bims-celmim 2025-05-25 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–05–25
twenty-two papers selected by
Marc Segarra Mondejar

Hepatic glutamic-oxaloacetic transaminase (GOT2) promotes mitochondrial respiration energized at complex II and alters whole body metabolism.
Metabolic Profiling of Tumor and Immune Cells Integrating Seahorse and Flow Cytometry.
De novo serine biosynthesis is protective in mitochondrial disease.
Adaptation of mitochondrial bioenergetics to coenzyme Q deficiency in human endothelial cells after chronic exposure to bisphosphonates.
Perturbation-response analysis of in silico metabolic dynamics revealed hard-coded responsiveness in the cofactors and network sparsity.
Adenine nucleotide translocase 2 silencing promotes metabolic reprogramming in P19 embryonal carcinoma stem cells.
Pex30-dependent membrane contact sites maintain ER lipid homeostasis.
Dynamic single-cell metabolomics reveals cell-cell interaction between tumor cells and macrophages.
Analysis of the Expression and Complexes Assembly of the Mitochondrial Respiratory Chain Proteins in the Fission Yeast Schizosaccharomyces pombe.
SMIM20 promotes complex IV biogenesis and Ca2+ signaling in mice heart.
Metabolomics and machine learning identify urine metabolic characteristics and potential biomarkers for severe Mycoplasma pneumoniae pneumonia.
A pathway to sight.
Dual Ribosome Profiling reveals metabolic limitations of cancer and stromal cells in the tumor microenvironment.
Loss of insulin signaling in microglia impairs cellular uptake of Aβ and neuroinflammatory response exacerbating AD-like neuropathology.
Mitochondrial aldehyde dehydrogenase restores the migratory capacity inhibited by high glucose-induced hyperosmolality.
Small-molecule inhibitors of 6-phosphofructo-1-kinase simultaneously suppress lactate and superoxide generation in cancer cells.
Image-guided targeting of mitochondrial metabolism sensitizes pediatric malignant rhabdoid tumors to low-dose radiotherapy.
Turn-on fluorescent glucose transport bioprobe enables wash-free real-time monitoring of glucose uptake activity in live cells and small organisms.
Unravelling cysteine-deficiency-associated rapid weight loss.
Phosphatidic acid drives spatiotemporal distribution of Pex30 at ER-LD contact sites.
Isocitrate dehydrogenase 1 primes group-3 medulloblastomas for cuproptosis.
Abiotic lipid metabolism enables membrane plasticity in artificial cells.

J Biol Chem. 2025 May 21. pii: S0021-9258(25)02111-8. [Epub ahead of print] 110261

Hepatic glutamic-oxaloacetic transaminase (GOT2) promotes mitochondrial respiration energized at complex II and alters whole body metabolism.

Brian D Fink, Ritu Som, Adam J Rauckhorst, Eric B Taylor, Liping Yu, William I Sivitz.

  The mitochondrial enzyme, glutamic-oxaloacetic transaminase (GOT2), catalyzes the reaction between oxaloacetate and glutamate generating aspartate and alpha-ketoglutarate (α-KG). Glutamate can also be directly converted to α-KG by glutamate dehydrogenase. We investigated mitochondrial and systemic effects of an inducible liver specific-mouse GOT2 knockout (KO). We observed no differences in body mass or percent fat mass in KO mice, however, KO mice had lower fasting glucose and liver tissue contained more fat. Respiration by liver mitochondria energized at complex II by succinate + glutamate was decreased in KO compared to wildtype (WT) mice at low inner membrane potential (ΔΨ) as induced by titration with ADP. Metabolite studies by NMR showed that at low versus high ΔΨ, GOT2KO mitochondria energized by succinate + glutamate generated more oxaloacetate (a potent inhibitor of succinate dehydrogenase, SDH) and less aspartate. Respiration and mitochondrial metabolites energized by pyruvate + malate or palmitoyl-carnitine + malate did not differ between KO and WT mice. Respiration by GOT2KO mitochondria energized by glutamate + malate was decreased at all levels of ΔΨ. Pathway analysis of LC-MS profile data in liver tissue of KO versus WT mice revealed differential enrichment of the malate aspartate shuttle, TCA cycle, aspartate metabolism, glutamate metabolism, and gluconeogenesis. In summary, GOT2KO impaired potential-dependent complex II energized O2 flux likely due at least in part to oxaloacetate inhibition of SDH.

Keywords:  Mitochondria; glutamic-oxaloacetic transaminase-2; liver; mitochondrial complex II; mitochondrial inner membrane potential; oxaloacetate; respiration; succinate dehydrogenase

DOI:  https://doi.org/10.1016/j.jbc.2025.110261
Methods Mol Biol. 2025 ;2930 103-126

Metabolic Profiling of Tumor and Immune Cells Integrating Seahorse and Flow Cytometry.

Nienke B Goedhart, Helga Simon-Molas.

  Studying metabolism in the different cellular compartments of the tumor microenvironment (TME) is crucial to identify the specific metabolic signatures that contribute to tumor progression. Additionally, TME-driven metabolic changes can disrupt the essential metabolic processes involved in immune cell function, hindering immunotherapy success. Extracellular flux analysis (Seahorse) is a well-established approach used to characterize cellular metabolism. When combined with flow cytometry-based measurements, it offers a comprehensive view of the metabolic signatures within the different cellular compartments of the TME. Here we provide a detailed description on the procedures of Seahorse analysis and complementary flow cytometry-based metabolic readouts on tumor cells and T cells in the context of cancer, which can also be applied to other physiological and pathological situations.

Keywords:  Extracellular flux analysis; Flow cytometry; Immunotherapy; Metabolism; Mitochondria; Tumor microenvironment

DOI:  https://doi.org/10.1007/978-1-0716-4558-1_9
Cell Rep. 2025 May 15. pii: S2211-1247(25)00481-4. [Epub ahead of print]44(5): 115710

De novo serine biosynthesis is protective in mitochondrial disease.

Christopher B Jackson, Anastasiia Marmyleva, Geoffray Monteuuis, Ryan Awadhpersad, Takayuki Mito, Nicola Zamboni, Takashi Tatsuta, Amy E Vincent, Liya Wang, Nahid A Khan, Thomas Langer, Christopher J Carroll, Anu Suomalainen.

  The importance of serine as a metabolic regulator is well known for tumors and is also gaining attention in degenerative diseases. Recent data indicate that de novo serine biosynthesis is an integral component of the metabolic response to mitochondrial disease, but the roles of the response have remained unknown. Here, we report that glucose-driven de novo serine biosynthesis maintains metabolic homeostasis in energetic stress. Pharmacological inhibition of the rate-limiting enzyme, phosphoglycerate dehydrogenase (PHGDH), aggravated mitochondrial muscle disease, suppressed oxidative phosphorylation and mitochondrial translation, altered whole-cell lipid profiles, and enhanced the mitochondrial integrated stress response (ISRmt) in vivo in skeletal muscle and in cultured cells. Our evidence indicates that de novo serine biosynthesis is essential to maintain mitochondrial respiration, redox balance, and cellular lipid homeostasis in skeletal muscle with mitochondrial dysfunction. Our evidence implies that interventions activating de novo serine synthesis may protect against mitochondrial failure in skeletal muscle.

Keywords:  CP: Metabolism; de novo serine synthesis; mitochondrial disease; mitochondrial integrated stress response; mitochondrial translation; tissue specificity; treatment

DOI:  https://doi.org/10.1016/j.celrep.2025.115710
Sci Rep. 2025 May 22. 15(1): 17734

Adaptation of mitochondrial bioenergetics to coenzyme Q deficiency in human endothelial cells after chronic exposure to bisphosphonates.

Adrianna Budzinska, Lukasz Galganski, Krzysztof Wojcicki, Wieslawa Jarmuszkiewicz.

  Nitrogen-containing bisphosphonates (N-BPs), widely used in bone disease therapy, inhibit the mevalonate pathway, which affects coenzyme Q (CoQ) biosynthesis and may compromise mitochondrial function, particularly in endothelial cells where oxidative stress and mitochondrial dysfunction contribute to cardiovascular disease. This study examined the effects of chronic six-day exposure of human endothelial cells to N-BPs on mitochondrial bioenergetic functions, focusing on drug-induced mitochondrial CoQ (mtCoQ) deficiency. Compared with the mitochondria of control cells, those of endothelial cells treated with 5 µM alendronate or 1 µM zoledronate presented a significant 45-50% decrease in total mtCoQ pool, loss of reduced (mtCoQH2) antioxidant mtCoQ pool, and elevated mitochondrial antioxidant protein superoxide dismutase 2 (SOD2) and uncoupling protein 2 (UCP2) levels. Exposing endothelial cells to N-BPs also led to an overall reduction in mitochondrial substrate oxidation, except for increased fatty acid oxidation. Additionally, the mitochondria of N-BP-treated endothelial cells presented decreased respiratory rates, membrane potential, and ATP synthesis efficiency, and increased H2O2 production resulting from increased mtCoQ reduction during the oxidation of complex I (CI) and CII substrates. N-BP-induced mtCoQ deficiency also resulted in rearranged respiratory chain supercomplexes, particularly downregulation of the III2 + IV supercomplex, and decreased CII, CIII, and CV protein levels and activities. Despite the N-BP-induced decrease in a-heme levels, maximal CIV activity remained unaffected in endothelial mitochondria. These findings highlight the role of N-BPs in disrupting mtCoQ redox homeostasis and associated bioenergetic functions in endothelial mitochondria.

Keywords:  Alendronate; Bisphosphonates; Coenzyme Q; Endothelial cells; Mitochondrial respiration; Zoledronate

DOI:  https://doi.org/10.1038/s41598-025-02710-8
Elife. 2025 May 20. pii: RP98800. [Epub ahead of print]13

Perturbation-response analysis of in silico metabolic dynamics revealed hard-coded responsiveness in the cofactors and network sparsity.

Yusuke Himeoka, Chikara Furusawa.

  Homeostasis is a fundamental characteristic of living systems. Unlike rigidity, homeostasis necessitates that systems respond flexibly to diverse environments. Understanding the dynamics of biochemical systems when subjected to perturbations is essential for the development of a quantitative theory of homeostasis. In this study, we analyze the response of bacterial metabolism to externally imposed perturbations using kinetic models of Escherichia coli's central carbon metabolism in nonlinear regimes. We found that three distinct kinetic models consistently display strong responses to perturbations; in the strong responses, minor initial discrepancies in metabolite concentrations from steady-state values amplify over time, resulting in significant deviations. This pronounced responsiveness is a characteristic feature of metabolic dynamics, especially since such strong responses are seldom seen in toy models of the metabolic network. Subsequent numerical studies show that adenyl cofactors consistently influence the responsiveness of the metabolic systems across models. Additionally, we examine the impact of network structure on metabolic dynamics, demonstrating that as the metabolic network becomes denser, the perturbation response diminishes-a trend observed commonly in the models. To confirm the significance of cofactors and network structure, we constructed a simplified metabolic network model underscoring their importance. By identifying the structural determinants of responsiveness, our findings offer implications for bacterial physiology, the evolution of metabolic networks, and the design principles for robust artificial metabolism in synthetic biology and bioengineering.

Keywords:  E. coli; computational biology; kinetic model; metabolism; network; systems biology; systems modeling

DOI:  https://doi.org/10.7554/eLife.98800
Biochim Biophys Acta Mol Basis Dis. 2025 May 15. pii: S0925-4439(25)00250-9. [Epub ahead of print]1871(6): 167902

Adenine nucleotide translocase 2 silencing promotes metabolic reprogramming in P19 embryonal carcinoma stem cells.

Gabriela L Oliveira, Jaromir Novak, Zuzana Nahacka, Petra Brisudova, Sandra I Mota, Jiri Neuzil, Paulo J Oliveira, Ricardo Marques.

  Although controversial, cancer stem cells (CSCs) are thought to be one tumor component, being characterized by their strong self-renewal and survival properties. Cancer cells, CSCs included, are thought to rely mostly on glycolysis, even in the presence of oxygen, which confers them adaptive advantages. Adenine nucleotide translocator 2 (ANT2), responsible for the exchange of ADP and ATP in the mitochondrial inner membrane, has been correlated with a higher glycolytic metabolism and is known to be overexpressed in cancer cells. Using P19 embryonal carcinoma stem cells, we inhibited ANT2 translation by using siRNA. ANT2 protein levels were shown to be overexpressed in P19 undifferentiated cells (P19SCs) when compared to their differentiated counterparts (P19dCs). Furthermore, we showed here that the OXPHOS machinery and mitochondrial membrane potential are compromised after ANT2 depletion, leading to a metabolic adaptation towards a less oxidative phenotype. Interestingly, hexokinase II levels were downregulated, which was also accompanied by decreased cell growth, and reduced ability to form spheroids. Our findings underscore ANT2 as a key regulator of metabolic remodeling and cell survival of cancer stem-like cells, suggesting its potential as a therapeutic target for controlling CSC-driven tumor progression.

Keywords:  ANT2; Hexokinase II; Metabolism; Mitochondria; Spheroids; cancer stem cells

DOI:  https://doi.org/10.1016/j.bbadis.2025.167902
J Cell Biol. 2025 Jul 07. pii: e202409039. [Epub ahead of print]224(7):

Pex30-dependent membrane contact sites maintain ER lipid homeostasis.

Joana Veríssimo Ferreira, Yara Ahmed, Tiaan Heunis, Aamna Jain, Errin Johnson, Markus Räschle, Robert Ernst, Stefano Vanni, Pedro Carvalho.

In eukaryotic cells, communication between organelles and the coordination of their activities depend on membrane contact sites (MCS). How MCS are regulated under the dynamic cellular environment remains poorly understood. Here, we investigate how Pex30, a membrane protein localized to the endoplasmic reticulum (ER), regulates multiple MCS in budding yeast. We show that Pex30 is critical for the integrity of ER MCS with peroxisomes and vacuoles. This requires the dysferlin (DysF) domain on the Pex30 cytosolic tail. This domain binds to phosphatidic acid (PA) both in vitro and in silico, and it is important for normal PA metabolism in vivo. The DysF domain is evolutionarily conserved and may play a general role in PA homeostasis across eukaryotes. We further show that the ER-vacuole MCS requires a Pex30 C-terminal domain of unknown function and that its activity is controlled by phosphorylation in response to metabolic cues. These findings provide new insights into the dynamic nature of MCS and their coordination with cellular metabolism.

DOI: https://doi.org/10.1083/jcb.202409039
Nat Commun. 2025 May 16. 16(1): 4582

Dynamic single-cell metabolomics reveals cell-cell interaction between tumor cells and macrophages.

Yi Zhang, Mingying Shi, Mingxuan Li, Shaojie Qin, Daiyu Miao, Yu Bai.

Single-cell metabolomics reveals cell heterogeneity and elucidates intracellular molecular mechanisms. However, general concentration measurement of metabolites can only provide a static delineation of metabolomics, lacking the metabolic activity information of biological pathways. Herein, we develop a universal system for dynamic metabolomics by stable isotope tracing at the single-cell level. This system comprises a high-throughput single-cell data acquisition platform and an untargeted isotope tracing data processing platform, providing an integrated workflow for dynamic metabolomics of single cells. This system enables the global activity profiling and flow analysis of interlaced metabolic networks at the single-cell level and reveals heterogeneous metabolic activities among single cells. The significance of activity profiling is underscored by a 2-deoxyglucose inhibition model, demonstrating delicate metabolic alteration within single cells which cannot reflected by concentration analysis. Significantly, the system combined with a neural network model enables the metabolomic profiling of direct co-cultured tumor cells and macrophages. This reveals intricate cell-cell interaction mechanisms within the tumor microenvironment and firstly identifies versatile polarization subtypes of tumor-associated macrophages based on their metabolic signatures, which is in line with the renewed diversity atlas of macrophages from single-cell RNA-sequencing. The developed system facilitates a comprehensive understanding single-cell metabolomics from both static and dynamic perspectives.

DOI: https://doi.org/10.1038/s41467-025-59878-w
J Vis Exp. 2025 May 02.

Analysis of the Expression and Complexes Assembly of the Mitochondrial Respiratory Chain Proteins in the Fission Yeast Schizosaccharomyces pombe.

Guangchun Lu, Jinjie Shang, Gang Feng.

The mitochondrial respiratory chain is crucial for cellular energy metabolism, serving as the core of oxidative phosphorylation. The mitochondrial respiratory chain comprises five enzyme complexes and their interacting supercomplexes. Analysis of the expression and complexes assembly of these proteins is vital to understanding mitochondrial function. This can be studied by combining biochemical and genetic methods in an excellent model organism fission yeast Schizosaccharomyces pombe (S. pombe), which provides a compensatory system to budding yeast for studies of mitochondrial biology. Here, we present a detailed protocol for the isolation of S. pombe mitochondria and analysis of expression levels and complexes assembly of the mitochondrial respiratory proteins by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and blue native-PAGE (BN-PAGE). Briefly, mitochondria from the wild-type and gene mutants are purified, and then their complexes are solubilized and subjected to SDS-PAGE/BN-PAGE and immunoblotting. This method enables the characterization of a gene's novel function in the mitochondrial respiratory chain.

DOI: https://doi.org/10.3791/68336
Cell Rep. 2025 May 20. pii: S2211-1247(25)00494-2. [Epub ahead of print]44(6): 115723

SMIM20 promotes complex IV biogenesis and Ca2+ signaling in mice heart.

Angela Boshnakovska, Julius Ryan Pronto, Tanja Gall, Abhishek Aich, Jan Prochazka, Zuzana Nichtova, Radislav Sedlacek, Izzatullo Sobitov, Sofia Ainatzi, Christof Lenz, Dörthe M Katschinski, Henning Urlaub, Niels Voigt, Peter Rehling, Laura S Kremer.

  Mitochondria are key to cellular energetics, metabolism, and signaling. Their dysfunction is linked to devastating diseases, including mitochondrial disorders, diabetes, neurodegenerative diseases, cardiac disorders, and cancer. Here, we present a knockout mouse model lacking the complex IV assembly factor SMIM20/MITRAC7. SMIM20-/- mice display cardiac pathology with reduced heart weight and cardiac output. Heart mitochondria present with reduced levels of complex IV associated with increased complex I activity, have altered fatty acid oxidation, and display elevated levels of ROS production. Interestingly, mutant mouse ventricular myocytes show unphysiological Ca2+ handling, which can be attributed to the increase in mitochondrial ROS production. Our study presents an example of a tissue-specific phenotype in the context of OXPHOS dysfunction. Moreover, our data suggest a link between complex IV dysfunction and Ca2+ handling at the endoplasmic reticulum through ROS signaling.

Keywords:  CP: Cell biology; CP: Molecular biology; OXPHOS; assembly factor; cytochrome c oxidase; mitochondria; mitochondrial disease

DOI:  https://doi.org/10.1016/j.celrep.2025.115723
Sci Rep. 2025 May 16. 15(1): 17090

Metabolomics and machine learning identify urine metabolic characteristics and potential biomarkers for severe Mycoplasma pneumoniae pneumonia.

Lin Li, Wang Haijun, Chen Tianyu, Wang Wenjing, Wang Zi, Cheng Yibing.

  To study the differences in the urine metabolome between pediatric patients with severe Mycoplasma pneumoniae pneumonia (SMPP) and those with general Mycoplasma pneumoniae pneumonia (GMPP) via non-targeted metabolomics method, and potential biomarkers were explored through machine learning (ML) algorithms. The urine metabonomics data of 48 children with SMPP and 85 children with GMPP were collected via high performance liquid chromatography‒mass spectrometry (HPLC-MS/MS). The differential metabolites between the two groups were obtained via principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA), and the significant metabolic pathways were screened via enrichment analysis. Potential biomarkers were identified using the random forest algorithm, and their relationships with clinical indicators were subsequently analyzed. A total of 136 significantly differential metabolites were identified in the urine samples from SMPP and GMPP. Of these, 68 metabolites were upregulated, and 68 were downregulated, predominantly belonging to the amino acid group. A total of 6 differential metabolic pathways were enriched, including Galactose metabolism, Pantothenate and CoA biosynthesis, Cysteine and methionine metabolism, Biotin metabolism, Glycine, serine and threonine metabolism, Arginine biosynthesis. Three significant potential biomarkers were identified through machine learning: 3-Hydroxyanthranilic acid (3-HAA), L-Kynurenine, and 16(R)-HETE. The area under the receiver operating characteristic curve (AUC) for this three-metabolite panel was 0.9142. There are great differences in the urine metabolome between SMPP and GMPP children, with multiple metabolic pathways being abnormally expressed. Three metabolites have been identified as potential biomarkers for the early detection of SMPP.

Keywords:  Machine learning; Metabolomics; Potential biomarkers; Severe Mycoplasma pneumoniae pneumonia; Urine

DOI:  https://doi.org/10.1038/s41598-025-01895-2
Elife. 2025 May 21. pii: e107193. [Epub ahead of print]14

A pathway to sight.

Katherine J Wert.

  The breakdown of glutamine is an important metabolic pathway for the health and survival of rod photoreceptors within the retina.

Keywords:  cell biology; glutaminase; metabolism; mouse; neurodegeneration; neuroscience; photoreceptor; vision

DOI:  https://doi.org/10.7554/eLife.107193
Nat Commun. 2025 May 19. 16(1): 4652

Dual Ribosome Profiling reveals metabolic limitations of cancer and stromal cells in the tumor microenvironment.

Daniela Aviles-Huerta, Rossella Del Pizzo, Alexander Kowar, Ali Hyder Baig, Giuliana Palazzo, Ekaterina Stepanova, Cinthia Claudia Amaya Ramirez, Sara D'Agostino, Edoardo Ratto, Catarina Pechincha, Nora Siefert, Helena Engel, Shangce Du, Silvia Cadenas-De Miguel, Beiping Miao, Victor M Cruz-Vilchez, Karin Müller-Decker, Ilaria Elia, Chong Sun, Wilhelm Palm, Fabricio Loayza-Puch.

The tumor microenvironment (TME) influences cancer cell metabolism and survival. However, how immune and stromal cells respond to metabolic stress in vivo, and how nutrient limitations affect therapy, remains poorly understood. Here, we introduce Dual Ribosome Profiling (DualRP) to simultaneously monitor translation and ribosome stalling in multiple tumor cell populations. DualRP reveals that cancer-fibroblast interactions trigger an inflammatory program that reduces amino acid shortages during glucose starvation. In immunocompetent mice, we show that serine and glycine are essential for optimal T cell function and that their deficiency impairs T cell fitness. Importantly, immune checkpoint blockade therapy imposes amino acid restrictions specifically in T cells, demonstrating that therapies create distinct metabolic demands across TME cell types. By mapping codon-resolved ribosome stalling in a cell‑type‑specific manner, DualRP uncovers metabolic crosstalk that shapes translational programs. DualRP thus offers a powerful, innovative approach for dissecting tumor cell metabolic interplay and guiding combined metabolic-immunotherapeutic strategies.

DOI: https://doi.org/10.1038/s41467-025-59986-7
Proc Natl Acad Sci U S A. 2025 May 27. 122(21): e2501527122

Loss of insulin signaling in microglia impairs cellular uptake of Aβ and neuroinflammatory response exacerbating AD-like neuropathology.

Wenqiang Chen, Xiangyu Liu, Vitor Rosetto Muñoz, C Ronald Kahn.

  Insulin receptors are present on cells throughout the body, including the brain. Dysregulation of insulin signaling in neurons and astrocytes has been implicated in altered mood, cognition, and the pathogenesis of Alzheimer's disease (AD). To define the role of insulin signaling in microglia, the primary phagocytes in the brain critical for maintenance and damage repair, we created mice with an inducible microglia-specific insulin receptor knockout (MG-IRKO). RiboTag profiling of microglial mRNAs revealed that loss of insulin signaling results in alterations of gene expression in pathways related to innate immunity and cellular metabolism. In vitro, loss of insulin signaling in microglia results in metabolic reprogramming with an increase in glycolysis and impaired uptake of Aβ. In vivo, MG-IRKO mice exhibit alterations in mood and social behavior, and when crossed with the 5xFAD mouse model of AD, the resultant mice exhibit increased levels of Aβ plaque and elevated neuroinflammation. Thus, insulin signaling in microglia plays a key role in microglial cellular metabolism and the ability of the cells to take up Aβ, such that reduced insulin signaling in microglia alters mood and social behavior and accelerates AD pathogenesis. Together, these data indicate key roles of insulin action in microglia and the potential of targeting insulin signaling in microglia in treatment of AD.

Keywords:  Alzheimer’s disease; insulin; metabolism; microglia; neuroinflammation

DOI:  https://doi.org/10.1073/pnas.2501527122
Sci Rep. 2025 May 22. 15(1): 17741

Mitochondrial aldehyde dehydrogenase restores the migratory capacity inhibited by high glucose-induced hyperosmolality.

Chi-Cheng Huang, Yuh-Lien Chen, Chung-Liang Chien.

  Cell migration, which is often impaired under high glucose (HG) conditions, plays a crucial role in the pathogenesis of various diabetic complications. This study investigates the role of mitochondrial aldehyde dehydrogenase (ALDH2) in the HG-induced migratory inhibition. Using fibroblasts sub-cultured in HG medium as a cell model of chronic hyperglycemia, we found that prolonged exposure to HG stress inhibited cell migration via a novel mechanism independent of oxidative stress or cell death. By increasing osmolality, HG induced perinuclear clustering of mitochondria, enhanced focal adhesion maturation, and caused the cells to be less responsive to migratory cues. The pharmacological inhibition of ALDH2 exaggerated this phenomenon, while ALDH2 overexpression protected cells from the migratory impairment caused by HG-induced hyperosmolality. Cells with ALDH2 overexpression exhibited less mature focal adhesions and longer mitochondrial network, suggesting that ALDH2 might preserve mitochondrial integrity to facilitate the focal adhesion turnover during cell migration.

Keywords:  Aldehyde dehydrogenase; Cell migration; Cytoskeleton; Focal adhesion; Hyperglycemia; Hyperosmolality; Mitochondria

DOI:  https://doi.org/10.1038/s41598-025-02022-x
PLoS One. 2025 ;20(5): e0321998

Small-molecule inhibitors of 6-phosphofructo-1-kinase simultaneously suppress lactate and superoxide generation in cancer cells.

Samo Lešnik, Janez Konc, Tina Vodopivec, Katja Čamernik, Urška Karolina Potokar, Matic Legiša.

Deregulated energy metabolism is a hallmark of cancer, characterized by increased glycolytic flux. Cancer-specific modification of 6-phosphofructo-1-kinase (PFK) impairs its ability to regulate the enzyme's activity which increases glycolytic flux. Consequently, excessive cytosolic NADH formation triggers a harmful redox imbalance in cancer cells, which is rapidly neutralized by the formation of lactic acid and superoxide (SOX). To learn more about deregulated glycolysis in cancer cells, a supercomputer used the atomic model of the crystal structure of human PFK1 for virtual screening a database of 4.5 million compounds by docking with the catalytic binding sites of the enzyme. The screening revealed two compounds capable of reducing modified, cancer-specific PFK1 activity and simultaneously suppressing lactate and SOX formation. A dose-dependent inhibition was observed in the cells treated by compounds in the following tumorigenic cells: Jurkat (Acute T cells leukemia); Caco-2 (colorectal adenocarcinoma); COLO 829 (melanoma); and MDA-MB-231 (breast gland adenocarcinoma). In addition, two selected compounds assessed for cytostatic and cytotoxic activity showed no negative effects on tumorigenic cells. However, during incubation, the strengths of inhibitions continuously decreased, both during lactate and SOX formation. No such effects were observed if compounds were sequentially submitted to the cells at low concentrations every 24 hours. Additional experiments performed by Jurkat cells revealed reduced respiration and glycolysis rates in the cells treated with compounds concerning the untreated cells. Inhibition of modified cancer-specific PFK1 activity reduces deregulated glycolytic flux, prevents abundant cytosolic NADH formation, and restores redox balance thus simultaneously preventing the formation of deleterious effects of lactate and SOX, two crucial players in cancer initiation and development.

DOI: https://doi.org/10.1371/journal.pone.0321998
Sci Adv. 2025 May 23. 11(21): eadv2930

Image-guided targeting of mitochondrial metabolism sensitizes pediatric malignant rhabdoid tumors to low-dose radiotherapy.

Wenxi Xia, Esther Need, Carmine Schiavone, Neetu Singh, Jiemin Huang, Matthew Goff, Joseph Cave, David L Gillespie, Randy L Jensen, Mark D Pagel, Prashant Dogra, Sixiang Shi, Shreya Goel.

Tumor hypoxia leads to radioresistance and markedly worse clinical outcomes for pediatric malignant rhabdoid tumors (MRTs). Our transcriptomics and bioenergetic profiling data reveal that mitochondrial oxidative phosphorylation is a metabolic vulnerability of MRT and can be exploited to overcome consumptive hypoxia by repurposing an FDA-approved antimalarial drug, atovaquone (AVO). We then establish the utility of oxygen-enhanced-multispectral optoacoustic tomography, a label-free, ionizing radiation-free imaging modality, to visualize and quantify spatiotemporal changes in tumor hypoxia in response to AVO. We show a potent but transient increase in tumor oxygenation upon AVO treatment that results in complete elimination of tumors in all tested mice when combined with 10-gray radiotherapy, a dose several times lower than the current clinic standard. Last, we use translational mathematical modeling for systematic evaluation of dosing regimens, administration timing, and therapeutic synergy in a virtual patient cohort. Together, our work establishes a framework for safe and pediatric patient-friendly image-guided metabolic radiosensitization of rhabdoid tumors.

DOI: https://doi.org/10.1126/sciadv.adv2930
RSC Chem Biol. 2025 May 12.

Turn-on fluorescent glucose transport bioprobe enables wash-free real-time monitoring of glucose uptake activity in live cells and small organisms.

Monica S Hensley, David Hutchings, Aldelrahman Ismail, Marina Tanasova.

The direct link between sugar uptake and metabolic diseases highlights the iminent need for molecular tools to detect and evaluate alterations in sugar uptake efficiency as approaches to identify disease-relevant metabolic alterations. However, the strict requirements of facilitative glucose transporters regarding substrate binding and translocation pose challenges for developing effective fluorescence molecular probes. Based on the state-of-the-art understanding of glucose recognition by facilitative transporters (GLUTs), we designed a glucopyranoside mimic - GluRho - that delivers the "turn-on" rhodamine B to live cells via glucose transport, including major transporters GLUTs 1-4. The high binding affinity achieved through the secondary interaction between the fluorophore and a GLUT protein supports the delivery of the probe in nutrient-rich conditions, facilitating its use as a tool for a direct assessment of glucose GLUT activity in live cells and organisms and across various experimental settings, including uptake evaluation in the presence of sugars or GLUT activity modulators. The lack of metabolic contribution to the probe uptake due to the elimination of the phosphorylation site contributes to the high efficacy of the GluRho probe in reflecting alterations in glucose uptake efficiency in live cells, between cell lines, and in multicellular model organisms, such as Drosophila melanogaster. The molecular modeling analysis of GluRho complexes with GLUT1 and GLUT2 provided essential information on GLUT-probe interactions, highlighting the residues facilitating the effective binding and translocation of the probe through transporters, thus setting the basis for developing glucose-based glycoconjugates as a cargo-delivering platform.

DOI: https://doi.org/10.1039/d4cb00239c
Nature. 2025 May 21.

Unravelling cysteine-deficiency-associated rapid weight loss.

Alan Varghese, Ivan Gusarov, Begoña Gamallo-Lana, Daria Dolgonos, Yatin Mankan, Ilya Shamovsky, Mydia Phan, Rebecca Jones, Maria Gomez-Jenkins, Eileen White, Rui Wang, Drew R Jones, Thales Papagiannakopoulos, Michael E Pacold, Adam C Mar, Dan R Littman, Evgeny Nudler.

Around 40% of the US population and 1 in 6 individuals worldwide have obesity, with the incidence surging globally1,2. Various dietary interventions, including carbohydrate, fat and, more recently, amino acid restriction, have been explored to combat this epidemic3-6. Here we investigated the impact of removing individual amino acids on the weight profiles of mice. We show that conditional cysteine restriction resulted in the most substantial weight loss when compared to essential amino acid restriction, amounting to 30% within 1 week, which was readily reversed. We found that cysteine deficiency activated the integrated stress response and oxidative stress response, which amplify each other, leading to the induction of GDF15 and FGF21, partly explaining the phenotype7-9. Notably, we observed lower levels of tissue coenzyme A (CoA), which has been considered to be extremely stable10, resulting in reduced mitochondrial functionality and metabolic rewiring. This results in energetically inefficient anaerobic glycolysis and defective tricarboxylic acid cycle, with sustained urinary excretion of pyruvate, orotate, citrate, α-ketoglutarate, nitrogen-rich compounds and amino acids. In summary, our investigation reveals that cysteine restriction, by depleting GSH and CoA, exerts a maximal impact on weight loss, metabolism and stress signalling compared with other amino acid restrictions. These findings suggest strategies for addressing a range of metabolic diseases and the growing obesity crisis.

DOI: https://doi.org/10.1038/s41586-025-08996-y
J Cell Biol. 2025 Jul 07. pii: e202405162. [Epub ahead of print]224(7):

Phosphatidic acid drives spatiotemporal distribution of Pex30 at ER-LD contact sites.

Morgan House, Karan Khadayat, Thomas N Trybala, Nikhil Nambiar, Elizabeth Jones, Steven M Abel, Joshua Baccile, Amit S Joshi.

Lipid droplets (LDs) are ubiquitous neutral lipid storage organelles that form at discrete subdomains in the ER bilayer. The assembly of these ER subdomains and the mechanism by which proteins are recruited to them is poorly understood. Here, we investigate the spatiotemporal distribution of Pex30 at the ER-LD membrane contact sites (MCSs). Pex30, an ER membrane-shaping protein, has a reticulon homology domain, a dysferlin (DysF) domain, and a Duf4196 domain. Deletion of SEI1, which codes for seipin, a highly conserved protein required for LD biogenesis, results in accumulation of Pex30 and phosphatidic acid (PA) at ER-LD contact sites. We show that PA recruits Pex30 at ER subdomains by binding to the DysF domain. The distribution of Pex30 as well as PA is also affected by phosphatidylcholine (PC) levels. We propose that PA regulates the spatiotemporal distribution of Pex30 at ER subdomains that plays a critical role in driving the formation of LDs in the ER membrane.

DOI: https://doi.org/10.1083/jcb.202405162
Cancer Cell. 2025 May 12. pii: S1535-6108(25)00172-2. [Epub ahead of print]

Isocitrate dehydrogenase 1 primes group-3 medulloblastomas for cuproptosis.

Derek Dang, Akash Deogharkar, John McKolay, Kyle S Smith, Pooja Panwalkar, Simon Hoffman, Wentao Tian, Sunjong Ji, Ana P Azambuja, Siva Kumar Natarajan, Joanna Lum, Jill Bayliss, Katie Manzeck, Stefan R Sweha, Erin Hamanishi, Matthew Pun, Diya Patel, Sagar Rau, Olamide Animasahun, Abhinav Achreja, Martin P Ogrodzinski, Jutta Diessl, Jennifer Cotter, Debra Hawes, Fusheng Yang, Robert Doherty, Andrea T Franson, Allison R Hanaford, Charles G Eberhart, Eric H Raabe, Brent A Orr, Robert J Wechsler-Reya, Brandon Chen, Costas A Lyssiotis, Yatrik M Shah, Sophia Y Lunt, Ruma Banerjee, Alexander R Judkins, John R Prensner, Carl Koschmann, Sebastian M Waszak, Deepak Nagrath, Marcos Simoes-Costa, Paul A Northcott, Sriram Venneti.

  MYC-driven group-3 medulloblastomas (MBs) are malignant pediatric brain cancers without cures. To define actionable metabolic dependencies, we identify upregulation of dihydrolipoyl transacetylase (DLAT), the E2-subunit of pyruvate dehydrogenase complex (PDC) in a subset of group-3 MB with poor prognosis. DLAT is induced by c-MYC and targeting DLAT lowers TCA cycle metabolism and glutathione synthesis. We also note upregulation of isocitrate dehydrogenase 1 (IDH1) gene expression in group-3 MB patient tumors and suppression of IDH1 epigenetically reduces c-MYC and downstream DLAT levels in multiple c-MYC amplified cancers. DLAT is a central regulator of cuproptosis (copper-dependent cell death) induced by the copper ionophore elesclomol. DLAT expression in group-3 MB cells correlates with increased sensitivity to cuproptosis. Elesclomol is brain-penetrant and suppresses tumor growth in vivo in multiple group-3 MB animal models. Our data uncover an IDH1/c-MYC dependent vulnerability that regulates DLAT levels and can be targeted to kill group-3 MB by cuproptosis.

Keywords:  cancer metabolism; cell death; copper; cuproptosis; elesclomol; epigenetics; pediatric brain tumor; protein lipoylation

DOI:  https://doi.org/10.1016/j.ccell.2025.04.013
Nat Chem. 2025 May 22.

Abiotic lipid metabolism enables membrane plasticity in artificial cells.

Alessandro Fracassi, Andrés Seoane, Roberto J Brea, Hong-Guen Lee, Alexander Harjung, Neal K Devaraj.

The plasticity of living cell membranes relies on complex metabolic networks fueled by cellular energy. These metabolic processes exert direct control over membrane properties such as lipid composition and morphological plasticity, which are essential for cellular functions. Despite notable progress in the development of artificial systems mimicking natural membranes, the realization of synthetic membranes capable of sustaining metabolic cycles remains a challenge. Here we present an abiotic phospholipid metabolic network that generates and maintains dynamic artificial cell membranes. Chemical coupling agents drive the in situ synthesis of transiently stable non-canonical phospholipids, leading to the formation and maintenance of phospholipid membranes. We find that phospholipid metabolic cycles can drive lipid self-selection, favouring the enrichment of specific lipid species. Moreover, we demonstrate that controlling lipid metabolism can induce reversible membrane phase transitions, facilitating lipid mixing between distinct populations of artificial membranes. Our work demonstrates that a simple lipid metabolic network can drive dynamic behaviour in artificial membranes, offering insights into mechanisms for engineering functional synthetic compartments.

DOI: https://doi.org/10.1038/s41557-025-01829-5