mountain sickness (AMS). Recent studies reported that molecular clock could control mitochondrial pathways to involve hypoxic and inflammatory responses. Excessively released mitochondrial DNA (mtDNA) acts as a damage-associated molecular pattern (DAMP) to trigger inflammation in many diseases. Herein, we subjected mice at a simulated altitude of 5500 m for 3 days and found that the expression levels of inflammatory cytokines were significantly increased in mouse pulmonary arteries, accompanied by mtDNA release and NLRP3 inflammasome activation in the pulmonary artery smooth muscle cells (PASMCs). RNA-sequencing and loss- and gain-of function experiments indicated that the core clock component BMAL1 regulated mtDNA leakage in PASMCs, and smooth muscle-specific Bmal1 knockout significantly alleviated the pulmonary arterial inflammation under acute high-altitude hypoxia. Mechanically, BMAL1 as a transcription factor directly promoted the transcriptional expression of Voltage-dependent anion channel 1 (VDAC1) and exacerbated the VDAC1-mediated mtDNA leakage under hypoxia, which activated NLRP3 inflammasome signaling in PASMCs and induced vascular inflammation. Our work provides mechanistic insights into the hypoxia-induced inflammation in PASMCs and may provide a novel therapeutic approaching for targeting BMAL1-VDAC1 in AMS.

Keywords:   Bmal1 ; High-altitude hypoxia; Inflammatory response; MtDNA leakage

DOI:  https://doi.org/10.1007/s10495-025-02138-5
Cell Commun Signal. 2025 Jun 21. 23(1): 301

AIM2 activation mediated by RIPK1/3-dependent mitochondrial DNA release drives Aβ1-40-Induced retinal pigment epithelium injury.

Xiaoxu Huang, Tongqi Li, Guanran Zhang, Jieqiong Chen, Tong Li, Shiqi Yang, Qiyu Bo, Xiaohuan Zhao, Xiaoling Wan, Xinyue Zhu, Bo Yu, Xiaodong Sun, Junran Sun.

   BACKGROUND: The retinal pigment epithelium (RPE) degeneration and subsequent retinal atrophy are hallmarks of age-related macular degeneration (AMD). Amyloid-beta (Aβ), the primary component of amyloid plaques in Alzheimer's disease (AD), is also present within drusen and is considered a critical factor contributing to RPE degeneration in AMD. Recent findings indicate that Aβ-induced inflammation plays a role in RPE degeneration. The aim of this study was to explore the molecular players and the precise mechanisms involved in this process, particularly the potential role of the absent in melanoma 2 (AIM2)-like receptors (ALRs) inflammasome.
METHODS: An animal model of Aβ1-40-induced RPE injury was established. Fundus photography, electrophysiology and hematoxylin-eosin staining were used to evaluate the morphological and functional RPE damage. Transcriptome sequencing was used to detect the differentially expressed genes between Aβ1-40 group and control group. The transcriptional and protein expression levels of AIM2 pathway and RIPK family members were detected. Adeno-associated virus vector 2/2 (AAV2/2)-shAIM2 was constructed to knockdown AIM2 expression in mice RPE cells. Aβ1-40-treated ARPE-19 cells and hRPE cells were employed to analyze the regulatory effects of RIPK family on mitochondrial DNA (mtDNA) release and AIM2 pathway activation.
RESULTS: Aβ induces RPE damage through stimulation of AIM2 inflammasome and augmentation of caspase-1 and interleukin-1β (IL-1β). Knocking down AIM2 inhibits the release of inflammatory cytokines and alleviates the degeneration of the retina and RPE. Simultaneously, Aβ triggers the activation of RIPK1/RIPK3 kinases, as manifested by heightened protein expression and phosphorylation. Inhibiting RIPK1/RIPK3 phosphorylation dampens AIM2 inflammasome activity and curtails IL-1β secretion. Mechanistically, RIPK1/RIPK3 inhibition attenuates Aβ-induced Drp1(S616) hyperphosphorylation, consequently reducing mitochondrial fission and the efflux of mitochondrial DNA (mtDNA) into the cytosol. The diminished mtDNA release is responsible for attenuated AIM2 activation and subsequent inactivation of the stimulator of interferon genes (STING)/nuclear factor-kappa-B (NF-κB) signaling cascade.
CONCLUSIONS: Our study is the first to validate AIM2's contribution in Aβ-induced RPE pathology and underscore the significance of the RIPK1/RIPK3-induced mtDNA release in modulating inflammatory responses, shedding light on the underlying mechanisms and potential therapeutics of AMD.

Keywords:  AIM2; Age-related macular degeneration; Amyloid β; RIPK1; RIPK3; Retinal pigment epithelial cells

DOI:  https://doi.org/10.1186/s12964-025-02294-w
Int J Mol Sci. 2025 Jun 07. pii: 5481. [Epub ahead of print]26(12):

Flow Cytometric Quantification of Mitochondrial Properties: A High-Throughput Approach for Single Organelle Analysis.

Andrew J Piasecki, Hannah C Sheehan, Jonathan L Tilly, Dori C Woods.

  Recent advances in flow cytometry facilitate the detection of subcellular components, such as organelles and vesicles. Fluorescence-activated mitochondria sorting (FAMS) is a flow cytometry-based technique that allows for quantitative analysis and sorting of mitochondria as individual organelles from various tissues and in vitro cell culture. This manuscript details three novel applications of this technique to study mitochondrial function on an organelle-specific level, which is not possible with other approaches. Specifically, we detail the further development and versatility of this nanoscaled flow cytometry approach, including assays to quantitatively assess mitochondrial subpopulations, mitochondrial protein translocation, and both free-floating and EV-encapsulated secreted mitochondria. We demonstrate a multi-parameter quantitative assay for the analysis of mitochondrial autophagy using antibodies targeting the proteins PINK1 and Parkin corresponding to ΔΨM and further show how these can be assessed for mtDNA content on a single organelle level. Further, we establish parameters for the size and surface marker-based analysis of EVs, many of which contain identifiable and respiring mitochondria, as well as free-floating respiratory-competent mitochondria. These results display the versatility of nanoscaled flow cytometry in terms of both sample input and target organelle and provide an important methodological means for the quantitative assessment of mitochondrial features.

Keywords:  extracellular vesicle sorting; flow cytometry; fluorescence-activated mitochondria sorting; mitochondria; organelle sorting

DOI:  https://doi.org/10.3390/ijms26125481
Nat Aging. 2025 Jun 27.

Age-dependent accumulation of mitochondrial tRNA mutations in mouse kidneys linked to mitochondrial kidney diseases.

Leping Zhang, Zhe Xu, Jia Jing, Guoshi Chai, Guanglei Xie, Yanfei Ru, Qunyu Lv, Xiang Zuo, Qian Zhang, Jiatong Chen, He Jin, Ning Liu, Minghua Kong, Bin Shen, Mingxi Liu, Lei Jiang, Xi Wang, Yanxiao Zhang, Min Jiang.

Heteroplasmic pathogenic mitochondrial DNA (mtDNA) mutations are key drivers of mitochondrial diseases, yet their tissue-specific and cell-specific accumulation patterns during aging and the mechanistic links to pathology remain poorly understood. In this study, we employed DddA-derived cytosine base editor technology to generate three mouse models harboring distinct pathogenic mitochondrial tRNA mutations. These mutations exhibited age-dependent accumulation in the kidneys, leading to severe kidney defects that well recapitulate human mitochondrial kidney disease. Mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (mtscATAC-seq) revealed unique heteroplasmy dynamics across different kidney cell types: podocytes exhibited a positive selection for mutant mtDNA, whereas tubular epithelial cells displayed neutral drift of mutations during aging. Integrative analyses combining mtscATAC-seq, single-cell RNA sequencing and spatially enhanced resolution omics sequencing further identified molecular changes in high-mutant defective cells, including increased AP-1 family transcription factor activity, tubular epithelial cell proliferation and immune activation, which contribute to disease progression. Our study underscores the importance of kidney function monitoring in patients with mitochondrial disease, particularly in older adults, and establishes robust preclinical models to facilitate the development of therapeutic strategies.

DOI: https://doi.org/10.1038/s43587-025-00909-y
Mol Cell. 2025 Jun 24. pii: S1097-2765(25)00500-3. [Epub ahead of print]

Interaction with AK2A links AIFM1 to cellular energy metabolism.

Robin Alexander Rothemann, Egor Pavlenko, Mrityunjoy Mondal, Sarah Gerlich, Pavel Grobushkin, Sebastian Mostert, Julia Racho, Konstantin Weiss, Dylan Stobbe, Katharina Stillger, Kim Lapacz, Silja Lucia Salscheider, Carmelina Petrungaro, Dan Ehninger, Thi Hoang Duong Nguyen, Jörn Dengjel, Ines Neundorf, Daniele Bano, Simon Poepsel, Jan Riemer.

  Apoptosis-inducing factor 1 (AIFM1) is a flavoprotein essential for mitochondrial function and biogenesis. Its interaction with MIA40/CHCHD4, the central component of the mitochondrial disulfide relay, accounts for some, but not all, aspects of AIFM1 function. We provide a high-confidence AIFM1 interactome that elucidates functional partners within the mitochondrial intermembrane space. We found that AIFM1 binding to adenylate kinase 2 (AK2), an essential enzyme that maintains cellular adenine nucleotide pools, depends on the AK2 C-terminal domain. High-resolution cryoelectron microscopy (cryo-EM) and biochemical analyses showed that both MIA40 and AK2A bind the AIFM1 C-terminal β-sheet domain. Their binding enhances NADH oxidoreductase activity by locking an active dimer conformation and, in the case of MIA40, affecting the cofactor-binding site. The AIFM1-AK2A interaction is important during mitochondrial respiration because AIFM1 serves as a recruiting hub within the IMS, regulating mitochondrial bioenergetic output by creating hotspots of metabolic enzymes.

Keywords:  AIFM1; AK2; ATP; ATP transport; MIA40/CHCHD4; MICOS; metabolism; mitochondria

DOI:  https://doi.org/10.1016/j.molcel.2025.05.036
Respir Res. 2025 Jun 21. 26(1): 219

Inhibition of the ATP synthase c subunit ameliorates HDM/LPS-induced inflammatory responses in asthmatic bronchial epithelial cells by blocking the mPTP-mtDNA-cGAS-STING axis.

Decai Wang, Chao Liu, Chen Bao, Jiannan Hu, Ziling Li, Xinyue Ma, Yunfei Zhu, Shuyun Xu.

  The ATP synthase c subunit (c subunit) constitutes the mitochondrial permeability transition pore (mPTP). The extended opening of the mPTP is crucial in the development of various human illnesses. Nevertheless, it remains unclear whether the c subunit regulates the prolonged opening of the mPTP to attenuate inflammatory responses in asthma. This study sought to clarify the impact of the c subunit on inflammatory responses and to examine the therapeutic effects of 1,3,8-triazaspiro [4.5] decane derivatives (PP10), a c subunit inhibitor, in human bronchial epithelial (HBE) cells induced by house dust mite (HDM) and lipopolysaccharide (LPS), as well as in a mouse model. The findings indicated that the expression of the c subunit is elevated in asthmatic patients, HDM/LPS-induced HBE cells, and asthmatic mice. The inhibition of the c subunit by PP10 alleviated the prolonged opening of mPTP, then blocked the release of mitochondrial DNA (mtDNA) and cyclic GMP-AMP synthase (cGAS)-interferon response cGAMP interactor (STING) pathway activation in HDM/LPS-induced HBE cells. Furthermore, PP10 decreased the secretion of inflammatory cytokines and ameliorated airway inflammation in HDM/LPS-induced HBE cells and asthmatic animals, respectively. The data collectively suggest that the c subunit triggers an inflammatory response by promoting the sustained opening of mPTP, leading to the activation of the mtDNA-GAS-STING pathway in HDM/LPS-induced HBE cells. Inhibition of the c-subunit attenuates inflammatory responses in HDM/LPS-induced cells or mouse models. Clinical trial number Not applicable.

Keywords:  ATP synthase c subunit; Airway epithelial cells; Asthma; Inflammatory responses; Mitochondria; Mitochondrial permeability transition pore

DOI:  https://doi.org/10.1186/s12931-025-03299-2
J Cell Biol. 2025 Aug 04. pii: e202408025. [Epub ahead of print]224(8):

A substrate-interacting region of Parkin directs ubiquitination of the mitochondrial GTPase Miro1.

Joanna Koszela, Anne Rintala-Dempsey, Giulia Salzano, Viveka Pimenta, Outi Kamarainen, Mads Gabrielsen, Aasna L Parui, Gary S Shaw, Helen Walden.

Mutations in the E3 ubiquitin ligase Parkin gene have been linked to early onset Parkinson's disease. Besides many other roles, Parkin is involved in clearance of damaged mitochondria via mitophagy-a process of particular importance in dopaminergic neurons. Upon mitochondrial damage, Parkin accumulates at the outer mitochondrial membrane and is activated, leading to ubiquitination of many mitochondrial substrates and recruitment of mitophagy effectors. While the activation mechanisms of autoinhibited Parkin have been extensively studied, it remains unknown how Parkin recognizes its substrates for ubiquitination. Here, we characterize a conserved region in the flexible linker between the Ubl and RING0 domains of Parkin, which is indispensable for Parkin interaction with the mitochondrial GTPase Miro1. Our results may explain fast kinetics of Miro1 ubiquitination by Parkin in recombinant assays and provide a biochemical explanation for Miro1-dependent Parkin recruitment to the mitochondrial membrane observed in cells. Our findings are important for understanding mitochondrial homeostasis and may inspire new therapeutic avenues for Parkinson's disease.

DOI: https://doi.org/10.1083/jcb.202408025
Nucleic Acid Ther. 2025 Jun 18.

Exosome-Mediated Mitochondrial Delivery of Antisense Oligonucleotides.

Dora von Trentini, Ivan J Dmochowski.

  We present a general method for in-cellulo delivery of 2'-O-methyl (2'-OMe) RNA oligonucleotides (oligos) to mitochondria for antisense applications, with potential for implementation in other mitochondrial DNA (mtDNA)-targeted therapies. Exosomes, which are nanoscale, naturally occurring extracellular vesicles (EVs), have been employed for biotechnology applications in oligonucleotide delivery in recent years. We discovered that exosomes from fetal bovine serum (FBS) can be used as a simple and biologically compatible delivery agent of 2'-OMe RNA antisense oligonucleotides to cellular mitochondria, leading to target protein knockdown. While most RNA interference and antisense mechanisms occur in the cytoplasm or nucleus, the need for mitochondrial targeting has become increasingly apparent. Mitochondrial disease describes a variety of currently incurable syndromes that especially affect organs requiring significant energy including the muscles, heart, and brain. Many of these syndromes result from mutations in mtDNA, which codes for the 13 proteins of the oxidative phosphorylation system and are thus often implicated in inherited metabolic disorders.

Keywords:  2′-OMe RNA; antisense oligonucleotides; exosome-based delivery; extracellular vesicles; fetal bovine serum; mitochondrial localization

DOI:  https://doi.org/10.1089/nat.2024.0067
Exp Mol Med. 2025 Jun 26.

Changes in mitochondrial thymidine metabolism and mtDNA copy number during induced pluripotency.

Hyun Kyu Kim, Yena Song, Minji Kye, Byeongho Yu, Hyung Kyu Choi, Sung-Hwan Moon, Man Ryul Lee.

Somatic cell reprogramming into human induced pluripotent stem cells entails significant intracellular changes, including modifications in mitochondrial metabolism and a decrease in mitochondrial DNA copy number. However, the mechanisms underlying this decrease in mitochondrial DNA copy number during reprogramming remain unclear. Here we aimed to elucidate these underlying mechanisms. Through a meta-analysis of several RNA sequencing datasets, we identified genes responsible for the decrease in mitochondrial DNA. We investigated the functions of these identified genes and assessed their regulatory mechanisms. In particular, the expression of the thymidine kinase 2 gene (TK2), located in the mitochondria and required for mitochondrial DNA synthesis, is decreased in human pluripotent stem cells as compared with its expression in somatic cells. TK2 was significantly downregulated during reprogramming and markedly upregulated during differentiation. Collectively, this decrease in TK2 levels induces a decrease in mitochondrial DNA copy number and contributes to shaping the metabolic characteristics of human pluripotent stem cells. However, contrary to our expectations, treatment with a TK2 inhibitor impaired somatic cell reprogramming. These results suggest that decreased TK2 expression may result from metabolic conversion during somatic cell reprogramming.

DOI: https://doi.org/10.1038/s12276-025-01476-3
Mol Cell. 2025 Jun 20. pii: S1097-2765(25)00472-1. [Epub ahead of print]

Microprotein SMIM26 drives oxidative metabolism via serine-responsive mitochondrial translation.

Jiemin Nah, Sreya Mahendran, Baptiste Kerouanton, Liang Cui, Daniella H Hock, Alfredo Cabrera-Orefice, Kyle Dunlap, David Robinson, Desmond W H Tung, Sze Huey Leong, Kiat-Yi Tan, Sonia P Chothani, Jingjing Sun, Agnieszka Dziegowska, Grazyna Leszczynska, Owen J L Rackham, Ilka Wittig, Peter Dedon, Gregory S Ducker, David A Stroud, Lena Ho.

  Mitochondrial small open reading frame (ORF)-encoded microproteins (SEPs) are key regulators and components of the electron transport chain (ETC). Although ETC complex I assembly is tightly coupled to nutrient availability, including serine, the coordinating mechanism remains unknown. A genome-wide CRISPR screen targeting SEPs revealed that deletion of the LINC00493-encoded microprotein SMIM26 sensitizes cells to one-carbon restriction. SMIM26 interacts with mitochondrial serine transporters SFXN1/2 and the mitoribosome, forming a functional triad that facilitates translation of the complex I subunit mt-ND5. SMIM26 loss impairs serine import, reduces folate intermediates, and disrupts key mitochondrial tRNA modifications (τm5U and τm5s²U), resulting in ND5 translation failure and complex I deficiency. SMIM26 deletion is embryonic lethal in mice and impedes tumor growth in a xenograft model of folate-dependent acute myeloid leukemia. These findings define SMIM26 as a critical integrator of one-carbon flux and complex I biogenesis and establish a paradigm for localized mitochondrial translation through transporter-ribosome interactions.

Keywords:  complex I; electron transport chain; micropeptides; mitochondria; mitochondrial translation; one-carbon pathway; oxidative phosphorylation; small ORF-encoded peptides

DOI:  https://doi.org/10.1016/j.molcel.2025.05.033
bioRxiv. 2025 May 10. pii: 2025.05.09.649859. [Epub ahead of print]

Specificity and mechanism of the double-stranded RNA-specific J2 monoclonal antibody.

Charles Bou-Nader, Kevin M Juma, Ankur Bothra, Andrew J Brasington, Rodolfo Ghirlando, Motoshi Suzuki, David N Garboczi, Stephen H Leppla, Jinwei Zhang.

Double-stranded (ds) RNAs are major structural components of the transcriptome, hallmarks of viral infection, and primary triggers of innate immune responses. The J2 monoclonal antibody is the gold-standard method to discover and map endogenous dsRNAs across subcellular locations and cell surfaces, detect exogenous RNAs in viral infection, and surveil mRNA prophylactics and therapeutics for inflammatory dsRNAs. To define its epitope, specificity, and mechanism, we determine a 2.85 Å co-crystal structure of J2 antigen-binding fragment (Fab) bound to dsRNA. J2 uses its heavy and light chains in tandem to track the dsRNA minor groove, recognizing a staggered 8-bp duplex. J2 is exquisitely selective for dsRNAs, requires 14 bp for robust binding, and exhibits greatly diminished binding for GC-rich dsRNAs. J2 and R-loop-specific S9.6 antibody share a common recognition strategy distinct from intracellular dsRNA-binding proteins. This study provides mechanistic insights into dsRNA recognition and establishes a framework for reliable application and data interpretation of the J2 antibody in RNA discovery.

DOI: https://doi.org/10.1101/2025.05.09.649859
Poult Sci. 2025 Jun 12. pii: S0032-5791(25)00678-9. [Epub ahead of print]104(9): 105434

PHB1 and PHB2 positively regulate IFN-β production by targeting MAVS in ducks.

Jinlu Liu, Shuwen Luo, Guoyao Wang, Xuming Hu, Guohong Chen, Qi Xu.

  PHB1 and PHB2, two subunits of the mitochondrial prohibitin complex, are critical regulators of antiviral innate immunity. Ducks, as natural reservoirs for RNA viruses, exhibit unique antiviral mechanisms. RIG-I is a key receptor for recognizing RNA viruses in ducks. However, the roles of PHB1 and PHB2 in the RIG-I-MAVS-IFN-β signaling pathway remain unclear. Here, we characterized the duPHB1 and PHB2 structure and functional domains, which contains similar N-terminal transmembrane domain, PHB domain and coil-coiled C-terminal domain, revealing high conservation with avian and mammalian orthologs. Both genes were ubiquitously expressed in duck tissues, with elevated levels in immune-related organs (e.g., pancreas, thymus) and tissues with high metabolic activity and tissue regeneration ability (e.g., heart, liver and muscle) post-NDV infection. We next sought to investigate the functional roles by which duPHB1 and duPHB2 triggered antiviral innate immune response. Overexpression of duPHB1/2 in DEFs enhanced MAVS activation and IFN-β production upon 5'ppp dsRNA stimulation, while siRNA-mediated knockdown suppressed these effects. Co-transfection of duPHB1 and duPHB2 synergistically amplified MAVS-dependent IFN-β induction. Crucially, MAVS depletion abolished PHB1/2-mediated IFN-β upregulation, demonstrating their dependence on MAVS signaling. Our findings establish duPHB1/2 as key regulators of mitochondrial-mediated antiviral responses in ducks, providing insights into avian innate immunity.

Keywords:  Ducks; IFN-β; Innate immunity; PHB1; PHB2

DOI:  https://doi.org/10.1016/j.psj.2025.105434
Nat Rev Cardiol. 2025 Jun 22.

Immunometabolism in heart failure.

Ioanna Andreadou, Alessandra Ghigo, Panagiota-Efstathia Nikolaou, Filip K Swirski, James T Thackeray, Gerd Heusch, Gemma Vilahur.

The interaction between inflammation and metabolism (immunometabolism) is a crucial factor in the pathophysiology of heart failure, whether the cardiac failure originates from ischaemic injury or systemic metabolic disorders, and whether it is associated with reduced or preserved ejection fraction. Ischaemia, metabolic stress and comorbidity-driven systemic inflammation attract innate and adaptive immune cells to the myocardium and induce their polarization towards pro-inflammatory or anti-inflammatory phenotypes through cell-intrinsic metabolic shifts involving oxidative phosphorylation and anaerobic glycolysis. These infiltrating immune cells modulate cardiac and systemic metabolism. The bidirectional metabolic crosstalk between immune cells and parenchymal and stromal cardiac cells contributes to adverse cardiac remodelling. In turn, ischaemic injury and deregulated metabolism stimulate bone marrow and extramedullary myelopoiesis, which increases immune cell recruitment and perpetuates a non-resolving chronic inflammatory state. Pharmacological interventions targeting metabolism have shown promise for improving outcomes in patients with heart failure, but immunomodulatory approaches face multiple challenges. Understanding the complex metabolic pathways and cell-cell interactions that regulate immunometabolism in heart failure is essential to identify new therapies that shift the balance from maladaptive to cardioprotective immune responses. In this Review, we provide a comprehensive overview of the intricate cellular and molecular mechanisms that govern immunometabolism in heart failure and discuss potential approaches to non-invasively monitor and treat patients with heart failure.

DOI: https://doi.org/10.1038/s41569-025-01165-8