bims-celmim 2025-05-18 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–05–18
25 papers selected by
Marc Segarra Mondejar

Mitochondrial HSP90 paralog TRAP1 deletion drives glutamine addiction in tumor cells via destablization of the Cys/Glu antiporter SLC7A11/xCT.
Mitochondria-membranous organelle contacts at a glance.
Adipocyte metabolic state regulates glial phagocytic function.
Real-Time Measurement of Mitochondrial Function and Glycolysis in Lymphoblastoid Cell Lines.
Snapshots of mitochondrial fission imaged by cryo-scanning transmission electron tomography.
Metabolic pathway analysis of tumors using stable isotopes.
Quality control of un-imported mitochondrial proteins at a glance.
Mitochondrial metabolism is rapidly re-activated in mature neutrophils to support stimulation-induced response.
Split genetically encoded calcium indicators for interorganellar junctions.
Beta cells intrinsically sense and limit their secretory activity via mTORC1-RhoA signaling.
Regulation of synaptic mitochondria by extracellular vesicles and its implications for neuronal metabolism and synaptic plasticity.
Dual-Organelle-Targeted Fluorescent Probe for Lipid Droplets and Endoplasmic Reticulum Using Bay-Region Substituted Perylene Diimides.
ALDH4A1 functions as an active component of the MPC complex maintaining mitochondrial pyruvate import for TCA cycle entry and tumour suppression.
Single-cell mitochondrial morphomics reveals cellular heterogeneity and predicts complex I, III, and ATP synthase Inhibition responses.
Molecular machineries shaping the mitochondrial inner membrane.
Estrogen-related receptors regulate innate and adaptive muscle mitochondrial energetics through cooperative and distinct actions.
Tobacco Smoking Rewires Cell Metabolism by Inducing GAPDH Succinylation to Promote Lung Cancer Progression.
The role of glutamate dehydrogenase in the ageing brain.
The mitophagy receptors BNIP3 and NIX mediate tight attachment and expansion of the isolation membrane to mitochondria.
Mitochondria regulate MR1 protein expression and produce self-metabolites that activate MR1-restricted T cells.
To transfer mitochondria or not to transfer mitochondria: ADP does the trick.
Label-free multimodal optical biopsy reveals biomolecular and morphological features of diabetic kidney tissue in 2D and 3D.
Urine metabolite profiling in Indian males exposed to high-altitude: a longitudinal pilot study.
A fluorescent sensor for real-time monitoring of DPP8/9 reveals crucial roles in immunity and cancer.
Novel Mitochondria-Targeted NIR Cyanine Cy750M-C1 Nanoparticles for Chemotherapy against Triple-Negative Breast Cancer.

Mol Cancer Res. 2025 May 16.

Mitochondrial HSP90 paralog TRAP1 deletion drives glutamine addiction in tumor cells via destablization of the Cys/Glu antiporter SLC7A11/xCT.

Abhinav Joshi, Li Dai, Marisa Maisiak, Sunmin Lee, Elizabeth Lopez, Takeshi Ito, Len Neckers.

TRAP1, the mitochondrial isoform of HSP90, has emerged as a key regulator of cancer cell metabolism, yet the mechanisms by which it rewires nutrient utilization remain poorly understood. We previously reported that TRAP1 loss increases glutamine dependency of mitochondrial respiration following glucose withdrawal. Here, we investigate how TRAP1 deletion impacts glucose metabolism and the mechanisms enabling glutamine retention to support mitochondrial respiration via reductive carboxylation and the oxidative TCA cycle. TRAP1 knockout (KO) in bladder and prostate cancer cells recapitulates the carbon source-specific metabolic rewiring previously observed. Stable isotope tracing reveals that although glucose oxidation remains functional, TRAP1 KO reduces overall glucose uptake and its contribution to glycolysis and the pentose phosphate pathway. This effect is consistent across multiple cell lines. Concurrently, TRAP1-deficient cells exhibit increased glutamine retention and reliance, potentially due to downregulation of the cystine/glutamate antiporter SLC7A11/xCT. Supporting this, xCT overexpression reduces glutamine-dependent respiration in TRAP1 KO cells. qPCR and proteasome inhibition assays suggest xCT is regulated post-translationally via protein stability. Notably, xCT suppression does not trigger ferroptosis, indicating a selective adaptation rather than induction of cell death. Together, our findings suggest that TRAP1 loss decreases glucose uptake while preserving its metabolic fate, promoting glutamine conservation through xCT downregulation to maintain mitochondrial respiration without inducing ferroptosis. Implications: These results reveal a TRAP1-dependent mechanism of metabolic rewiring in cancer cells and identify xCT-mediated glutamine conservation as a key adaptive response, underscoring TRAP1 as a potential metabolic vulnerability and therapeutic target in tumors with altered nutrient utilization.

DOI: https://doi.org/10.1158/1541-7786.MCR-24-0194
J Cell Sci. 2025 May 01. pii: jcs263895. [Epub ahead of print]138(9):

Mitochondria-membranous organelle contacts at a glance.

Antigoni Diokmetzidou, Luca Scorrano.

  Mitochondrial contact sites are specialized interfaces where mitochondria physically interact with other organelles. Stabilized by molecular tethers and defined by unique proteomic and lipidomic profiles, these sites enable direct interorganellar communication and functional coordination, playing crucial roles in cellular physiology and homeostasis. Recent advances have expanded our knowledge of contact site-resident proteins, illuminated the dynamic and adaptive nature of these interfaces, and clarified their contribution to pathophysiology. In this Cell Science at a Glance article and the accompanying poster, we summarize the mitochondrial contacts that have been characterized in mammals, the molecular mechanisms underlying their formation, and their principal functions.

Keywords:  Contact sites; Mitochondria; Organelles

DOI:  https://doi.org/10.1242/jcs.263895
Cell Rep. 2025 May 14. pii: S2211-1247(25)00475-9. [Epub ahead of print]44(5): 115704

Adipocyte metabolic state regulates glial phagocytic function.

Mroj Alassaf, Aditi Madan, Sunidhi Ranganathan, Shannon Marschall, Jordan J Wong, Zachary H Goldberg, Ava E Brent, Akhila Rajan.

  Excess dietary sugar profoundly impacts organismal metabolism and health, yet it remains unclear how metabolic adaptations in adipose tissue influence other organs, including the brain. Here, we show that a high-sugar diet (HSD) in Drosophila reduces adipocyte glycolysis and mitochondrial pyruvate uptake, shifting metabolism toward fatty acid oxidation and ketogenesis. These metabolic changes trigger mitochondrial oxidation and elevate antioxidant responses. Adipocyte-specific manipulations of glycolysis, lipid metabolism, or mitochondrial dynamics non-autonomously modulate Draper expression in brain ensheathing glia, key cells responsible for neuronal debris clearance. Adipocyte-derived ApoB-containing lipoproteins maintain basal Draper levels in glia via LpR1, critical for effective glial phagocytic activity. Accordingly, reducing ApoB or LpR1 impairs glial clearance of degenerating neuronal debris after injury. Collectively, our findings demonstrate that dietary sugar-induced shifts in adipocyte metabolism substantially influence brain health by modulating glial phagocytosis, identifying adipocyte-derived ApoB lipoproteins as essential systemic mediators linking metabolic state with neuroprotective functions.

Keywords:  ApoB; CP: Metabolism; CP: Neuroscience; Drosophila; OxPhos; adipokine; glycolysis; high-sugar diet; injury-response; ketogenesis; lipid metabolism; mitochondria; neurodegeneration; pyronic sensor

DOI:  https://doi.org/10.1016/j.celrep.2025.115704
Methods Mol Biol. 2025 ;2920 173-202

Real-Time Measurement of Mitochondrial Function and Glycolysis in Lymphoblastoid Cell Lines.

Tina Katsaros, Daniel Missailidis, Sarah J Annesley.

  Cells require energy in the form of ATP to function. The two main ways in which cells generate energy in mammalian cells is through glycolysis and oxidative phosphorylation (OXPHOS). Glycolysis takes place in the cytosol and involves the breakdown of glucose molecules, generating ATP and pyruvate, while OXPHOS takes place in the mitochondria and is responsible for producing the majority of ATP for the cell. A dysregulation of these cellular processes has been reported in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). In order to understand the mechanisms of the disease, it is imperative to understand how the bioenergetic pathways are altered in ME/CFS. Here we describe a method for measuring mitochondrial function and glycolytic function using the Agilent Seahorse Extracellular Flux Analyzer. We have optimized these assays for use in actively proliferating lymphoblastoid cell lines that are generated from blood cells. This assay measures oxygen consumption rate and extracellular acidification rates providing an overview of mitochondrial function and efficiency and glycolytic rate and capacity, respectively. These assays are performed on live, intact cells, and enable us to view different components and measurements of energy metabolism through the injection of different compounds that stimulate or inhibit various sections of these pathways. The below method details an optimized glycolysis and mitochondrial assay for 96-well plates with modifications noted for use in 24-well plates.

Keywords:  Agilent seahorse XF analyzer; Glycolysis; Lymphoblastoid cell lines; Mitochondria; Myalgic encephalomyelitis/chronic fatigue syndrome

DOI:  https://doi.org/10.1007/978-1-0716-4498-0_11
J Cell Sci. 2025 May 01. pii: jcs263639. [Epub ahead of print]138(9):

Snapshots of mitochondrial fission imaged by cryo-scanning transmission electron tomography.

Peter Kirchweger, Sharon Grayer Wolf, Neta Varsano, Tali Dadosh, Guenter P Resch, Michael Elbaum.

  Mitochondria undergo constant remodeling via fission, fusion, extension and degradation. Fission, in particular, depends on the accumulation of mitochondrial fission factor (MFF) and subsequent recruitment of the dynamin-related protein DRP1 (also known as DNM1L). We used cryo-scanning transmission electron tomography (cryo-STET) to investigate mitochondrial morphologies in MFF mutant (MFF-/-) mouse embryonic fibroblast (MEF) cells in ATP-depleting conditions that normally induce fission. The capability of cryo-STET to image through the cytoplasmic volume to a depth of 1 µm facilitated visualization of intact mitochondria and their surroundings. We imaged changes in mitochondrial morphology and cristae structure, as well as contacts with the endoplasmic reticulum (ER), degradative organelles and the cytoskeleton at stalled fission sites. We found disruption of the outer mitochondrial membrane at contact sites with the ER and degradative organelles at sites of mitophagy. We identified fission sites where the inner mitochondrial membrane is already separated while the outer membrane is still continuous. Although MFF is a general fission factor, these observations demonstrate that mitochondrial fission can proceed to the final stage in its absence. The use of cryo-STET allays concerns about the loss of structures due to sample thinning required for tomography using cryo-transmission electron microscopy.

Keywords:  Cryo-ET; Cryo-FM; Cryo-STET; Mitochondrial dynamics; Mitochondrial fission; Mitochondrial fission factor

DOI:  https://doi.org/10.1242/jcs.263639
Semin Cancer Biol. 2025 May 08. pii: S1044-579X(25)00063-X. [Epub ahead of print]113 9-24

Metabolic pathway analysis of tumors using stable isotopes.

Qiufen Bi, Junzhang Zhao, Jun Nie, Fang Huang.

  Metabolic reprogramming is pivotal in malignant transformation and cancer progression. Tumor metabolism is shaped by a complex interplay of both intrinsic and extrinsic factors that are not yet fully elucidated. It is of great value to unravel the complex metabolic activity of tumors in patients. Metabolic flux analysis (MFA) is a versatile technique for investigating tumor metabolism in vivo, it has increasingly been applied to the assessment of metabolic activity in cancer in the past decade. Stable-isotope tracing have shown that human tumors use diverse nutrients to fuel central metabolic pathways, such as the tricarboxylic acid cycle and macromolecule synthesis. Precisely how tumors use different fuels, and the contribution of alternative metabolic pathways in tumor progression, remain areas of intensive investigation. In this review, we systematically summarize the evidence from in vivo stable- isotope tracing in tumors and describe the catabolic and anabolic processes involved in altered tumor metabolism. We also discuss current challenges and future perspectives for MFA of human cancers, which may provide new approaches in diagnosis and treatment of cancer.

Keywords:  Cancer metabolism; Metabolic flux analysis; Stable-isotope tracing

DOI:  https://doi.org/10.1016/j.semcancer.2025.05.002
J Cell Sci. 2025 May 01. pii: jcs263757. [Epub ahead of print]138(9):

Quality control of un-imported mitochondrial proteins at a glance.

Megan Balzarini, John Kim, Hilla Weidberg.

  Mitochondria are metabolic hubs that are essential for cellular homeostasis. Most mitochondrial proteins are translated in the cytosol and imported into the organelle. However, import machineries can become overwhelmed or disrupted by physiological demands, mitochondrial damage or diseases, such as metabolic and neurodegenerative disorders. Impaired import affects mitochondrial function and causes un-imported pre-proteins to accumulate not only in the cytosol but also in other compartments, including the endoplasmic reticulum and nucleus. Quality control pathways have evolved to mitigate the accumulation of these mistargeted proteins and prevent proteotoxicity. In this Cell Science at a Glance article and the accompanying poster, we summarize the fate of un-imported mitochondrial proteins and the compartment-specific quality control pathways that regulate them.

Keywords:  Mitochondrial protein import; Mitochondrial stress; Protein quality control

DOI:  https://doi.org/10.1242/jcs.263757
Front Immunol. 2025 ;16 1572927

Mitochondrial metabolism is rapidly re-activated in mature neutrophils to support stimulation-induced response.

Jorgo Lika, James A Votava, Rupsa Datta, Carlos A Mellado Fritz, Aleksandr M Kralovec, Frances M Smith, Anna Huttenlocher, Melissa C Skala, Jing Fan.

   Introduction: Neutrophils are highly abundant innate immune cells that are constantly produced from myeloid progenitors in the bone marrow. Differentiated neutrophils can perform an arsenal of effector functions critical for host defense. This study aims to quantitatively understand neutrophil mitochondrial metabolism throughout differentiation and activation, and to elucidate the impact of mitochondrial metabolism on neutrophil functions.
Methods: To study metabolic remodeling throughout neutrophil differentiation, murine ER-Hoxb8 myeloid progenitor-derived neutrophils and human induced pluripotent stem cell-derived neutrophils were assessed as models. To study the metabolic remodeling upon neutrophil activation, differentiated ER-Hoxb8 neutrophils and primary human neutrophils were activated with various stimuli, including ionomycin, monosodium urate crystals, and phorbol 12-myristate 13-acetate. Characterization of cellular metabolism by isotopic tracing, extracellular flux analysis, metabolomics, and fluorescence-lifetime imaging microscopy revealed dynamic changes in mitochondrial metabolism.
Results: As neutrophils mature, mitochondrial metabolism decreases drastically, energy production is offloaded from oxidative phosphorylation, and glucose oxidation through the TCA cycle is substantially reduced. Nonetheless, mature neutrophils retain the capacity for mitochondrial metabolism. Upon stimulation with certain stimuli, TCA cycle is rapidly activated. Mitochondrial pyruvate carrier inhibitors reduce this re-activation of the TCA cycle and inhibit the release of neutrophil extracellular traps. Treatment with these inhibitors also impacts neutrophil redox status, migration, and apoptosis without significantly changing overall bioenergetics.
Conclusions: Together, these results demonstrate that mitochondrial metabolism is dynamically remodeled and plays a significant role in neutrophils. Furthermore, these findings point to the therapeutic potential of mitochondrial pyruvate carrier inhibitors in a range of conditions where dysregulated neutrophil response drives inflammation and contributes to pathology.

Keywords:  TCA cycle; metabolism; mitochondria; neutrophil; neutrophil extracellular traps

DOI:  https://doi.org/10.3389/fimmu.2025.1572927
Proc Natl Acad Sci U S A. 2025 May 20. 122(20): e2415268122

Split genetically encoded calcium indicators for interorganellar junctions.

Shunit Olszakier, Wessal Hussein, Ronit Heinrich, Michael Andreyanov, Achinoam Blau, Yara Otor, Jackie Schiller, Shai Kellner, Shai Berlin.

  Genetically encoded calcium indicators (GECIs) have revolutionized the study of cellular calcium signaling, offering powerful tools for real-time optical monitoring of calcium dynamics. Although contemporary GECIs can be targeted to various organelles, there are no means to obtain active and functional GECIs exclusively at interorganellar junctions. To address this gap, we have developed a toolbox of split versions of green and red GECIs designed to reassemble only when the two "halves" come into proximity. We developed split probes to investigate interorganellar connectivity and activity between mitochondria and the ER (via split-MEGIC) or between the plasma membrane and the ER (via split-sf-MEMBER). We employ the various split-sensors to image neural Ca2+ activity in vitro and in vivo and, in the process, identify Mito-ER junctions and calcium activity within individual dendritic spines by use of split-MEGIC.

Keywords:  calcium; neurons; organelle; spine; split

DOI:  https://doi.org/10.1073/pnas.2415268122
Cell Rep. 2025 May 09. pii: S2211-1247(25)00418-8. [Epub ahead of print]44(5): 115647

Beta cells intrinsically sense and limit their secretory activity via mTORC1-RhoA signaling.

Saar Krell, Amit Hamburg, Ofer Gover, Kfir Molakandov, Gil Leibowitz, Kfir Sharabi, Michael D Walker, Aharon Helman.

  Precise regulation of insulin secretion by pancreatic β cells is essential to prevent excessive insulin release. Here, we show that the nutrient sensor mechanistic Target of Rapamycin Complex 1 (mTORC1) is rapidly activated by glucose in β cells via the insulin secretion machinery, positioning mTORC1 as a sensor of β cell activity. Acute pharmacological inhibition of mTORC1 during glucose stimulation enhances insulin release, suggesting that mTORC1 acts as an intrinsic feedback regulator that restrains insulin secretion. Phosphoproteomic profiling reveals that mTORC1 modulates the phosphorylation of proteins involved in actin remodeling and vesicle trafficking, with a prominent role in the RhoA-GTPase pathway. Mechanistically, mTORC1 promotes RhoA activation and F-actin polymerization, limiting vesicle movement and dampening the second phase of insulin secretion. These findings identify a glucose-mTORC1-RhoA signaling axis that forms an autonomous feedback loop to constrain insulin exocytosis, providing insight into how β cells prevent excessive insulin release and maintain metabolic balance.

Keywords:  CP: Metabolism; CP: Molecular biology; RhoA-GTPase; Torin-1; actin remodeling; activity sensor; autonomous regulation; insulin secretion; mTORC1; negative feedback loop; pancreatic β cell; rapamycin

DOI:  https://doi.org/10.1016/j.celrep.2025.115647
J Cereb Blood Flow Metab. 2025 May 14. 271678X251337630

Regulation of synaptic mitochondria by extracellular vesicles and its implications for neuronal metabolism and synaptic plasticity.

Yuzhou Zeng, Anna Antoniou.

  Mitochondrial metabolism in neurons is necessary for energetically costly processes like synaptic transmission and plasticity. As post-mitotic cells, neurons are therefore faced with the challenge of maintaining healthy functioning mitochondria throughout lifetime. The precise mechanisms of mitochondrial maintenance in neurons, and particularly in morphologically complex dendrites and axons, are not fully understood. Evidence from several biological systems suggests the regulation of cellular metabolism by extracellular vesicles (EVs), secretory lipid-enclosed vesicles that have emerged as important mediators of cell communication. In the nervous system, neuronal and glial EVs were shown to regulate neuronal circuit development and function, at least in part via the transfer of protein and RNA cargo. Interestingly, EVs have been implicated in diseases characterized by altered metabolism, such as cancer and neurodegenerative diseases. Furthermore, nervous system EVs were shown to contain proteins related to metabolic processes, mitochondrial proteins and even intact mitochondria. Here, we present the current knowledge of the mechanisms underlying neuronal mitochondrial maintenance, and highlight recent evidence suggesting the regulation of synaptic mitochondria by neuronal and glial cell EVs. We further discuss the potential implications of EV-mediated regulation of mitochondrial maintenance and function in neuronal circuit development and synaptic plasticity.

Keywords:  Exosomes; extracellular vesicles; metabolism; mitochondria; synaptic plasticity

DOI:  https://doi.org/10.1177/0271678X251337630
Chemistry. 2025 May 13. e202500772

Dual-Organelle-Targeted Fluorescent Probe for Lipid Droplets and Endoplasmic Reticulum Using Bay-Region Substituted Perylene Diimides.

Jinping Liu, Xiaoyu Bu, Zikang Yang, Linshuai Yang, Qi Ai, Baoxiang Gao.

  In the complex cellular microenvironment, lipid droplets (LDs) and the endoplasmic reticulum (ER) are essential for maintaining cellular homeostasis. Their interactions are crucial for regulating processes such as lipid metabolism. Nevertheless, simultaneously monitoring these two organelles remains a challenging task. In this study, a dual-organelle-targeted perylene diimides (PDIs) based probe, LD-ER-PDI, by incorporating a 2-azetidinone substituent in the bay-region and two distinct targeting groups for LDs and ER at opposite ends of the imide positions was development, enabling discrimination between LDs and ER. Moreover, it can effectively visualize the dynamic behaviors of LDs and ER under starvation and oleic acid-treated conditions and also allows real-time monitoring of LDs formation from the ER. This work not only provides a valuable tool for studying the dynamic interactions between LDs and ER but also highlights a strategy for designing dual-organelle-targeted fluorescent probes.

Keywords:  Perylene diimides * Dual-organelle-targeted probe * Lipid droplets * Endoplasmic reticulum * Fluorescent imaging

DOI:  https://doi.org/10.1002/chem.202500772
Nat Cell Biol. 2025 May;27(5): 847-862

ALDH4A1 functions as an active component of the MPC complex maintaining mitochondrial pyruvate import for TCA cycle entry and tumour suppression.

Che-Chia Hsu, Chi-Yun Wang, Rajesh Kumar Manne, Zhen Cai, Vasudevarao Penugurti, Rajni Kant, Ling Bai, Bo-Syong Pan, Tingjin Chen, Yuan-Ru Chen, Hsin-En Wu, Yan Jin, Haiwei Gu, Chia-Yang Li, Hui-Kuan Lin.

MPC1 and MPC2 are two well-known components of the mitochondrial pyruvate carrier (MPC) complex maintaining MPC activity to transport pyruvate into mitochondria for tricarboxylic acid (TCA) cycle entry in mammalian cells. It is currently unknown whether there is an additional MPC component crucially maintaining MPC complex activity for pyruvate mitochondrial import. Here we show that ALDH4A1, a proline-metabolizing enzyme localized in mitochondria, serves as a previously unrecognized MPC component maintaining pyruvate mitochondrial import and the TCA cycle independently of its enzymatic activity. Loss of ALDH4A1 in mammalian cells impairs pyruvate entry to mitochondria, resulting in defective TCA cycle entry. ALDH4A1 forms an active trimeric complex with MPC1-MPC2 to maintain the integrity and oligomerization of MPC1-MPC2 and facilitates pyruvate transport in an in vitro system. ALDH4A1 displays tumour suppression by maintaining MPC complex activity. Our study identifies ALDH4A1 as an essential component of MPC for pyruvate mitochondrial import, TCA cycle entry and tumour suppression.

DOI: https://doi.org/10.1038/s41556-025-01651-8
Sci Rep. 2025 May 14. 15(1): 16715

Single-cell mitochondrial morphomics reveals cellular heterogeneity and predicts complex I, III, and ATP synthase Inhibition responses.

Ratneswary Sutharsan, Maddi Biaut Hontaas, Yan Li, Hao Xiong, Hartwig Preckel, Carolyn M Sue, Gautam Wali.

Mitochondrial heterogeneity drives diverse cellular responses in neurodegenerative diseases, complicating the evaluation of mitochondrial dysfunction. In this study, we describe a high-throughput imaging and analysis approach to investigate cell-to-cell mitochondrial variability. We applied known mitochondrial function inhibitors - rotenone, antimycin, and oligomycin to inhibit complexes I, III, and V (ATP synthase) function in human induced pluripotent stem cell-derived cortical neurons, a model commonly used in neurodegenerative disease research. We captured a large number of cell images and extracted a diverse range of mitochondrial morphological features related to shape, size, texture, and spatial distribution, for an unbiased and comprehensive analysis of mitochondrial morphology. Group-level cell analysis, which examines the collective responses of cells exposed to the same mitochondrial inhibitor, showed that cells treated with rotenone, antimycin, or oligomycin clustered together based on their shared morphological changes. Rotenone and antimycin, both targeting different complexes of the electron transport chain, formed sub-clusters within a larger cluster. In contrast, oligomycin, which inhibits ATP synthase, resulted in a distinct cluster likely due to its differing effect on ATP production. Single-cell analysis using dimensionality reduction techniques revealed distinct subpopulations of cells with varying degrees of sensitivity to each mitochondrial inhibitor, identifying the most affected cells. Mitochondrial feature differential expression analysis showed that neurite-related mitochondrial features, such as intensity and size, were more severely impacted than cell body-related mitochondrial features, particularly with rotenone and antimycin, which target the electron transport chain. In contrast, oligomycin which affects ATP synthesis by directly inhibiting ATP synthase showed relatively less severe alterations in neurite-related mitochondrial features, highlighting a distinct effect of the mode of action between inhibitors. By incorporating the most affected cells into machine learning models, we significantly improved the prediction accuracy of mitochondrial dysfunction outcomes - 81.97% for antimycin, 75.12% for rotenone, and 94.42% for oligomycin. This enhancement underscores the value of targeting highly responsive cell subpopulations, offering a more precise method for evaluating mitochondrial modulators and therapeutic interventions in neurodegenerative diseases.

DOI: https://doi.org/10.1038/s41598-025-99972-z
Nat Rev Mol Cell Biol. 2025 May 14.

Molecular machineries shaping the mitochondrial inner membrane.

Oliver Daumke, Martin van der Laan.

Mitochondria display intricately shaped deep invaginations of the mitochondrial inner membrane (MIM) termed cristae. This peculiar membrane architecture is essential for diverse mitochondrial functions, such as oxidative phosphorylation or the biosynthesis of cellular building blocks. Conserved protein nano-machineries such as F1Fo-ATP synthase oligomers and the mitochondrial contact site and cristae organizing system (MICOS) act as adaptable protein-lipid scaffolds controlling MIM biogenesis and its dynamic remodelling. Signal-dependent rearrangements of cristae architecture and MIM fusion events are governed by the dynamin-like GTPase optic atrophy 1 (OPA1). Recent groundbreaking structural insights into these nano-machineries have considerably advanced our understanding of the functional architecture of mitochondria. In this Review, we discuss how the MIM-shaping machineries cooperate to control cristae and crista junction dynamics, including MIM fusion, in response to cellular signalling pathways. We also explore how mutations affecting MIM-shaping machineries compromise mitochondrial functions.

DOI: https://doi.org/10.1038/s41580-025-00854-z
Proc Natl Acad Sci U S A. 2025 May 20. 122(20): e2426179122

Estrogen-related receptors regulate innate and adaptive muscle mitochondrial energetics through cooperative and distinct actions.

Weiwei Fan, Tae Gyu Oh, Hui J Wang, Lillian Crossley, Mingxiao He, Hunter Robbins, Chandra Koopari, Yang Dai, Morgan L Truitt, Christopher Liddle, Ruth T Yu, Annette R Atkins, Michael Downes, Ronald M Evans.

  Mitochondrial energy metabolism is vital for muscle function and is tightly controlled at the transcriptional level, both in the basal state and during adaptive muscle remodeling. The importance of the transcription factors estrogen-related receptors (ERRs) in controlling innate mitochondrial energetics has been recently demonstrated. However, whether different ERR isoforms display distinct functions in glycolytic versus oxidative myofibers is largely unknown. Moreover, their roles in regulating exercise-induced adaptive mitochondrial biogenesis remain unclear. Using muscle-specific single and combinatorial knockout mouse models, we have identified both cooperative and distinct roles of the ERR isoforms ERRα and ERRγ in regulating mitochondrial energy metabolism in different muscles. We demonstrate the essential roles of both these ERRs in mediating adaptive mitochondrial biogenesis in response to exercise training. We further show that PGC1α-induced mitochondrial biogenesis is completely abolished in primary myotubes with ERRα deletion but not ERRγ, highlighting distinct roles of these two isoforms in adaptive mitochondrial remodeling. Mechanistically, we find that both ERRs directly bind to the majority of mitochondrial energetic genes and control their expression, largely through collaborative binding to the same genomic loci. Collectively, our findings reveal critical and direct regulatory roles of ERRα and ERRγ in governing both innate and adaptive mitochondrial energetics in skeletal muscle.

Keywords:  PGC1; energy metabolism; estrogen-related receptor; mitochondria; muscle

DOI:  https://doi.org/10.1073/pnas.2426179122
Cancer Res. 2025 May 14.

Tobacco Smoking Rewires Cell Metabolism by Inducing GAPDH Succinylation to Promote Lung Cancer Progression.

Kun Wang, Jingzhuo Li, Hai Zhang, Hongyan Ma, Hong-Yong Cui, Huai-Qiang Ju, Jing Zhang, Qing-Zhi Ma, Ming Zhao, Qing-Mei Zeng, Jie Zou, Xiu-Xuan Sun, Gang Nan, Meirui Qian, Lin Jing, Yiming Li, Cai-Feng Xiong, Qiu-Zi Yang, Hao Wang, Jian-Li Jiang, Zhi-Nan Chen, Liang Chen, Wan Huang.

Patient behavior and physiology can directly affect cancer metabolism. Smoking is the leading risk factor for non-small cell lung cancer (NSCLC). Here, we identified that smoking modulates lung cancer cell metabolism through altered protein post-translational modification. Proteomic analyses identified elevated K251 succinylation (K251-Su) of GAPDH, a key enzyme in glycolysis, in NSCLC samples, and GAPDH K251-Su was significantly higher in patients who smoke compared to non-smokers. Exposure of lung cancer cells to cigarette smoke extract led to increased uptake of glutamine and enhanced GAPDH K251-Su. Glutamine uptake by cancer cells in hypoxic and nutrient-deficient microenvironments provided succinyl-CoA donors for GAPDH succinylation at K251, which was catalyzed by acyltransferase p300. K251-Su increased GAPDH stability by suppressing TRIM4-mediated K254 ubiquitination. GAPDH K251-Su enhanced glycolysis and glutamine reductive carboxylation to meet the demands for cell growth and to support survival in hypoxic and nutrient-depleted conditions, promoting tumor growth and metastasis. These findings indicate that tobacco smoking mediates metabolic reprogramming of cancer cells through succinylation of GAPDH to drive NSCLC progression.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-3525
Front Pharmacol. 2025 ;16 1586655

The role of glutamate dehydrogenase in the ageing brain.

Tao Zhou, Haichuan Wang.

  The homeostasis of glutamate, the primary excitatory neurotransmitter in the brain and is crucial for normal brain function. The mitochondrial enzyme glutamate dehydrogenase (GDH) connects the multifunctional amino acid glutamate, which is intimately related to glutamate metabolism, to the Krebs cycle. As a result, GDH reglutes the synthesis and uptake of the chemical messenger glutamate in neuroendocrine cells, playing a crucial role in the metabolism of proteins and carbohydrates. Nonetheless, brain ageing and numerous neurodegenerative diseases, including Parkinson's disease and Alzheimer's disease, have been linked to GDH malfunction or dysregulation. In this review, we summarize the dynamics of GDH levels in the ageing brain and provide additional details about the role of GDH in the ageing brain. Understanding the metabolic mechanisms underlying glutamate homeostasis in the aging brain and how GDH regulates glutamate-dependent metabolic processes at synapses may lead to novel therapeutic approaches for neurodegenerative and psychiatric disorders, potentially slowing the aging process and promoting brain regeneration.

Keywords:  Alzheimer’s disease; Parkinson’s disease; ageing brain; glutamate dehydrogenase; glutamate metabolism

DOI:  https://doi.org/10.3389/fphar.2025.1586655
J Cell Biol. 2025 Jul 07. pii: e202408166. [Epub ahead of print]224(7):

The mitophagy receptors BNIP3 and NIX mediate tight attachment and expansion of the isolation membrane to mitochondria.

Shun-Ichi Yamashita, Ritsuko Arai, Hiroshi Hada, Benjamin Scott Padman, Michael Lazarou, David C Chan, Tomotake Kanki, Satoshi Waguri.

BNIP3 and NIX are the main receptors for mitophagy, but their mechanisms of action remain elusive. Here, we used correlative light EM (CLEM) and electron tomography to reveal the tight attachment of isolation membranes (IMs) to mitochondrial protrusions, often connected with ER via thin tubular and/or linear structures. In BNIP3/NIX-double knockout (DKO) HeLa cells, the ULK1 complex and nascent IM formed on mitochondria, but the IM did not expand. Artificial tethering of LC3B to mitochondria induced mitophagy that was equally efficient in DKO cells and WT cells. BNIP3 and NIX accumulated at the segregated mitochondrial protrusions via binding with LC3 through their LIR motifs but did not require dimer formation. Finally, the average distance between the IM and the mitochondrial surface in receptor-mediated mitophagy was significantly smaller than that in ubiquitin-mediated mitophagy. Collectively, these results indicate that BNIP3 and NIX are required for the tight attachment and expansion of the IM along the mitochondrial surface during mitophagy.

DOI: https://doi.org/10.1083/jcb.202408166
Proc Natl Acad Sci U S A. 2025 May 20. 122(20): e2418525122

Mitochondria regulate MR1 protein expression and produce self-metabolites that activate MR1-restricted T cells.

Gennaro Prota, Giuliano Berloffa, Wael Awad, Alessandro Vacchini, Andrew Chancellor, Verena Schaefer, Daniel Constantin, Dene R Littler, Rodrigo Colombo, Vladimir Nosi, Lucia Mori, Jamie Rossjohn, Gennaro De Libero.

  Mitochondria coordinate several metabolic pathways, producing metabolites that influence the immune response in various ways. It remains unclear whether mitochondria impact antigen presentation by the MHC-class-I-related antigen-presenting molecule, MR1, which presents small molecules to MR1-restricted T-lymphocytes. Here, we demonstrate that mitochondrial complex III and the enzyme dihydroorotate dehydrogenase are essential for the cell-surface expression of MR1 and for generating uridine- and thymidine-related compounds that bind to MR1 and are produced upon oxidation by reactive oxygen species. One mitochondria-derived immunogenic formylated metabolite we identified is 5-formyl-deoxyuridine (5-FdU). Structural studies indicate that 5-FdU binds in the A'-antigen-binding pocket of MR1, positioning the deoxyribose toward the surface of MR1 for TCR interaction. 5-FdU stimulates specific T cells and detects circulating T cells when loaded onto MR1-tetramers. 5-FdU-reactive cells resemble adaptive T cells and express the phenotypes of naïve, memory, and effector cells, indicating prior in vivo stimulation. These findings suggest that mitochondria may play a role in MR1-mediated immune surveillance.

Keywords:  MR1; T cells; antigen presentation; formylated metabolite; mitochondria

DOI:  https://doi.org/10.1073/pnas.2418525122
PLoS Biol. 2024 Aug;22(8): e3002754

To transfer mitochondria or not to transfer mitochondria: ADP does the trick.

Jaromir Novak, Jiri Neuzil.

Horizontal mitochondrial transfer (HMT) has emerged as a novel phenomenon in cell biology, but it is unclear how this process of intercellular movement of mitochondria is regulated. A new study in PLOS Biology reports that ADP released by stressed cells is a signal that triggers HMT.

DOI: https://doi.org/10.1371/journal.pbio.3002754
Nat Commun. 2025 May 15. 16(1): 4509

Label-free multimodal optical biopsy reveals biomolecular and morphological features of diabetic kidney tissue in 2D and 3D.

Anthony A Fung, Zhi Li, Craig Boote, Petar Markov, Joseph P Gaut, Sanjay Jain, Lingyan Shi.

Kidney disease, the ninth leading cause of death in the United States, suffers from poor diagnostic efficiency (10%). Traditional biopsies use molecular reagents to enhance diagnostic power but are limited by overlapping spatial and chromatic signals, product quality variability, and additional processing. To address these challenges without disrupting routine diagnostics, we implement label-free imaging modalities-stimulated Raman scattering (SRS), second harmonic generation (SHG), and two-photon fluorescence (TPF)-within a single setup. We identify morphological, lipidomic, and metabolic biomarkers in control and diabetic kidney samples at subcellular resolution. Label-free Stimulated Raman Histology (SRH) reveals distinct collagen morphology, mesangial-glomerular volumes, lipid saturation, redox status, and lipid-protein concentrations previously unrecognized in kidney diseases. Using the same tissue section enhances diagnostic value without compromising limited tissue. These multimodal biomarkers broadly deepen the understanding of kidney disease progression by integrating lipidomic, fibrotic, and metabolic data.

DOI: https://doi.org/10.1038/s41467-025-59163-w
Sci Rep. 2025 May 15. 15(1): 16981

Urine metabolite profiling in Indian males exposed to high-altitude: a longitudinal pilot study.

Manisha Kumari, Dolly Sharma, Anu Kumari, Mallesh Rao Eslavath, Chhavi Rai, Maramreddy Prasanna Kumar Reddy, Lilly Ganju, Rajeev Varshney, Ramesh Chand Meena.

  People who visit high-altitude for research and development work, pilgrimage, recreational purposes and deployments are exposed to different environmental conditions such as low temperature and atmospheric pressure, leading to hypoxia, high radiation, dry air, and non-availability of fresh food and vegetables. These environmental stressors have significant physiological effects on the human body. Among these challenges, hypobaric hypoxia at high-altitude affects aerobic metabolism and thereby reduces the supply of metabolic energy. Metabolic alterations may further lead to extreme environment related maladaptation as evidenced by alterations in the levels of metabolites and metabolic pathways. To investigate the variation in the metabolite profile, urine samples were collected from 16 individuals at baseline (BL, 210 m) and high-altitude (HA, 4200 m). Untargeted urinary metabolic profiling was performed by liquid chromatography-mass spectrometry (LC-MS) in conjunction with statistical analysis. Univariate and multivariate statistical analyses revealed 33 differentially abundant metabolites based on fold change, VIP score and p value. These distinct metabolites were primarily associated with pathways related to phenylalanine, tyrosine and tryptophan biosynthesis; metabolism of phenylalanine, biotin, tyrosine, cysteine and methionine along with alanine, aspartate and glutamate metabolism. Thes pathways are also linked with pentose and glucuronate interconversions, citrate cycle, vitamin B6 and porphyrin metabolism. Furthermore, receiver operating characteristic curve analysis detected five metabolites namely, 2-Tetrahydrothiopheneacetic acid, 1-Benzyl-7,8-dimethoxy-3-phenyl-3H-pyrazolo [3,4-c] isoquinoline, Abietin, 4,4'-Thiobis-2-butanone, and Hydroxyisovaleroyl carnitine with high range of sensitivity and specificity. In summary, this longitudinal study demonstrated novel metabolic variations in humans exposed to high-altitude, utilising the potential of LC-MS based metabolomics. Thus, the present findings shed light on the impact of hypoxic exposure on metabolic adaptation and provide a better understanding about the pathophysiological mechanisms underlying high-altitude illnesses correlated to tissue hypoxia.

Keywords:  High-altitude; Hypobaric hypoxia; Liquid chromatography-mass spectrometry; Longitudinal; Metabolism; Metabolites; Metabolomics

DOI:  https://doi.org/10.1038/s41598-025-00312-y
Life Sci Alliance. 2025 Aug;pii: e202403076. [Epub ahead of print]8(8):

A fluorescent sensor for real-time monitoring of DPP8/9 reveals crucial roles in immunity and cancer.

Konstantin Weiss, Yelizaveta Agarkova, Alexandra Zwosta, Sarah Hoevel, Ann-Kathrin Himmelreich, Magdalena Shumanska, Julia Etich, Gereon Poschmann, Bent Brachvogel, Ivan Bogeski, Dirk Mielenz, Jan Riemer.

Dipeptidyl peptidases 8 and 9 (DPP8/9) are critical for the quality control of mitochondrial and endoplasmic reticulum protein import, immune regulation, cell adhesion, and cell migration. Dysregulation of DPP8/9 is associated with pathologies including tumorigenesis and inflammation. Commonly, DPP8/9 activity is analysed by in vitro assays using artificial substrates, which allow neither continuously monitoring DPP8/9 activity in individual, living cells nor detecting effects from endogenous interactors and posttranslational modifications. Here, we developed DiPAK (for DPP8/9 activity sensor based on AK2), a ratiometric genetically encoded fluorescent sensor, which enables studying DPP8/9 activity in living cells. Using DiPAK, we determined the dynamic range of DPP8/9 activity in cells overexpressing or lacking DPP9. We identified distinct activity levels among melanoma cell lines and found that LPS-induced primary B-cell activation depends on DPP8/9 as the absence of DPP8/9 activity results in apoptotic but not pyroptotic cell death. Consistently, we observed increasing DPP8/9 activity during B-cell maturation. Overall, DiPAK is a versatile tool for real-time single-cell monitoring of DPP8/9 activity in a broad range of cells and organisms.

DOI: https://doi.org/10.26508/lsa.202403076
ACS Biomater Sci Eng. 2025 May 13.

Novel Mitochondria-Targeted NIR Cyanine Cy750M-C1 Nanoparticles for Chemotherapy against Triple-Negative Breast Cancer.

Zhilin Shen, Fenglin Zhang, Jiawang Yang, Kaihang Zhang, Feng Liang, Han Mu, Li Shi, Jijun Jiang, Yuanzhi Yang, Zhixuan Lin, Jie Gao, Ning Gao.

  Mitochondrial metabolism plays an important role in promoting cancer development, making mitochondria a novel promising target for cancer therapy. Current mitochondria-targeted fluorescent agents can specifically accumulate in the mitochondria of cancer cells and can be applied for cancer imaging and therapy. However, their clinical application is still limited due to the poor solubility and lower tumor-specific distribution. In the present study, we synthesized a novel NIR small-molecule dye, Cy750M-C1, and evaluated its optical properties, mitochondrial distribution, and anticancer activity. We also synthesized nanoparticles loading Cy750M-C1 (Cy750M-C1-FA-NPs) and demonstrated that Cy750M-C1-FA-NPs are specifically targeted to the tumor and dramatically inhibited tumor growth in vivo. The mechanistic study revealed that Cy750M-C1 specifically targeted mitochondria of TNBC cells, subsequently promoting ROS production through inhibition of mitochondrial complexes (complexes I, III, and IV) and OXPHOS and depletion of ATP, leading, in turn, to AMPK activation and Drp1 dephosphorylation mediating the mitochondrial translocation of Drp1 and BAX and ultimately inducing mitochondrial fission, caspase activation, as well as apoptosis. Overall, our data implicate that Cy750M-C1 could be developed as a novel anticancer agent with mitochondria-targeting ability and NIR fluorescence imaging and that Cy750M-C1-FA-NPs could also be considered as promising drug delivery carriers for antitumor agents.

Keywords:  NIR cyanine; chemotherapy; mitochondria; nanoparticles; triple-negative breast cancer; tumor targeting

DOI:  https://doi.org/10.1021/acsbiomaterials.5c00343