bims-celmim 2025-04-20 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–04–20
25 papers selected by
Marc Segarra Mondejar

Metabolic Screening of T Lymphocytes During Activation via SEAHORSE Extracellular Flux (XF) Analysis.
Metabolic rewiring caused by mitochondrial dysfunction promotes mTORC1-dependent skeletal aging.
Active control of mitochondrial network morphology by metabolism-driven redox state.
Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis.
Simultaneous in vivo multi-organ fluxomics reveals divergent metabolic adaptations in liver, heart, and skeletal muscle during obesity.
Analyzing Ex Vivo Metabolic Flux in Splenic and Cardiac Macrophages and Bone Marrow Monocytes.
Metabolic Profiling of Activated T Lymphocytes Using Single-Cell Energetic Metabolism by Profiling Translation Inhibition (SCENITH).
Metabolic Reprogramming of Glycolysis, Lipids, and Amino Acids in Tumors: Impact on CD8+ T Cell Function and Targeted Therapeutic Strategies.
Mitochondrial mayhem: Disrupting conserved N-terminal motifs in TANGO2 impacts its localization and function.
The unusual metabolism of germinal center B cells.
Analysis of Store-Operated Ca2+ Entry in Primary T Cells.
Progress in Understanding the Regulation of Glucose and Fructose Metabolism.
Mitochondrial classic metabolism and its often-underappreciated facets.
Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier.
Autophagy, ER-phagy and ER dynamics during cell differentiation.
SLC25A42 promotes gastric cancer growth by conferring ferroptosis resistance through enhancing CPT2-mediated fatty acid oxidation.
Mitochondrial function regulates cell growth kinetics to actively maintain mitochondrial homeostasis.
Integrated analysis of transcriptional and metabolic responses to mitochondrial stress.
Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering.
Identification of serum metabolite biomarkers and metabolic reprogramming mechanisms to predict recurrence in cholangiocarcinoma.
Distinct metabolome and flux responses in the retinal pigment epithelium to cytokines associated with age-related macular degeneration: comparison of ARPE-19 cells and eyecups.
Loss of VHL-mediated pRb regulation promotes clear cell renal cell carcinoma.
Spatial regulation of glucose and lipid metabolism by hepatic insulin signaling.
Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis.
Mitochondrial glutamine metabolism drives epileptogenesis in primary hippocampal neurons.

Methods Mol Biol. 2025 ;2904 243-258

Metabolic Screening of T Lymphocytes During Activation via SEAHORSE Extracellular Flux (XF) Analysis.

Gabriela F Gubert, Sophia M Hochrein, Katrin Sinning, Martin Vaeth.

  Upon activation, T cells undergo a profound reconfiguration of their metabolic profile, transitioning from a quiescent to a metabolically active state characterized by an increase in both aerobic glycolysis and mitochondrial respiration. Seahorse extracellular flux (XF) analysis is a powerful method for measuring the changes in fundamental metabolic pathways in real-time, including aerobic glycolysis and mitochondrial respiration of live T cells. This method allows a precise determination of mitochondrial performance and lactate secretion, which is measured as oxygen consumption rate (OCR) and glycolytic proton efflux rate (ECAR), respectively. By dynamically monitoring these metabolic changes, Seahorse XF analysis provides comprehensive insights into the metabolic dynamics of (activated) T cells across diverse experimental conditions or treatments.

Keywords:  Bioenergetic profile; ECAR; Glycolysis; Metabolic remodeling; Metabolism; Mitochondrial respiration; OCR; Seahorse; T cell activation

DOI:  https://doi.org/10.1007/978-1-0716-4414-0_17
Sci Adv. 2025 Apr 18. 11(16): eads1842

Metabolic rewiring caused by mitochondrial dysfunction promotes mTORC1-dependent skeletal aging.

Kristina Bubb, Julia Etich, Kristina Probst, Tanvi Parashar, Maximilian Schuetter, Frederik Dethloff, Susanna Reincke, Janica L Nolte, Marcus Krüger, Ursula Schlötzer-Schrehard, Julian Nüchel, Constantinos Demetriades, Patrick Giavalisco, Jan Riemer, Bent Brachvogel.

Decline of mitochondrial respiratory chain (mtRC) capacity is a hallmark of mitochondrial diseases. Patients with mtRC dysfunction often present reduced skeletal growth as a sign of premature cartilage degeneration and aging, but how metabolic adaptations contribute to this phenotype is poorly understood. Here we show that, in mice with impaired mtRC in cartilage, reductive/reverse TCA cycle segments are activated to produce metabolite-derived amino acids and stimulate biosynthesis processes by mechanistic target of rapamycin complex 1 (mTORC1) activation during a period of massive skeletal growth and biomass production. However, chronic hyperactivation of mTORC1 suppresses autophagy-mediated organelle recycling and disturbs extracellular matrix secretion to trigger chondrocytes death, which is ameliorated by targeting the reductive metabolism. These findings explain how a primarily beneficial metabolic adaptation response required to counterbalance the loss of mtRC function, eventually translates into profound cell death and cartilage tissue degeneration. The knowledge of these dysregulated key nutrient signaling pathways can be used to target skeletal aging in mitochondrial disease.

DOI: https://doi.org/10.1126/sciadv.ads1842
Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2421953122

Active control of mitochondrial network morphology by metabolism-driven redox state.

Gaurav Singh, Vineeth Vengayil, Aayushee Khanna, Swagata Adhikary, Sunil Laxman.

  Mitochondria are dynamic organelles that constantly change morphology. What controls mitochondrial morphology however remains unresolved. Using actively respiring yeast cells growing in distinct carbon sources, we find that mitochondrial morphology and activity are unrelated. Cells can exhibit fragmented or networked mitochondrial morphology in different nutrient environments independent of mitochondrial activity. Instead, mitochondrial morphology is controlled by the intracellular redox state, which itself depends on the nature of electron entry into the electron transport chain (ETC)-through complex I/II or directly to coenzyme Q/cytochrome c. In metabolic conditions where direct electron entry is high, reactive oxygen species (ROS) increase, resulting in an oxidized cytosolic environment and rapid mitochondrial fragmentation. Decreasing direct electron entry into the ETC by genetic or chemical means, or reducing the cytosolic environment rapidly restores networked morphologies. Using controlled disruptions of electron flow to alter ROS and redox state, we demonstrate minute-scale, reversible control between networked and fragmented forms in an activity-independent manner. Mechanistically, the fission machinery through Dnm1 responds in minute-scale to redox state changes, preceding the change in mitochondrial form. Thus, the metabolic state of the cell and its consequent cellular redox state actively control mitochondrial form.

Keywords:  electron transport chain; mitochondrial network; reactive oxygen species; redox state

DOI:  https://doi.org/10.1073/pnas.2421953122
Mol Cell. 2025 Apr 17. pii: S1097-2765(25)00196-0. [Epub ahead of print]85(8): 1487-1508

Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis.

Brandon Chen, Costas A Lyssiotis, Yatrik M Shah.

  Mitochondria serve as central hubs in cellular metabolism by sensing, integrating, and responding to metabolic demands. This integrative function is achieved through inter-organellar communication, involving the exchange of metabolites, lipids, and signaling molecules. The functional diversity of metabolite exchange and pathway interactions is enabled by compartmentalization within organelle membranes. Membrane contact sites (MCSs) are critical for facilitating mitochondria-organelle communication, creating specialized microdomains that enhance the efficiency of metabolite and lipid exchange. MCS dynamics, regulated by tethering proteins, adapt to changing cellular conditions. Dysregulation of mitochondrial-organelle interactions at MCSs is increasingly recognized as a contributing factor in the pathogenesis of multiple diseases. Emerging technologies, such as advanced microscopy, biosensors, chemical-biology tools, and functional genomics, are revolutionizing our understanding of inter-organellar communication. These approaches provide novel insights into the role of these interactions in both normal cellular physiology and disease states. This review will highlight the roles of metabolite transporters, lipid-transfer proteins, and mitochondria-organelle interfaces in the coordination of metabolism and transport.

Keywords:  endoplasmic reticulum; inter-organellar communication; mitochondria; organellar metabolism; organelle membrane contact sites

DOI:  https://doi.org/10.1016/j.molcel.2025.03.003
Cell Rep. 2025 Apr 16. pii: S2211-1247(25)00362-6. [Epub ahead of print]44(5): 115591

Simultaneous in vivo multi-organ fluxomics reveals divergent metabolic adaptations in liver, heart, and skeletal muscle during obesity.

Mohsin Rahim, Tomasz K Bednarski, Clinton M Hasenour, Deveena R Banerjee, Irina Trenary, Jamey D Young.

  We present an isotope-based metabolic flux analysis (MFA) approach to simultaneously quantify metabolic fluxes in the liver, heart, and skeletal muscle of individual mice. The platform was scaled to examine metabolic flux adaptations in age-matched cohorts of mice exhibiting varying levels of chronic obesity. We found that severe obesity increases hepatic gluconeogenesis and citric acid cycle flux, accompanied by elevated glucose oxidation in the heart that compensates for impaired fatty acid oxidation. In contrast, skeletal muscle fluxes exhibit an overall reduction in substrate oxidation. These findings demonstrate the dichotomy in fuel utilization between cardiac and skeletal muscle during worsening metabolic disease and demonstrate the divergent effects of obesity on metabolic fluxes in different organs. This multi-tissue MFA technology can be extended to address important questions about in vivo regulation of metabolism and its dysregulation in disease, which cannot be fully answered through studies of single organs or isolated cells/tissues.

Keywords:  CP: Metabolism; cardiac metabolism; fluxomics; isotope labeling; liver metabolism; metabolic flux analysis; metabolomics; muscle metabolism; obesity; steatotic liver disease; systems biology

DOI:  https://doi.org/10.1016/j.celrep.2025.115591
J Vis Exp. 2025 Mar 28.

Analyzing Ex Vivo Metabolic Flux in Splenic and Cardiac Macrophages and Bone Marrow Monocytes.

Erin B Taylor, Robert W Spitz, Katherine R O'Quinn, Alan J Mouton.

Metabolic reprogramming is a hallmark of monocyte/macrophage activation and polarization between pro- and anti-inflammatory states. For example, pro-inflammatory (i.e., M1-like) monocytes/macrophages display more reliance on anaerobic glycolysis and less reliance on mitochondrial oxidative phosphorylation, whereas anti-inflammatory (M2-like) macrophages display more reliance on glucose and fatty acid oxidation in the mitochondria. Here, we describe in-depth protocols for extracting macrophages from the two major monocyte/macrophage reservoirs in the body, the spleen and bone marrow, as well as injured tissues such as the heart following myocardial infarction. Macrophages or monocytes are extracted by immunomagnetic sorting by using antibody-tagged microbeads, which easily bind to cells without compromising their phenotypes. The extracted cells are then cultured in 96-well plates, followed by extracellular flux analysis using a metabolic flux analyzer. Both glycolysis and mitochondrial oxidative phosphorylation can be measured simultaneously in small numbers of cells (as little as 2-3 × 105 cells). This method can easily be performed in 1 day and produces reliable and repeatable results. Ultimately, these methods help to enhance our understanding of metabolic changes during immune and inflammatory responses to injury and disease, which could lead to the development of novel therapeutic targets for immunometabolic pathways.

DOI: https://doi.org/10.3791/67824
Methods Mol Biol. 2025 ;2904 259-271

Metabolic Profiling of Activated T Lymphocytes Using Single-Cell Energetic Metabolism by Profiling Translation Inhibition (SCENITH).

Katrin Sinning, Sophia M Hochrein, Gabriela F Gubert, Martin Vaeth.

  Metabolic reprogramming is increasingly recognized as a fundamental aspect of T cell activation, influencing the differentiation, proliferation, and effector functions of lymphocytes. Measuring and screening the metabolic states of activated T cells provide insights into the dynamic interplay between cellular metabolism and immune function. In the following chapter, we provide a simple protocol based on the publication of Argüello et al. [1] to analyze the metabolic state of activated T cells at the single-cell level using standard flow cytometry.

Keywords:  FACS; Glycolysis; Metabolism; Oxidative phosphorylation; SCENITH; T cells

DOI:  https://doi.org/10.1007/978-1-0716-4414-0_18
FASEB J. 2025 Apr 30. 39(8): e70520

Metabolic Reprogramming of Glycolysis, Lipids, and Amino Acids in Tumors: Impact on CD8+ T Cell Function and Targeted Therapeutic Strategies.

Panping Liang, Zedong Li, Zhengwen Chen, Zehua Chen, Tao Jin, Fengjun He, Xiaolong Chen, Hongfeng Gou, Kun Yang.

  Tumor cells undergo metabolic reprogramming to support their rapid proliferation and to adapt to the challenges of the tumor microenvironment (TME). This involves significant changes in glycolysis, lipid, and amino acid metabolism, which not only promote tumor survival but also impact CD8+ T cells within the TME. This review examines how these metabolic alterations affect CD8+ T cell function, particularly through competition for energy resources and microenvironmental changes. For instance, aerobic glycolysis in tumor cells depletes glucose and leads to lactate accumulation, both of which suppress CD8+ T cell activity. Additionally, changes in lipid metabolism affect the composition of cell membranes and disrupt signal transduction, impairing T cell function. Amino acid reprogramming, such as increased consumption of glutamine and arginine by tumor cells, further hinders the activity and proliferation of CD8+ T cells. We also explore therapeutic strategies that target these metabolic pathways in tumor cells, such as inhibitors of glycolysis and fatty acid synthesis, which may enhance the antitumor activity of CD8+ T cells. These approaches show promise in improving both T cell function and the effectiveness of immune checkpoint blockade therapies. By investigating the link between tumor metabolism and CD8+ T cell dysfunction, this review highlights mechanisms of tumor immune evasion. This understanding can guide the development of novel immunotherapies aimed at enhancing T cell function within the TME.

Keywords:  CD8+ T cell; fatty acids; glutamine; glycolysis; metabolic reprogramming

DOI:  https://doi.org/10.1096/fj.202403019R
J Cell Biol. 2025 May 05. pii: e202503010. [Epub ahead of print]224(5):

Mitochondrial mayhem: Disrupting conserved N-terminal motifs in TANGO2 impacts its localization and function.

Sarah E Sandkuhler, Samuel J Mackenzie.

TANGO2 deficiency in humans leads to progressive neurological impairment, punctuated by life-threatening metabolic crises. In this issue, Lujan and colleagues demonstrate that TANGO2 localizes within the mitochondrial lumen and binds acyl-CoA species, potentially implicating it as a lipid trafficking protein.

DOI: https://doi.org/10.1083/jcb.202503010
Trends Immunol. 2025 Apr 11. pii: S1471-4906(25)00058-4. [Epub ahead of print]

The unusual metabolism of germinal center B cells.

Caitlin J Gracie, Robert Mitchell, Julia C Johnstone, Alexander J Clarke.

  In the germinal center (GC), B cells undergo rounds of somatic hypermutation (SHM), proliferation, and positive selection to develop into high-affinity, long-lived plasma cells and memory B cells. It is well established that, upon activation, B cells significantly alter their metabolism, but until recently little was understood about their metabolism within the GC. In this review we discuss novel in vivo models in which GC B cell (GCBC) metabolism is disrupted; these have greatly increased our understanding of B cell metabolic phenotype. GCBCs are unusual in that, unlike almost all other rapidly proliferating immune cells, they use little glycolysis but prefer fatty acid oxidation (FAO) to fuel ATP synthesis, whilst preferentially utilizing glucose and amino acids as carbon and nitrogen sources for biosynthetic pathways.

Keywords:  B cell; germinal center; metabolism

DOI:  https://doi.org/10.1016/j.it.2025.02.015
Methods Mol Biol. 2025 ;2904 91-113

Analysis of Store-Operated Ca2+ Entry in Primary T Cells.

Sara T Granados, Sergei Yanushkevich, Jessica Lok, Axel R Concepcion.

  Calcium ions (Ca2+) are key second messengers for signal transduction in virtually all cells. In T cells, Ca2+ signals are generated upon T cell receptor (TCR) stimulation in a two-step integrated process known as Store-Operated Ca2+ Entry (SOCE), which involves the depletion of endoplasmic reticulum (ER) Ca2+ stores, followed by the influx of extracellular Ca2+ via Ca2+ release-activated Ca2+ (CRAC) channels. The Ca2+ influx generated by the opening of CRAC channels in T cells is essential for their metabolic reprogramming, proliferation, cytokine production, and adaptive immune response.In this book chapter, we review general concepts, discuss the rationale for using ratiometric Ca2+-sensitive chemical dyes to monitor SOCE in primary murine T cells, and weigh the advantages and disadvantages of the different methods that are currently available to detect cytosolic Ca2+ dynamics. We provide detailed protocols to measure SOCE in mouse T cells including flow cytometry, fluorescent microplate reader and single-cell imaging, and offer a general guideline on how to quantify SOCE in these cells. These protocols are easily adaptable to monitor cytosolic Ca2+ dynamics in human T cells and other cell types of interest.

Keywords:  Ca2+ signaling; FlexStation 3; Flow cytometry; Single-cell imaging; Store-Operated Ca2+ Entry; T cells

DOI:  https://doi.org/10.1007/978-1-0716-4414-0_7
Annu Rev Nutr. 2025 Apr 18.

Progress in Understanding the Regulation of Glucose and Fructose Metabolism.

Meng Zhao, Jameel Lone, Saranya Reghupaty, Karen Yasmin Linde-Garelli, Katrin J Svensson.

Hexoses, including glucose, fructose, and galactose, are six-carbon monosaccharides that play fundamental roles in mammalian metabolism, with glucose serving as the primary energy source and fructose and galactose metabolized through pathways converging with glucose metabolism. While glucose metabolism has been extensively studied over the past hundred years, the mechanisms of fructose metabolism and uptake, the transporters involved, and its roles in physiology and disease are far less explored. Recent data also suggest that excessive fructose intake can have detrimental effects on metabolic organs, including the liver. Emerging studies have uncovered novel regulatory mechanisms in glucose and fructose metabolism, including the role of posttranslational modifications of transporters and enzymes, and the discovery of regulators of transporters. Here, we highlight new findings on the regulation of glucose and fructose transporters and integrate recent molecular and clinical insights into how glucose and fructose contribute to metabolic diseases.

DOI: https://doi.org/10.1146/annurev-nutr-111824-012939
Biochim Biophys Acta Mol Basis Dis. 2025 Apr 10. pii: S0925-4439(25)00184-X. [Epub ahead of print] 167839

Mitochondrial classic metabolism and its often-underappreciated facets.

João P Moura, Paulo J Oliveira, Ana M Urbano.

  For many decades, mitochondria were essentially regarded as the main providers of the adenosine triphosphate (ATP) required to maintain the viability and function of eukaryotic cells, thus the widely popular metaphor "powerhouses of the cell". Besides ATP generation - via intermediary metabolism - these organelles have also traditionally been known, albeit to a lesser degree, for their notable role in biosynthesis, both as generators of biosynthetic intermediates and/or as the sites of biosynthesis. From the 1990s onwards, the concept of mitochondria as passive organelles providing the rest of the cell, from which they were otherwise isolated, with ATP and biomolecules on an on-demand basis has been challenged by a series of paradigm-shifting discoveries. Namely, it was shown that mitochondria act as signaling effectors to upregulate ATP generation in response to growth-promoting stimuli and that they are actively engaged, through signaling and epigenetics, in the regulation of a plethora of cellular processes, ultimately deciding cell function and fate. With the focus of mitochondrial research increasingly placed in these "non-classical" functions, the centrality of mitochondrial intermediary metabolism to biosynthesis and other mitochondrial functions tends to be overlooked. In this article, we revisit mitochondrial intermediary metabolism and illustrate how its intermediates, by-products and molecular machinery underpin other mitochondrial functions. A certain emphasis is given to frequently overlooked functions, namely the biosynthesis of iron‑sulfur (FeS) clusters, the only known function shared by all mitochondria and mitochondrion-related organelles. The generation of reactive oxygen species (ROS) and their putative role in signaling is also discussed in detail.

Keywords:  Educational article; Intermediary metabolism; Iron‑sulfur clusters; Metabolic energy; Mitochondrion-related organelles; ROS signaling

DOI:  https://doi.org/10.1016/j.bbadis.2025.167839
Sci Adv. 2025 Apr 18. 11(16): eadw1489

Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier.

Maximilian Sichrovsky, Denis Lacabanne, Jonathan J Ruprecht, Jessica J Rana, Klaudia Stanik, Mariangela Dionysopoulou, Alice P Sowton, Martin S King, Scott A Jones, Lee Cooper, Steven W Hardwick, Giulia Paris, Dimitri Y Chirgadze, Shujing Ding, Ian M Fearnley, Shane M Palmer, Els Pardon, Jan Steyaert, Vanessa Leone, Lucy R Forrest, Sotiria Tavoulari, Edmund R S Kunji.

The mitochondrial pyruvate carrier transports pyruvate, produced by glycolysis from sugar molecules, into the mitochondrial matrix, as a crucial transport step in eukaryotic energy metabolism. The carrier is a drug target for the treatment of cancers, diabetes mellitus, neurodegeneration, and metabolic dysfunction-associated steatotic liver disease. We have solved the structure of the human MPC1L/MPC2 heterodimer in the inward- and outward-open states by cryo-electron microscopy, revealing its alternating access rocker-switch mechanism. The carrier has a central binding site for pyruvate, which contains an essential lysine and histidine residue, important for its ΔpH-dependent transport mechanism. We have also determined the binding poses of three chemically distinct inhibitor classes, which exploit the same binding site in the outward-open state by mimicking pyruvate interactions and by using aromatic stacking interactions.

DOI: https://doi.org/10.1126/sciadv.adw1489
J Mol Biol. 2025 Apr 11. pii: S0022-2836(25)00217-7. [Epub ahead of print] 169151

Autophagy, ER-phagy and ER dynamics during cell differentiation.

Michele Cillo, Viviana Buonomo, Anna Vainshtein, Paolo Grumati.

  The endoplasmic reticulum (ER) is a multifunctional organelle essential for protein and lipid synthesis, ion transport and inter-organelle communication. It comprises a highly dynamic network of membranes that continuously reshape to support a wide range of cellular processes. During cellular differentiation, extensive remodelling of both ER architecture and its proteome is required to accommodate alterations in cell morphology and function. Autophagy, and ER-phagy in particular, plays a pivotal role in reshaping the ER, enabling cells to meet their evolving needs and adapt to developmental cues. Despite the ER's critical role in cellular differentiation, the mechanisms responsible for regulating its dynamics are not fully understood. Emerging evidence suggests that transcriptional and post-translational regulation play a role in fine-tuning ER-phagy and the unfolded protein response (UPR). This review explores the molecular basis of autophagy and ER-phagy, highlighting their role in ER remodelling during cellular differentiation. A deeper understanding of these processes could open new avenues for targeted therapeutic approaches in conditions where ER remodelling is impaired.

Keywords:  Cell Differentiation; Development; Endoplasmic Reticulum

DOI:  https://doi.org/10.1016/j.jmb.2025.169151
Cell Death Dis. 2025 Apr 17. 16(1): 309

SLC25A42 promotes gastric cancer growth by conferring ferroptosis resistance through enhancing CPT2-mediated fatty acid oxidation.

Haoying Wang, Weijia Dou, Mengxiao Liu, Weifang Wang, Ying Yang, Jibin Li, Zhenxiong Liu, Nan Wang.

Accumulating evidence has shown that the dysfunction of mitochondria, the multifunctional organelles in various cellular processes, is a pivotal event in the development of various diseases, including human cancers. Solute Carrier Family 25 Member 42 (SLC25A42) is a mitochondrial protein governing the transport of coenzyme A (CoA). However, the biological roles of SLC25A42 in human cancers are still unexplored. Here we uncovered that SLC25A42 is upregulated and correlated with a worse prognosis in GC patients. SLC25A42 promotes the proliferation of gastric cancer (GC) cells while suppresses apoptosis in vitro and in vivo. Mechanistically, SLC25A42 promotes the growth and inhibits apoptosis of GC cells by reprograming lipid metabolism. On the one hand, SLC25A42 enhances fatty acid oxidation-mediated mitochondrial respiration to provide energy for cell survival. On the other hand, SLC25A42 decreases the levels of free fatty acids and ROS to inhibit ferroptosis. Moreover, we found that SLC25A42 reprograms lipid metabolism in GC cells by upregulating the acetylation and thus the expression of CPT2. Collectively, our data reveal a critical oncogenic role of SLC25A42 in GCs and suggest that SLC25A42 represent a promising therapeutic target for GC.

DOI: https://doi.org/10.1038/s41419-025-07644-7
bioRxiv. 2025 Apr 01. pii: 2025.03.31.646474. [Epub ahead of print]

Mitochondrial function regulates cell growth kinetics to actively maintain mitochondrial homeostasis.

Leeba Ann Chacko, Hidenori Nakaoka, Richard Morris, Wallace Marshall, Vaishnavi Ananthanarayanan.

Mitochondria are not produced de novo in newly divided daughter cells, but are inherited from the mother cell during mitosis. While mitochondrial homeostasis is crucial for living cells, the feedback responses that maintain mitochondrial volume across generations of dividing cells remain elusive. Here, using a microfluidic yeast 'mother machine', we tracked several generations of fission yeast cells and observed that cell size and mitochondrial volume grew exponentially during the cell cycle. We discovered that while mitochondrial homeostasis relied on the 'sizer' mechanism of cell size maintenance, mitochondrial function was a critical determinant of the timing of cell division: cells born with lower than average amounts of mitochondria grew slower and thus added more mitochondria before they divided. Thus, mitochondrial addition during the cell cycle was tailored to the volume of mitochondria at birth, such that all cells ultimately contained the same mitochondrial volume at cell division. Quantitative modelling and experiments with mitochondrial DNA-deficient rho0 cells additionally revealed that mitochondrial function was essential for driving the exponential growth of cells. Taken together, we demonstrate a central role for mitochondrial activity in dictating cellular growth rates and ensuring mitochondrial volume homeostasis.

DOI: https://doi.org/10.1101/2025.03.31.646474
Cell Rep Methods. 2025 Apr 08. pii: S2667-2375(25)00063-3. [Epub ahead of print] 101027

Integrated analysis of transcriptional and metabolic responses to mitochondrial stress.

Liam P Kelley, Song-Hua Hu, Sarah A Boswell, Peter K Sorger, Alison E Ringel, Marcia C Haigis.

  Mitochondrial stress arises from a variety of sources, including mutations to mitochondrial DNA, the generation of reactive oxygen species, and an insufficient supply of oxygen or fuel. Mitochondrial stress induces a range of dedicated responses that repair damage and restore mitochondrial health. However, a systematic characterization of transcriptional and metabolic signatures induced by distinct types of mitochondrial stress is lacking. Here, we defined how primary human fibroblasts respond to a panel of mitochondrial inhibitors to trigger adaptive stress responses. Using metabolomic and transcriptomic analyses, we established integrated signatures of mitochondrial stress. We developed a tool, stress quantification using integrated datasets (SQUID), to deconvolute mitochondrial stress signatures from existing datasets. Using SQUID, we profiled mitochondrial stress in The Cancer Genome Atlas (TCGA) PanCancer Atlas, identifying a signature of pyruvate import deficiency in IDH1-mutant glioma. Thus, this study defines a tool to identify specific mitochondrial stress signatures, which may be applied to a range of systems.

Keywords:  CP: Metabolism; CP: Systems biology; cancer metabolism; integrated multi-omics; integrated stress response; metabolomics; mitochondria; mitochondrial stress response; mitochondrial unfolded protein response; stress signatures

DOI:  https://doi.org/10.1016/j.crmeth.2025.101027
Nat Commun. 2025 Apr 17. 16(1): 3401

Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering.

Koki Nakamura, Saeko Aoyama-Ishiwatari, Takahiro Nagao, Mohammadreza Paaran, Christopher J Obara, Yui Sakurai-Saito, Jake Johnston, Yudan Du, Shogo Suga, Masafumi Tsuboi, Makoto Nakakido, Kouhei Tsumoto, Yusuke Kishi, Yukiko Gotoh, Chulhwan Kwak, Hyun-Woo Rhee, Jeong Kon Seo, Hidetaka Kosako, Clint Potter, Bridget Carragher, Jennifer Lippincott-Schwartz, Franck Polleux, Yusuke Hirabayashi.

Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identify the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-electron tomography, and correlative light-electron microscopy. Single molecule tracking reveals highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and captures at MERCS. Overexpression of FKBP8 is sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrate their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.

DOI: https://doi.org/10.1038/s41467-025-58538-3
Sci Rep. 2025 Apr 14. 15(1): 12782

Identification of serum metabolite biomarkers and metabolic reprogramming mechanisms to predict recurrence in cholangiocarcinoma.

Piya Prajumwongs, Attapol Titapun, Vasin Thanasukarn, Apiwat Jareanrat, Natcha Khuntikeo, Nisana Namwat, Poramate Klanrit, Arporn Wangwiwatsin, Jarin Chindaprasirt, Supinda Koonmee, Prakasit Sa-Ngiamwibool, Nattha Muangritdech, Sittiruk Roytrakul, Watcharin Loilome.

  Cholangiocarcinoma (CCA) has high recurrence rates that severely limit long-term survival. Effective tools for accurate recurrence monitoring and diagnosis remain lacking. Metabolic reprogramming, a key driver of CCA growth and recurrence, is underutilized in cancer screening and management. This study aimed to identify metabolite-based biomarkers to evaluate recurrence severity, enhance disease management, and elucidate the molecular mechanisms underlying CCA recurrence. A comprehensive, non-targeted serum metabolomics analysis using ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry was conducted. Support Vector Machine (SVM) modeling was employed to develop a predictive framework based on metabolite biomarkers. The analysis revealed significant alterations in metabolomics and lipidomics across CCA recurrence subtypes. Notably, changes in metabolites such as amino acids, lipid-derived carnitines, and glycerophospholipids were associated with cancer progression through enhanced energy production and lipid remodeling. The SVM-constructed metabolite-based predictive model demonstrated predictive accuracy comparable to current clinical diagnostic standards. These findings provide novel insights into the metabolic mechanisms underlying CCA recurrence, addressing critical clinical challenges. By advancing early diagnostic approaches, particularly for preoperative detection, this study offers a reliable method for predicting recurrence in CCA patients. This enables effective treatment planning and supports the development of personalized therapeutic strategies, ultimately improving patient outcomes.

Keywords:  Cholangiocarcinoma; Metabolic reprogramming; Metabolite biomarkers; Recurrence; Support vector machine

DOI:  https://doi.org/10.1038/s41598-025-97641-9
Sci Rep. 2025 Apr 15. 15(1): 13012

Distinct metabolome and flux responses in the retinal pigment epithelium to cytokines associated with age-related macular degeneration: comparison of ARPE-19 cells and eyecups.

David S Hansman, Kelly Lim, Daniel Thomas, Robert J Casson, Daniel J Peet.

  Age-related macular degeneration (AMD) is associated with chronic inflammation of the retinal pigment epithelium (RPE) and elevated cytokines including TNFα, TGF-β, IL-6, and IL-1β. As a metabolic intermediary supporting aerobic glycolysis in the adjacent photoreceptors, the RPE's metabolic responses to inflammation and the optimal methods to study cytokine-driven metabolic programming remain unclear. We performed a rigorous comparison of ARPE-19 cells and rat eyecup metabolomes, revealing key distinctions. Rat eyecups exhibit higher levels of lactate and palmitate but depleted glutathione and high-energy nucleotides. Conversely, ARPE-19 cells are enriched with high-energy currency metabolites and the membrane phospholipid precursors phosphocholine and inositol. Both models showed contrasting responses to individual cytokines: ARPE-19 cells were more sensitive to TNFα, while eyecups responded more strongly to TGF-β2. Notably, a combined cytokine cocktail elicited stronger metabolic effects on ARPE-19 cells, more potently impacting both metabolite abundance (41 vs. 29) and glucose carbon flux (29 vs. 5), and influencing key RPE metabolites such as alanine, glycine, aspartate, proline, citrate, α-ketoglutarate, and palmitate. Overall, these findings position ARPE-19 cells as a more responsive platform for studying inflammatory cytokine effects on RPE metabolism and reveal critical RPE metabolites which may be linked with AMD pathogenesis.

Keywords:  Age-related macular degeneration; Cytokines; Metabolic ecosystem; Metabolism; Retina inflammation; Retinal pigment epithelium

DOI:  https://doi.org/10.1038/s41598-025-93882-w
Cell Death Dis. 2025 Apr 16. 16(1): 307

Loss of VHL-mediated pRb regulation promotes clear cell renal cell carcinoma.

Mercy Akuma, Minjun Kim, Chenxuan Zhu, Ellis Wiljer, Antoine Gaudreau-Lapierre, Leshan D Patterson, Lars Egevad, Simon Tanguay, Laura Trinkle-Mulcahy, William L Stanford, Yasser Riazalhosseini, Ryan C Russell.

The von Hippel-Lindau (VHL) tumor suppressor is a substrate-defining component of E3 ubiquitin ligase complexes that target cellular substrates for proteasome-mediated degradation. VHL inactivation by mutation or transcriptional silencing is observed in most sporadic cases of clear cell renal cell carcinoma (ccRCC). VHL loss in ccRCC leads to constitutive stabilization of E3 ligase substrates, including hypoxia inducible factor α (HIFα). HIFα stabilization upon VHL loss is known to contribute to ccRCC development through transactivation of hypoxia-responsive genes. HIF-independent VHL targets have been implicated in oncogenesis, although those mechanisms are less well-defined than for HIFα. Using proximity labeling to identify proteasomal-sensitive VHL interactors, we identified retinoblastoma protein (pRb) as a novel substrate of VHL. Mechanistically, VHL interacts with pRb in a proteasomal-sensitive manner, promoting its ubiquitin-mediated degradation. Concordantly, VHL-inactivation results in pRb hyperstabilization. Functionally, loss of pRb in ccRCC led to increased cell death, transcriptional changes, and loss of oncogenic properties in vitro and in vivo. We also show that downstream transcriptional changes induced by pRb hyperstabilization may contribute to ccRCC tumor development. Together, our findings reveal a novel VHL-related pathway which can be therapeutically targeted to inhibit ccRCC tumor development.

DOI: https://doi.org/10.1038/s41419-025-07623-y
Cell Metab. 2025 Apr 09. pii: S1550-4131(25)00207-4. [Epub ahead of print]

Spatial regulation of glucose and lipid metabolism by hepatic insulin signaling.

Baiyu He, Kyle D Copps, Oliver Stöhr, Beikl Liu, Songhua Hu, Shakchhi Joshi, Marcia C Haigis, Morris F White, Hao Zhu, Rongya Tao.

  Hepatic insulin sensitivity is critical for systemic glucose and lipid homeostasis. The liver is spatially organized into zones in which hepatocytes express distinct metabolic enzymes; however, the functional significance of this zonation to metabolic dysregulation caused by insulin resistance is undetermined. Here, we used CreER mice to selectively disrupt insulin signaling in periportal (PP) and pericentral (PC) hepatocytes. PP-insulin resistance has been suggested to drive combined hyperglycemia and excess lipogenesis in individuals with type 2 diabetes. However, PP-insulin resistance in mice impaired lipogenesis and suppressed high-fat diet (HFD)-induced hepatosteatosis, despite elevated gluconeogenesis and insulin. In contrast, PC-insulin resistance reduced HFD-induced PC steatosis while preserving normal glucose homeostasis, in part by shifting glycolytic metabolism from the liver to the muscle. These results demonstrate distinct roles of insulin in PP versus PC hepatocytes and suggest that PC-insulin resistance might be therapeutically useful to combat hepatosteatosis without compromising glucose homeostasis.

Keywords:  de novo lipogenesis; gluconeogenesis; hepatic glucose production; insulin resistance; insulin signaling; lipid metabolism; liver zonation; pericentral hepatocytes; periportal hepatocytes

DOI:  https://doi.org/10.1016/j.cmet.2025.03.015
Nat Commun. 2025 Apr 16. 16(1): 3306

Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis.

Kira A Young, Mohsen Hosseini, Jayna J Mistry, Claudia Morganti, Taylor S Mills, Xiurong Cai, Brandon T James, Griffin J Nye, Natalie R Fournier, Veronique Voisin, Ali Chegini, Aaron D Schimmer, Gary D Bader, Grace Egan, Marc R Mansour, Grant A Challen, Eric M Pietras, Kelsey H Fisher-Wellman, Keisuke Ito, Steven M Chan, Jennifer J Trowbridge.

The competitive advantage of mutant hematopoietic stem and progenitor cells (HSPCs) underlies clonal hematopoiesis (CH). Drivers of CH include aging and inflammation; however, how CH-mutant cells gain a selective advantage in these contexts is an unresolved question. Using a murine model of CH (Dnmt3aR878H/+), we discover that mutant HSPCs sustain elevated mitochondrial respiration which is associated with their resistance to aging-related changes in the bone marrow microenvironment. Mutant HSPCs have DNA hypomethylation and increased expression of oxidative phosphorylation gene signatures, increased functional oxidative phosphorylation capacity, high mitochondrial membrane potential (Δψm), and greater dependence on mitochondrial respiration compared to wild-type HSPCs. Exploiting the elevated Δψm of mutant HSPCs, long-chain alkyl-TPP molecules (MitoQ, d-TPP) selectively accumulate in the mitochondria and cause reduced mitochondrial respiration, mitochondrial-driven apoptosis and ablate the competitive advantage of HSPCs ex vivo and in vivo in aged recipient mice. Further, MitoQ targets elevated mitochondrial respiration and the selective advantage of human DNMT3A-knockdown HSPCs, supporting species conservation. These data suggest that mitochondrial activity is a targetable mechanism by which CH-mutant HSPCs gain a selective advantage over wild-type HSPCs.

DOI: https://doi.org/10.1038/s41467-025-57238-2
J Neurosci. 2025 Apr 14. pii: e0110252025. [Epub ahead of print]

Mitochondrial glutamine metabolism drives epileptogenesis in primary hippocampal neurons.

Helmut Kubista, Francesco Gentile, Klaus Schicker, Thomas Köcher, Stefan Boehm, Matej Hotka.

All available anti-seizure medications aim at symptomatic control of epilepsy, but there is no strategy to stop the development of the disease. The main reason is the lack of understanding of the epileptogenic mechanisms. Closing this knowledge gap is an essential prerequisite for developing disease-modifying therapies that can prevent the onset of epilepsy. Using primary co-cultures of hippocampal neurons and glial cells derived from rat pups of either sex, we show that epileptiform paroxysmal depolarization shifts (PDS) induce neuronal glucose hypometabolism which is compensated for by increased glutaminolysis. Glutaminolysis not only provides sufficient ATP to support electrical activity, but also leads to decreased vesicular glutamate release, thereby promoting neuronal hypersynchrony. Moreover, prolonged promotion of PDS increased neuronal arborization and synaptic density, which in combination with spontaneous recovery of neuronal glucose metabolism led to seizure-like discharge activity. Since inhibition of glutaminolysis did not prevent the PDS-induced morphogenesis, but eliminated seizure-like activity, we propose that glutaminolysis is a causative process linking neuronal metabolism with electrical activity thereby driving epileptogenesis.Significance statement The available pharmacotherapy for epilepsy provides symptomatic control of seizures by interfering with ictogenesis. However, understanding the preceding epileptogenic processes would offer an opportunity to intervene in the development of the disease. The electrical activity and glucose metabolism of the brain regions corresponding to the epileptic foci are disturbed long before the first seizures occur. The significance of the altered neuronal activity and metabolism is not well understood. We present evidence that abnormal neuronal electrical activity called paroxysmal depolarization shifts increase neuronal arborization and lead to metabolic shifts making neurons transiently rely on glutamine. We show that the interplay of these processes induces glucose hypometabolism, hyper-synchronization, and ultimately leads to seizure-like discharge activity, thus replicating several key features of epilepsy.

DOI: https://doi.org/10.1523/JNEUROSCI.0110-25.2025