bims-medica Biomed News
on Metabolism and diet in cancer
Issue of 2025–10–12
sixteen papers selected by
Brett Chrest, Wake Forest University



  1. J Cachexia Sarcopenia Muscle. 2025 Oct;16(5): e70090
       BACKGROUND: The coupling of oxygen consumption to ATP synthesis via oxidative phosphorylation (OXPHOS) is central for cellular energy homeostasis. Some studies suggest exercise training increases the efficiency of ATP synthesis, but the molecular mechanisms are unclear. We have previously shown that exercise remodels the lipid composition of mitochondrial membranes, and some of these changes in mitochondrial lipids might influence OXPHOS efficiency (ATP produced per O2 consumed, referred to as P/O). Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) is a transcriptional co-activator that coordinately regulates exercise-induced adaptations, including mitochondria. We hypothesized that increased PGC-1α activity might remodel mitochondrial membrane lipids and promote energy efficiency.
    METHODS: Mice with skeletal muscle-specific overexpression of PGC-1α (MCK-PGC-1α) and their wildtype littermates were used for this study. Lipid mass spectrometry and quantitative PCR were used to assess muscle mitochondrial lipid composition and their biosynthesis pathway. The abundance of OXPHOS enzymes was determined by Western blotting. High-resolution respirometry and fluorometry analyses were performed to characterize mitochondrial bioenergetics (ATP production, O2 consumption and P/O) for permeabilized fibres and isolated mitochondria. Respiratory supercomplexes were assessed by blue native PAGE.
    RESULTS: Lipidomic analyses of skeletal muscle mitochondria from wildtype and MCK-PGC-1α mice revealed that PGC-1α increases the concentrations of cone-shaped lipids such as phosphatidylethanolamine (PE; +25%, p < 0.0001), cardiolipin (CL; +184%, p < 0.0001) and lysophospholipids (+34%-94%, all p < 0.01), while decreasing the concentrations of phosphatidylcholine (PC; -4%, p = 0.0020), phosphatidylinositol (PI; -17%, p < 0.0001) and phosphatidic acid (PA; -35%, p < 0.0001). However, while PGC-1α overexpression increased the abundance of OXPHOS enzymes (two- to fourfold, p < 0.0001), the rate of O2 consumption (1.5-fold, p = 0.0030), or the respiratory supercomplexes (~1.5-fold, p < 0.01), P/O values were unaffected by PGC-1α overexpression in permeabilized fibres or isolated mitochondria.
    CONCLUSIONS: Collectively, overexpression of PGC-1α promotes the biosynthesis of mitochondrial PE and CL, but neither PGC-1α nor the mitochondrial membrane lipid remodelling induced in MCK-PGC-1α mice is sufficient to increase the efficiency of mitochondrial ATP synthesis. These findings indicate that PGC-1α-dependent mechanisms or changes in mitochondrial membrane lipids may be insufficient to alter P/O. While muscles from MCK-PGC-1α mice are known not to completely phenocopy adaptations with exercise training, our findings also highlight that there is a need to examine whether exercise training indeed improves P/O in mouse skeletal muscle.
    Keywords:  exercise; mitochondria; phospholipids; skeletal muscle
    DOI:  https://doi.org/10.1002/jcsm.70090
  2. Nat Commun. 2025 Oct 08. 16(1): 8952
      Cancer cells have the unique capability to upregulate the de novo nucleotide biosynthesis supporting cell survival under nucleotide deprivation. We probe the role of metabolic channeling and membrane-less metabolic compartmentalization by mitochondria-proximal dynamic de novo pyrimidine and purine biosynthesis metabolons, the pyrimidinosome and the purinosome, respectively. We designed in-cell stable isotope label incorporation assays (13C6 glucose, 15N2 glutamine) for detection of metabolic channeling, revealing the function and enzymatic composition of these complexes. Moreover, we discovered that the mitochondrially compartmentalized GOT2 dependent generation of aspartic acid feeds the channeled nucleotide synthesis instead of the bulk cytosolic pool or the GOT1 activity. While a low flux diffusive pathway generates the pathway intermediates in an accumulative process, it's the channeled pathway that successfully generates the end product nucleotides. Our results demonstrate how metabolic channeling and efficient de novo nucleotide biosynthesis is fueled by coordination of mitochondrially compartmentalized metabolic events with cytosolic metabolons in cancer cells.
    DOI:  https://doi.org/10.1038/s41467-025-64013-w
  3. Proc Natl Acad Sci U S A. 2025 Oct 14. 122(41): e2519902122
      Glycolytic enzymes sense metabolite levels to adapt rapidly to changing energy demands, but measuring the levels of these effectors with spatiotemporal precision in live cells has been challenging. We addressed this question in the context of neuronal depolarization, which activates glycolysis, focusing on the glycolysis inhibitor citrate. We engineered a pair of quantitative fluorescent biosensors for citrate that address several limitations (affinity, pH, Mg2+, and temperature) of existing citrate biosensors. Using two-photon fluorescence lifetime imaging, we found that free citrate in the cytosol of neurons in acute mouse brain slices declines two-to-threefold within seconds of neuronal activation and then returns to baseline over a few minutes. The stimulation-dependent citrate transient depends at least in part on the mitochondrial calcium uniporter. These types of live metabolite measurements are essential for achieving a nuanced understanding of the fast control of glycolysis.
    Keywords:  fluorescence lifetime; genetically encoded fluorescent biosensor; glycolytic regulation; mitochondrial calcium uniporter
    DOI:  https://doi.org/10.1073/pnas.2519902122
  4. Cell Death Discov. 2025 Oct 06. 11(1): 430
      Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype characterized by high recurrence rates and limited treatment options due to the absence of hormone receptors. Despite advancements in breast cancer research, effective therapies for TNBC remain inadequate, highlighting the need to elucidate subtype-specific metabolic vulnerabilities. TNBC cells exhibit a strong dependence on the exogenous amino acids cystine and glutamine, yet the interplay between these metabolic dependencies remains poorly understood. Here, we demonstrate that TNBC cells exhibit sensitivity to individual nutrient deprivation but can survive dual cystine and glutamine deprivation via distinct mechanisms. Exogenous glutamine primarily fuels glutamine anaplerosis, supporting TNBC cell proliferation. Notably, when exogenous glutamine is absent, restricted cystine uptake restores intracellular glutamate levels, fulfilling metabolic demands and sustaining TNBC cell growth. Under cystine deprivation, inhibition of glutaminolysis rescues TNBC cells by mitigating lipid peroxidation and reducing ROS production, whereas supplementation with the TCA cycle intermediates ɑ-ketoglutarate (ɑ-KG) and succinate induces profound cell death in both TNBC and luminal breast cancer cells under glutaminolysis blockade. Collectively, these findings highlight the metabolic interdependence of glutamine and cystine in TNBC, providing mechanistic insights into potential metabolic-targeted and dietary interventions for TNBC therapy.
    DOI:  https://doi.org/10.1038/s41420-025-02714-3
  5. Metabolism. 2025 Oct 06. pii: S0026-0495(25)00282-3. [Epub ahead of print] 156413
      4'-Phosphopantetheinyl (4'PP) groups are essential co-factors added to target proteins by phosphopantetheinyl transferase (PPTase) enzymes. Although mitochondrial 4'PP-modified proteins have been described for decades, a mitochondrially-localized PPTase has never been found in mammals. We discovered that the cytoplasmic PPTase aminoadipate semialdehyde dehydrogenase phosphopantetheinyl transferase (AASDHPPT) is required for mitochondrial respiration and oxidative metabolism. Loss of AASDHPPT results in failed 4'PP modification of the mitochondrial acyl carrier protein and blunted activity of the mitochondrial fatty acid synthesis (mtFAS) pathway. We found that in addition to its cytoplasmic localization, AASDHPPT localizes to the mitochondrial matrix via an N-terminal mitochondrial targeting sequence contained within the first 20 amino acids of the protein. Our data show that this novel mitochondrial localization of AASDHPPT is required to support mtFAS activity and oxidative metabolism. We further identify five variants of uncertain significance in AASDHPPT that are likely pathogenic in humans due to loss of mtFAS activity.
    Keywords:  Electron transport chain; Fatty acid synthesis; Metabolism; Mitochondria; Phosphopantetheine; Reductive carboxylation; Respiration
    DOI:  https://doi.org/10.1016/j.metabol.2025.156413
  6. Cancer Med. 2025 Oct;14(19): e71291
       BACKGROUND: RT4 bladder cancer cell line, derived from a nonmuscle-invasive low-grade subtype, is one of the few neoplastic cell lineages that maintain high expression of the candidate tumor suppressor ALDH1L1. Here, we investigated how differential ALDH1L1 expression affects cellular characteristics and tumorigenicity of RT4 cells as well as tumor metabotypes.
    METHODS: We characterized RT4 cells and two shRNA clones (sh506/low ALDH1L1 expression; sh572/ALDH1L1 is lost) for proliferation, migration, clonogenic capacity, and mitochondrial respiration. We have further evaluated the tumorigenic potential of RT4 cells and the two clones in nude mice and compared metabotypes of derived tumors using untargeted metabolomics.
    RESULTS: Both clones with diminished ALDH1L1 expression exhibited increased proliferation rates with doubling times of 19.4 h (sh506) and 23.2 h (sh572) versus 36.3 h for RT4 cells. Downregulation of ALDH1L1 expression also enhanced motility and clonogenic capacity. Proliferation and clonogenic capacity were highest for the sh506 clone (low ALDH1L1 expression), while motility was strongest for the sh572 clone (complete ALDH1L1 loss). Both clones showed altered energy metabolism, as indicated by a reduced basal oxygen consumption rate and enhanced maximal respiration rate following oligomycin treatment. Mouse xenograft tumors derived from ALDH1L1-deficient RT4 clones were significantly larger than RT4 cell-derived tumors. Of note, complete ALDH1L1 loss (sh572 clone) was less advantageous for tumor growth than the partial loss of the protein (sh506 clone). Untargeted metabolomics has shown that tumors with downregulated ALDH1L1 have altered the metabolism of fatty acids, amino acids, CoA, and acylcarnitines. Alterations in several key pathways, including glutathione metabolism (sh506), and TCA cycle (sh572), depend on the extent of ALDH1L1 downregulation.
    CONCLUSIONS: Our study underscores ALDH1L1 as a key metabolic regulator of proliferation, migration, and tumorigenicity in RT4 bladder cancer cells, suggesting that retaining low ALDH1L1 expression can provide a metabolic advantage for growth of aggressive tumors.
    Keywords:   ALDH1L1 ; RT4 bladder cancer cells; one‐carbon metabolism; untargeted metabolomics; xenograft tumors
    DOI:  https://doi.org/10.1002/cam4.71291
  7. FEBS Lett. 2025 Oct 10.
      Respiratory complex I (CI) is a multi-subunit membrane protein complex important for the production of ATP via the oxidative phosphorylation pathway. The structure of CI is roughly conserved across species and is composed of subunits that are either embedded in the membrane or are exposed to the aqueous environment that together form an overall L-shaped 'boot'. The conserved core of CI is generally composed of 14 subunits. Across species, various less conserved 'supernumerary' or 'accessory' subunits have been added. Accessory subunits vary in number across species and can include proteins that are unique to specific lineages. Additionally, there are structural variations in the core subunits between clades. In this Review, we compare seven representative CI structures from divergent eukaryotic lineages to identify what aspects of the CI core subunits are susceptible to variation and classify eukaryotic accessory subunits into those conserved from the last eukaryotic common ancestor (LECA) or those that are lineage specific. Impact statement Understanding the biodiversity and evolution of mitochondrial complex I will reveal patterns that may reflect metabolic niche and can be used to constrain quantitative models of molecular evolution.
    Keywords:  OXPHOS; bioenergetics; cellular respiration; complex I; cryoEM structures; evolution; last eukaryotic common ancestor; metabolism; mitochondria
    DOI:  https://doi.org/10.1002/1873-3468.70181
  8. Science. 2025 Oct 09. 390(6769): eadp7603
      Malignant tumors are characterized by diverse metabolic stresses, including nutrient shortages, hypoxia, and buildup of metabolic by-products. To understand how cancer cells adapt to such challenges, we conducted sequential CRISPR screens to identify genes that affect cellular fitness under specific metabolic stress conditions in cell culture and to then probe their relevance in pancreatic tumors. Comparative analyses of hundreds of fitness genes revealed that cancer metabolism in vivo was shaped by bioenergetic adaptations to tumor acidosis. Mechanistically, acidosis suppressed cytoplasmic activity of extracellular signal-regulated kinase (ERK), thereby preventing oncogene-induced mitochondrial fragmentation and promoting fused mitochondria. The resulting boost in mitochondrial respiration supported cancer cell adaptations to various metabolic stresses. Thus, acidosis is an environmental factor that alters energy metabolism to promote stress resilience in cancer.
    DOI:  https://doi.org/10.1126/science.adp7603
  9. Front Nutr. 2025 ;12 1651993
       Introduction: Obesity is caused by excessive storage of adipose tissue and leads to metabolic disorders. Uridine exerts modulatory effects on lipid metabolism, but the regulatory mechanism in obesity needs further research.
    Methods: In this study, the effects of uridine supplementation on lipid metabolism were investigated in high-fat diet-induced obese mice. Mice aged at 8 weeks were randomly grouped to receive a control diet (CON, n = 10) or a high-fat diet (HF, n = 24). After 6 weeks of feeding, the HF group was further divided, with half receiving 0.4 mg/mL uridine supplementation in drinking water (HUR, n = 12) for an additional 4 weeks, while the remaining HF mice continued without intervention.
    Results: The results showed that the uridine supplement reduced the liver weight and intra-abdominal white adipose tissue weight in obese mice (p < 0.05). Treatment with uridine and free fatty acid resulted in a significant increase in late and total apoptosis, accompanied by a decrease in early apoptosis of mouse liver organoids (p < 0.05). Moreover, uridine lowered serum levels of triglycerides (TG), total cholesterol (TC), high-density lipoprotein (HDL), leptin, and liver TG content (p < 0.05). In obese mice fed with uridine, the expression of key genes involved in lipid transport [activated fatty acid translocase/cd36 (Fat/cd36) and low-density lipid receptor (Ldlr)], pyrimidine de novo synthesis [dihydroorotate dehydrogenase (Dhodh)], pyrimidine metabolism [uridine phosphorylase 2 (Upp2), ribonucleoside-diphosphate reductase subunit M2 (Rrm2), and thymidine kinase 1 (Tk1)] was improved (p < 0.05). Furthermore, liver metabolomic analysis identified 37 differential metabolites between the HF and HUR groups, primarily enriched in arachidonic acid metabolism and α-linolenic acid metabolism.
    Discussion: These findings indicated that uridine supplementation can improve lipid metabolism in obese mice by regulating hepatic gene expression and metabolic pathways.
    Keywords:  apoptosis; lipid metabolism; metabolomics; obese mice; uridine
    DOI:  https://doi.org/10.3389/fnut.2025.1651993
  10. Am J Physiol Cell Physiol. 2025 Oct 10.
      Skeletal muscle is the main consumer of glucose after a mixed meal, and resistance exercise further increases muscle glucose uptake. Emerging evidence suggests that glucose uptake in muscles is not only stored as glycogen or used as a fuel but can also be incorporated into other biomass during growth. We aimed to study the utilization of glucose-derived carbons for protein, RNA, and lipid synthesis during human skeletal muscle (HSkM) cell growth. We also investigated whether muscle growth in vivo by resistance training (RT) affects the abundance of metabolites and enzymes required for these processes in human muscle. We found that differentiated HSkM cells incorporated glucose-derived carbon into proteins, RNA, and lipids, and anabolic stimulation further increased these processes. Liquid chromatography-mass spectrometry metabolomics and proteomics revealed that 10 weeks of RT in humans increased essential metabolites and enzymes for nucleotide, serine, and glycine synthesis, including phosphoglycerate dehydrogenase (PHGDH) in muscle. We also examined whether the PHGDH enzyme, starting the serine synthesis pathway branching from glycolysis, is sufficient and essential for human muscle protein, RNA, and lipid anabolism. We found that PHGDH inhibitors decreased protein synthesis and glucose-derived carbon incorporation into macromolecules, whereas manipulation of PHGDH abundance had mixed effects. Moreover, PHGDH was revealed to be important for myogenesis. The data suggest that glucose is not only used for ATP generation but also as a building block in human muscle cell growth. The results open new avenues for studies investigating the mechanisms of RT and muscle growth in improving muscle glucose metabolism.
    Keywords:  Metabolomics; Myogenesis; PHGDH; Proteomics; Resistance training
    DOI:  https://doi.org/10.1152/ajpcell.00525.2025
  11. NPJ Metab Health Dis. 2024 May 27. 2(1): 6
      The ability of mitochondria to transform the energy we obtain from food into cell phosphorylation potential has long been appreciated. However, recent decades have seen an evolution in our understanding of mitochondria, highlighting their significance as key signal-transducing organelles with essential roles in immunity that extend beyond their bioenergetic function. Importantly, mitochondria retain bacterial motifs as a remnant of their endosymbiotic origin that are recognised by innate immune cells to trigger inflammation and participate in anti-microbial defence. This review aims to explore how mitochondrial physiology, spanning from oxidative phosphorylation (OxPhos) to signalling of mitochondrial nucleic acids, metabolites, and lipids, influences the effector functions of phagocytes. These myriad effector functions include macrophage polarisation, efferocytosis, anti-bactericidal activity, antigen presentation, immune signalling, and cytokine regulation. Strict regulation of these processes is critical for organismal homeostasis that when disrupted may cause injury or contribute to disease. Thus, the expanding body of literature, which continues to highlight the central role of mitochondria in the innate immune system, may provide insights for the development of the next generation of therapies for inflammatory diseases.
    DOI:  https://doi.org/10.1038/s44324-024-00008-3
  12. Eur J Neurosci. 2025 Oct;62(7): e70270
      Increasing plasma levels of ketone bodies via supplementation has been recently found to modulate the neurometabolic profile in the healthy human brain. Here, we aimed to explore the physiological consequences of these neurometabolic changes by assessing visual cortical function. Ten young adult human volunteers (mean age 27 years, range 23-34) were orally administered a single dose of a β-hydroxybutyrate (βHB) ester (one of the main ketone bodies), and we measured neurometabolic change after supplementation. We used Electroencephalography (EEG) to assess cortical responsivity to visual stimuli and endogenous rhythms, and magnetic resonance spectroscopy (MRS) to quantify glutamate and GABA+ concentrations in the occipital cortex. βHB supplementation increased the amplitude of steady-state visual evoked potentials and increased resting-state EEG alpha power (8-13 Hz). These electrophysiological changes were paralleled by an increase in glutamate (but not GABA+) concentration in the occipital cortex. The glutamate increase was correlated with the increased steady-state visual evoked potentials amplitude. This suggests that acute βHB supplementation increases the excitability of the brain cortex, as assessed neurometabolically and electrophysiologically. We discuss how these effects of acute supplementation may differ from the long-term effects of chronic interventions in healthy or pathological brains.
    Keywords:  GABA; glutamate; ketone bodies; magnetic resonance spectroscopy; steady‐state visual evoked potentials
    DOI:  https://doi.org/10.1111/ejn.70270
  13. STAR Protoc. 2025 Oct 08. pii: S2666-1667(25)00540-4. [Epub ahead of print]6(4): 104134
      Cellular metabolism dictates immune cell function, yet we lack tools to functionally profile immunometabolism in low-yield, complex samples. We present a flow cytometry-based protocol for measuring cellular energetics through noncanonical amino acid tagging (CENCAT) in human peripheral blood and murine tissue immune cells. We describe steps for sample preparation, metabolic inhibition, protein synthesis analysis using click chemistry, immunophenotyping, and calculation of metabolic dependencies. For complete details on the use and execution of this protocol, please refer to Vrieling et al.1.
    Keywords:  Cell Biology; Cell culture; Cell isolation; Flow Cytometry; Immunology; Metabolism; Molecular Biology; Molecular/Chemical Probes
    DOI:  https://doi.org/10.1016/j.xpro.2025.104134
  14. J Biol Chem. 2025 Oct 07. pii: S0021-9258(25)02648-1. [Epub ahead of print] 110796
      The gram-negative opportunistic pathogen Fusobacterium nucleatum encodes an electron transfer flavoprotein (ETF) within a 6-gene cluster that also includes genes for a D-lactate dehydrogenase (Ldh), butyryl-CoA dehydrogenase (Bcd), and LrgAB. Herein, we demonstrate that ETF functions as a canonical ETF, transferring two electrons from Ldh following oxidation of D-lactate to Bcd for the reduction of crotonyl-CoA to butyryl-CoA. Steady-state kinetic analysis of the LdhFN/ETFFN/BcdFN reaction (lactate + crotonyl-CoA → pyruvate + butyryl-CoA) yielded a kcat of 2.5 ± 0.1 s-1 and a KM of 0.65 ± 0.04 μM and 5.2 ± 0.5 μM for D-lactate and butyryl-CoA, respectively. As observed in homologous ETFs, the FAD cofactor of ETF forms the red anionic semiquinone (FAD•-) but the Eo' values (versus the normal hydrogen electrode) of -70 mV (FAD/FAD•-) and = -122 mV (FAD•-/FADH-) are more compressed and negative compared to other ETFs, indicating the flavoprotein is physiologically primed to accept two electrons from Ldh. Similarly, reductive titration of Ldh shows that its FAD cofactor also forms the red anionic semiquinone, but the Eo' values for FAD/FAD•- (-109 mV) and FAD•-/FADH- (-115 mV) are even more closely spaced. We discuss how F. nucleatum potentially uses this lactate utilization gene cluster to maintain redox homeostasis during oxidative stress and how beneficial gut anaerobes of the Lachnospiraceae family with similar gene clusters employ either a canonical or bifurcating ETF for the conversion of lactate (and acetate) to butyrate.
    Keywords:  D-lactate dehydrogenase; Fusobacterium nucleatum; LrgAB; butyryl-CoA dehydrogenase; electron transfer flavoprotein
    DOI:  https://doi.org/10.1016/j.jbc.2025.110796
  15. Nat Commun. 2025 Oct 08. 16(1): 8932
      Chemotherapy is often a primary treatment for cancer. However, resistance leads to therapeutic failure. Acetylation dynamics play important regulatory roles in cancer cells, but the mechanisms by which acetylation mediates therapy resistance remain poorly understood. Here, using acetylome-focused RNA interference (RNAi) screening, we find that acetylation induced by mitochondrial dihydrolipoyl transacetylase (DLAT), independent of the pyruvate dehydrogenase complex, is pivotal in promoting resistance to chemotherapeutics, such as cisplatin. Mechanistically, DLAT acetylates methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) at lysine 44 and promotes 10-formyl-tetrahydrofolate (10-formyl-THF) and consequent mitochondrially encoded cytochrome c oxidase II (MT-CO2) induction. DLAT signaling is elevated in cancer patients refractory to chemotherapy or chemoimmunotherapy. A decoy peptide DMp39, designed to target DLAT signaling, effectively sensitizes cancer cells to cisplatin in patient-derived xenograft models. Collectively, our study reveals the crucial role of DLAT in shaping chemotherapy resistance, which involves an interplay between acetylation signaling and metabolic reprogramming, and offers a unique decoy peptide technology to overcome chemotherapy resistance.
    DOI:  https://doi.org/10.1038/s41467-025-63892-3
  16. Trends Endocrinol Metab. 2025 Oct 06. pii: S1043-2760(25)00198-5. [Epub ahead of print]
      Methionine restriction (MetR) attenuates the severity of numerous age-related diseases and extends lifespan across multiple species. Implementing MetR in humans remains challenging due to the low palatability of MetR diets, unfavorable side effects associated with continuous dietary MetR, and interindividual variation in factors that can diminish its efficacy, including microbiota activity, compensatory effects from cysteine, and methionine transfer from neighboring cells. Several novel approaches that target methionine metabolism have been developed - including small molecules, synthetic biotics, and xenotopic tools - with some already translated into early-stage clinical trials. In this review, we discuss a variety of approaches that either produce or mimic MetR, as well as their potential applications for human healthspan improvement.
    Keywords:  MetR; MetR mimetics; SAAR; cancer; cysteine; healthspan; lifespan; metabolic health
    DOI:  https://doi.org/10.1016/j.tem.2025.09.006