bims-medica 2025-11-23 papers

bims-medica

Biomed News

on Metabolism and diet in cancer

Issue of 2025–11–23
23 papers selected by
Brett Chrest, Wake Forest University

Succinate puts the brakes on de novo purine synthesis.
Pre-Analytical Considerations in the simultaneous quantification of Ketone Bodies, Lactate, pyruvate and TCA cycle intermediates.
DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency.
Hepatocyte mitochondrial NAD+ content is limiting for liver regeneration.
Short-term effect of Ketogenic diet and Low-calorie diet on Ketometabolism and lipid metabolism.
Complex II inhibition suppresses RSL3-induced ferroptosis by restoring mitochondrial bioenergetics.
Branched chain amino acids and their aberrant metabolism in cancer.
Mitochondrial NAD+ gradient sustained by membrane potential and transport.
SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.
Comparative Evaluation of Hyperpolarized [13C]pyruvate and [13C]lactate for Imaging Neuronal and Glioma Metabolism.
Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.
How one nutrient controls cell size.
Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis.
Targeted Metabolomic Methods for 13C Stable Isotope Labeling with Uniformly Labeled Glucose and Glutamine Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS).
Quantifying Mitochondrial Metabolism and Metabolic Fluxes in Soft Agar Cultures.
Single-Cell Lineage Tracing Uncovers Resistance Signatures and Sensitizing Strategies to FLT3 Inhibitors in Acute Myeloid Leukemia.
Metformin inhibits mitochondrial complex I in intestinal epithelium to promote glycemic control.
Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I.
Knockdown of SUCLG2 inhibits glioblastoma proliferation and promotes apoptosis through LMNA acetylation and the mediation of H4K16la lactylation.
Activation of the pentose phosphate pathway flux by hydrogen peroxide is not regulated by NADPH-mediated feedback inhibition.
Phase 1a/b Multi-Center Study of BPM31510IV Targeting Mitochondrial Metabolism/Warburg Effect as Monotherapy and Combination Chemotherapy in Solid Tumor Patients.
Exploiting Metabolic Vulnerabilities in Cancer with a Dual-Transporter-Targeted 2-Deoxyglucose Analogue for Low-Dose, Potent Antitumor Activity.
Prognostic significance of cytogenetic and molecular features in pediatric acute myeloid leukemia: a meta-analysis.

Mol Cell. 2025 Nov 20. pii: S1097-2765(25)00861-5. [Epub ahead of print]85(22): 4109-4110

Succinate puts the brakes on de novo purine synthesis.

Timothy C Kenny, Kıvanç Birsoy.

In this issue of Molecular Cell, Nengroo et al.1 report that the tricarboxylic acid (TCA) cycle enzyme succinate dehydrogenase (SDH) is essential for de novo purine synthesis, revealing a previously unrecognized metabolic dependency in cancer that can be leveraged therapeutically.

DOI: https://doi.org/10.1016/j.molcel.2025.10.020
Clin Biochem. 2025 Nov 13. pii: S0009-9120(25)00185-7. [Epub ahead of print]141 111056

Pre-Analytical Considerations in the simultaneous quantification of Ketone Bodies, Lactate, pyruvate and TCA cycle intermediates.

Kaitlyn Berchier, Chiara Nyffeler, Stephen Bruce, Clothilde Roux, Jean-Marc Nuoffer, Matthias Gautschi, Alexander Laemmle, Déborah Mathis.

   BACKGROUND: Accurate quantification of small metabolites such as ketone bodies (KB: β-hydroxybutyrate (BHB), acetoacetate (AcAc)), pyruvate (Pyr), lactate (Lac) and tricarboxylic acid (TCA) cycle intermediates is essential for diagnostics, therapy monitoring and metabolic research. These metabolites serve as energy substrates and signaling molecules, with their interpretation often relying on physiologically meaningful ratios (Lac/Pyr, BHB/AcAc). However, their chemical instability and susceptibility to rapid post-collection metabolism pose significant pre-analytical challenges.
METHOD: We developed an LC-MS/MS method for the simultaneous quantification of KB, Pyr, Lac and TCA cycle intermediates, and systematically evaluated pre-analytical factors affecting their stability and accuracy. We compared lithium-heparin (LH), ethylenediaminetetraacetic acid (EDTA), sodium fluoride/EDTA (NaF/EDTA) and sodium citrate (NaCit) collection tubes and deproteinized whole blood (depWB) using perchloric acid. Stability was assessed in whole blood at RT over 24 h, as well as in LH and depWB at various temperatures (RT, 4 °C, -20 °C) over 7 days.
RESULTS: Pyr, Lac, AcAc and fumarate were most labile, while BHB and citrate were stable across matrices. LH-plasma with prompt centrifugation showed minimal metabolic alterations, while NaF/EDTA effectively stabilized Lac but compromised Pyr and TCA cycle intermediates. DepWB improved Lac/Pyr ratio reliability but introduced higher variability and matrix effects. NaCit induced unexpected metabolic shifts, suggesting in-vitro TCA cycle activity.
CONCLUSIONS: Our findings highlight the critical impact of anticoagulants and processing conditions on metabolite stability. LH-plasma provides the best compromise for quantifying KB, Pyr and TCA cycle intermediates when processed rapidly, while depWB remains preferable for accurate Lac/Pyr ratio determination despite its higher variability.

Keywords:  Deproteinized blood; Ketone bodies; LC-MS/MS; Lactate/pyruvate ratio; Perchloric acid; TCA cycle intermediates

DOI:  https://doi.org/10.1016/j.clinbiochem.2025.111056
Cancer Discov. 2025 Nov 20.

DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency.

Thomas Köhnke, Daiki Karigane, Eleanor Hilgart, Amy C Fan, Kensuke Kayamori, Masashi Miyauchi, Cailin T Collins, Fabian P Suchy, Athreya Rangavajhula, Yang Feng, Yusuke Nakauchi, Eduardo Martinez-Montes, Jonas L Fowler, Kyle M Loh, Hiromitsu Nakauchi, Michael A Koldobskiy, Andrew P Feinberg, Ravindra Majeti.

Genetic mutations are being thoroughly mapped in human cancers, yet a fundamental question in cancer biology is whether such mutations are functionally required for cancer initiation, maintenance of established cancer, or both. Here, we study this question in the context of human acute myeloid leukemia (AML), where DNMT3AR882 missense mutations often arise early, in pre-leukemic clonal hematopoiesis, and corrupt the DNA methylation landscape to initiate leukemia. We developed CRISPR-based methods to directly correct DNMT3AR882 mutations in leukemic cells obtained from patients. Surprisingly, DNMT3AR882 mutations were largely dispensable for disease maintenance. Replacing DNMT3AR882 mutants with wild-type DNMT3A did not impair the ability of AML cells to engraft in vivo, and minimally altered DNA methylation. Taken together, DNMT3AR882 mutations are initially necessary for AML initiation, but are largely dispensable for disease maintenance. The notion that initiating oncogenes differ from those that maintain cancer has important implications for cancer evolution and therapy.

DOI: https://doi.org/10.1158/2159-8290.CD-24-1604
Nat Metab. 2025 Nov 20.

Hepatocyte mitochondrial NAD+ content is limiting for liver regeneration.

Sarmistha Mukherjee, Ricardo A Velázquez Aponte, Caroline E Perry, Won Dong Lee, Kevin A Janssen, Marc Niere, Gabriel K Adzika, Mu-Jie Lu, Hsin-Ru Chan, Xiangyu Zou, Beishan Chen, Nicole Bye, Teresa Xiao, Jin-Seon Yook, Oniel Salik, David W Frederick, Ryan B Gaspar, Khanh V Doan, James G Davis, Joshua D Rabinowitz, Douglas C Wallace, Nathaniel W Snyder, Shingo Kajimura, Xiaolu A Cambronne, Mathias Ziegler, Joseph A Baur.

Nicotinamide adenine dinucleotide (NAD+) precursor supplementation shows metabolic and functional benefits in rodent models of disease and is being explored as potential therapeutic strategy in humans. However, the wide range of processes that involve NAD+ in every cell and subcellular compartment make it difficult to narrow down the mechanisms of action. Here we show that the rate of liver regeneration is closely associated with the concentration of NAD+ in hepatocyte mitochondria. We find that the mitochondrial NAD+ concentration in hepatocytes of male mice is determined by the expression of the transporter SLC25A51 (MCART1). The heterozygous loss of SLC25A51 modestly decreases mitochondrial NAD+ content in multiple tissues and impairs liver regeneration, whereas the hepatocyte-specific overexpression of SLC25A51 is sufficient to enhance liver regeneration comparably to the effect of systemic NAD+ precursor supplements. This benefit is observed even though NAD+ levels are increased only in mitochondria. Thus, the hepatocyte mitochondrial NAD+ pool is a key determinant of the rate of liver regeneration.

DOI: https://doi.org/10.1038/s42255-025-01408-5
J Nutr Biochem. 2025 Nov 18. pii: S0955-2863(25)00350-X. [Epub ahead of print] 110188

Short-term effect of Ketogenic diet and Low-calorie diet on Ketometabolism and lipid metabolism.

Flora Bahrami, Elija Buetler, Katrin Freiburghaus, Patcharamon Seubnooch, Lia Bally, Jonathan Maurer, Christa E Flück, Reiner Wiest, Mojgan Masoodi.

  The ketogenic diet (KD) has shown therapeutic potential for epilepsy, neuroprotective effects, and, more recently, metabolic complications. In this study, we explored the impact of the KD on the promotion of ketometabolism and the improvement of dyslipidemia. To this end, we investigated the outcomes of two different diets, eucaloric KD and low-calorie diet (LCD), on ketogenesis, circulating intact lipids, bile acids, and neuro and pancreatic peptides. Based on our results, the concentration of ketone bodies, namely 3-hydroxybutyric acid, increased significantly by an average of 10 and 2 times for KD and LCD, respectively. Additionally, the concentration of several triglyceride (TAG) species decreased up to 98.3% and 99.1% for KD and LCD, respectively, while these reductions were only significant for LCD. Moreover, our results showed that three days of KD led to an increase in the baseline concentration of pancreatic polypeptide 3-36, which suggests that short-term KD has the potential to suppress the appetite. Finally, no significant change in the baseline and kinetic postprandial concentration of bile acid species was observed during the KD. In conclusion, our findings suggest that the ketogenic diet, being less restrictive than the low-calorie diet, has a greater impact on ketometabolism. However, while KD reduces TAG species, this reduction is not statistically significant, unlike the significant decrease observed with LCD.

Keywords:  Calorie restriction; Dietary intervention; Dyslipidemia; Ketogenesis; Ketometabolism

DOI:  https://doi.org/10.1016/j.jnutbio.2025.110188
Biochem Biophys Res Commun. 2025 Nov 14. pii: S0006-291X(25)01686-9. [Epub ahead of print]792 152970

Complex II inhibition suppresses RSL3-induced ferroptosis by restoring mitochondrial bioenergetics.

Sun Chul Lee, Soo Kyung Lee, Hyun Kim, Kyu-Sang Park.

  The mitochondrial electron transport chain (ETC) serves as the main site of cellular energy production and a major source of reactive oxygen species (ROS) generation, which can contribute to the lipid peroxidation associated with ferroptosis. However, the critical roles of mitochondria in ferroptosis are still being debated, and the consequences for cell survival vary depending on different ferroptosis inducers or mitochondrial modulators. In the neuroblastoma clonal cells SH-SY5Y, we demonstrated that inhibition of mitochondrial Complex II by 2-thenoyltrifluoroacetone (TTFA) markedly suppressed RSL3-induced ferroptotic lipid peroxidation and cell death. RSL3, a known inhibitor of glutathione peroxidase 4 (GPX4), significantly increased the mitochondrial membrane potential and superoxide production while reducing ATP-linked oxygen consumption. Co-treatment with TTFA effectively attenuated RSL3-induced mitochondrial hyperpolarization, lowered mitochondrial ROS generation, and restored respiratory activities - particularly enhanced ATP-linked oxygen consumption and reduced proton leak. Consistently, TTFA restored ATP production suppressed by RSL3. In contrast, inhibition of Complex I by rotenone did not suppress superoxide production and lipid peroxidation induced by RSL3, although it provided some protection against RSL3-mediated cytotoxicity. These findings suggest that inhibition of Complex II confers protection against ferroptosis by maintaining mitochondrial redox balance and protecting mitochondrial energy metabolism. In addition, our results uncover a novel mitochondrial mechanism underlying RSL3-induced oxidative stress and ferroptosis that can be modulated through targeted regulation of the ETC.

Keywords:  2-thenoyltrifluoroacetone; ATP-linked respiration; Ferroptosis; Mitochondrial electron transport chain; Mitochondrial superoxide; RSL3

DOI:  https://doi.org/10.1016/j.bbrc.2025.152970
Trends Cancer. 2025 Nov 18. pii: S2405-8033(25)00255-9. [Epub ahead of print]

Branched chain amino acids and their aberrant metabolism in cancer.

Morgan L Brown, Xuanyan Cai, M Celeste Simon.

  Cancer cells require sufficient nutrients to support biomass generation, rapid proliferation, and survival. Thus, extensive reprogramming of amino acid metabolism is necessary for tumor initiation and progression under strenuous conditions. One metabolic pathway that has garnered attention is branched chain amino acid (BCAA) catabolism, a pathway that is highly altered across malignancies. This review examines current insights into how circulating BCAAs and their aberrant catabolic enzymes impact both cancer cells and the surrounding tumor microenvironment.

Keywords:  branched chain amino acids; cancer metabolism; nutrient supplementation; tumor microenvironment

DOI:  https://doi.org/10.1016/j.trecan.2025.10.004
Sci Adv. 2025 Nov 21. 11(47): eaea7460

Mitochondrial NAD+ gradient sustained by membrane potential and transport.

Shivansh Goyal, Scott N Lyons, Xiaolu A Cambronne.

SLC25A51 is required for the replenishment of free nicotinamide adenine dinucleotide (oxidized form) (NAD+) into mammalian mitochondria. However, it is not known how SLC25A51 imports this anionic molecule to sustain elevated NAD+ concentrations in the matrix. Understanding this would reveal regulatory mechanisms used to maintain critical bioenergetic gradients for cellular respiration, oxidative mitochondrial reactions, and mitochondrial adenosine triphosphate (ATP) production. In this work, mutational analyses and localized NAD+ biosensors revealed that the mitochondrial membrane potential (ΔΨm) works in concert with charged residues in the carrier's inner pore to enable sustained import of NAD+ against its electrochemical gradient into the matrix. Dissipation of the ΔΨm or mutation of select residues in SLC25A51 led to equilibration of NAD+ from the matrix. Corroborating data were obtained with the structurally distinct mitochondrial NAD+ carrier from Saccharomyces cerevisiae (ScNdt1p) and mitochondrial ATP transport suggesting a shared mechanism of charge compensation and electrogenic transport in these mitochondrial carrier family members.

DOI: https://doi.org/10.1126/sciadv.aea7460
Nat Commun. 2025 Nov 20. 16(1): 10198

SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.

Cecilia Colson, Yujue Wang, James Atherton, Nisha Rani Dahiya, Davood Kharaghani, Xiaoyang Su.

Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We develop a metabolomic-transcriptomic association analysis, and we find that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrate that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the peroxisome membrane to facilitate GABA production. Taken together, our results reveal a biochemical mechanism where SLC45A4 controls GABA production.

DOI: https://doi.org/10.1038/s41467-025-62721-x
ACS Sens. 2025 Nov 21.

Comparative Evaluation of Hyperpolarized [13C]pyruvate and [13C]lactate for Imaging Neuronal and Glioma Metabolism.

Jun Chen, Maheen Zaidi, Jaideep Chaudhary, Zohreh Erfani, Sarah Al Nemri, Erik J Plautz, Xiaodong Wen, Erin H Seeley, Brenda L Bartnik-Olson, Ian R Corbin, Jae Mo Park.

  Glucose and lactate are primary substrates in cerebral energy metabolism. Hyperpolarized [1-13C]pyruvate has become a powerful imaging agent for metabolic neuroimaging due to its central role in glucose and lactate metabolism, ability to cross the blood-brain barrier, and translational utility in neurological disorders. In particular, [1-13C]pyruvate enables an assessment of mitochondrial metabolism in the cerebral cortex through its conversion to [13C]bicarbonate. While it is not yet confirmed that production of [13C]bicarbonate primarily reflects neuronal metabolism, the higher affinity of neuronal transporters for lactate over pyruvate has motivated interest in hyperpolarized lactate as a more physiologic probe of neuronal metabolism. Here, we identify the predominant cellular source of [13C]bicarbonate and evaluate [1-13C]lactate as an imaging agent for neuronal metabolic imaging. Ex vivo NMR and mass spectrometry imaging of brain tissue collected after bolus injection of [U-13C3]pyruvate revealed that pyruvate dehydrogenase dominates pyruvate carboxylase in the cortex, supporting the neuronal origin of [13C]bicarbonate production. Although the bicarbonate fraction among the total 13C products in vivo was higher following hyperpolarized [1-13C]lactate injection, the signal sensitivity was markedly reduced due to lactate's shorter T1 and larger endogenous pool. Isotopomer analysis of brain tissue harvested 2 min after injection of [U-13C3]pyruvate or [U-13C3]lactate showed comparable labeling of mitochondrial intermediates. In glioma-bearing rats, in vivo imaging revealed an elevated pyruvate-to-lactate ratio within the tumor, highlighting altered redox and transport dynamics in malignancy. These findings demonstrate that both hyperpolarized [1-13C]pyruvate and [1-13C]lactate can effectively probe neuronal and glioma metabolism, although pyruvate outperforms lactate in detecting pyruvate dehydrogenase flux.

Keywords:  hyperpolarization; lactate metabolism; mass spectrometry imaging; neuroimaging; neuron

DOI:  https://doi.org/10.1021/acssensors.5c03203
Cell. 2025 Nov 19. pii: S0092-8674(25)01233-4. [Epub ahead of print]

Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.

Alexander C Lewis, Emily Gruber, Rheana Franich, Jessica Armstrong, Madison J Kelly, Carlos M Opazo, Yau C Low, Léa Flippe, Kevin Wijanarko, Caitlin L Rowe, Celeste H Mawal, Alexandra Birrell, Joan So, Srimayee Vaidyanathan, Keziah Ting, Liana N Semcesen, Karena Last, Ching-Seng Ang, Giovanna Pomilio, Fiona C Brown, Andrew H Wei, Jason A Powell, Elizabeth S Ng, Ann E Frazier, Kate McArthur, Najoua Lalaoui, David A Stroud, Kristin K Brown, Ricky W Johnstone, Lev M Kats.

  The ubiquitous metabolite heme has diverse enzymatic and signaling functions in most mammalian cells. Through integrated analyses of mouse models, human cell lines, and primary patient samples, we identify de novo heme biosynthesis as a selective dependency in acute myeloid leukemia (AML). The dependency is underpinned by a propensity of AML cells, and especially leukemic stem cells (LSCs), to downregulate heme biosynthesis enzymes (HBEs), which promotes their self-renewal. Inhibition of HBEs causes the collapse of mitochondrial Complex IV and dysregulates the copper-chaperone system, inducing cuproptosis, a form of programmed cell death brought about by the oligomerization of lipoylated proteins by copper. Moreover, we identify pathways that are synthetic lethal with heme biosynthesis, including glycolysis, which can be leveraged for combination strategies. Altogether, our work uncovers a heme rheostat that is connected to gene expression and drug sensitivity in AML and implicates HBE inhibition as a trigger of cuproptosis.

Keywords:  acute myeloid leukemia; cuproptosis; heme biosynthesis; metabolic vulnerability; metabolism; mitochondrial Complex IV

DOI:  https://doi.org/10.1016/j.cell.2025.10.028
Elife. 2025 Nov 19. pii: e109482. [Epub ahead of print]14

How one nutrient controls cell size.

Angela Montero, Lydia W S Finley.

  The metabolic fate of a nutrient called pyruvate determines how big cells become.

Keywords:  D. melanogaster; biochemistry; cell biology; cell growth; chemical biology; genetics; hepatocytes; human; pyruvate metabolism; redox state; translation

DOI:  https://doi.org/10.7554/eLife.109482
bioRxiv. 2025 Sep 29. pii: 2025.09.28.674326. [Epub ahead of print]

Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis.

Vasileios Chortis, Kleiton Silva Borges, Cong-Hui Yao, Claudio Ribeiro, Luis Fernando Nagano, Mesut Berber, Alessandro Prete, Lukáš Najdekr, Michail E Klontzas, Andris Jankevics, Pedro Vendramini, Jean Lucas Kremer, Liam Kelley, Sathuwarman Raveenthiraraj, Stylianos Tsagarakis, Magdalena Macech, Ivana D Pupovac, Thomas G Papathomas, Betul Haykir, Catherine Winder, Marcus Quinkler, M Conall Dennedy, Grethe Å Ueland, Felix Beuschlein, Antoine Tabarin, Martin Fassnacht, Angela E Taylor, Darko Kastelan, Urszula Ambroziak, Dimitra A Vassiliadi, Katja Kiseljak-Vassiliades, Irina Bancos, Diana L Carlone, Warwick B Dunn, Wiebke Arlt, Marcia C Haigis, David T Breault.

Dysregulation of cellular metabolism is a hallmark of cancer, which remains poorly understood in adrenocortical carcinoma (ACC). Here, we dissected ACC metabolism by integrating transcriptional profiling from human and mouse ACC, targeted tissue metabolomics from a mouse ACC model, and untargeted serum metabolomics from a large patient cohort, providing cross-species validation of metabolic rewiring in ACC. This study revealed global metabolic dysregulation, involving glutamine-dependent pathways such as non-essential amino-acid and hexosamine biosynthesis, nucleotide metabolism, and glutathione biosynthesis, suggesting glutamine catabolism is a critical metabolic vulnerability in ACC. Treatment with glutamine antagonists 6-Diazo-5-Oxo-L-Norleucine (DON) and JHU-083 elicited robust anti-tumor responses. Mechanistic studies revealed DON's anti-tumor effect was primarily driven by selective inhibition of glutamine-fueled de novo nucleotide biosynthesis. Additionally, DON led to DNA damage, which yielded potent synergism with inhibition of the DNA damage response pathway. Collectively, this work highlights glutamine metabolism as a central metabolic dependency and therapeutic target in ACC.

DOI: https://doi.org/10.1101/2025.09.28.674326
J Proteome Res. 2025 Nov 20.

Targeted Metabolomic Methods for 13C Stable Isotope Labeling with Uniformly Labeled Glucose and Glutamine Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS).

Erin Q Jennings, W Kimryn Rathmell, Jeffrey C Rathmell.

  Heavy carbon labeling has emerged as a popular way to study metabolic diseases. However, most carbon labeling techniques use untargeted mass spectrometry, which typically requires dependence on a research core and specialized software. By combining published 13C labeling patterns and known enzyme reactions, an optimized targeted mass spectrometry method was generated to measure stable isotope labeling with carbon-13 through glycolysis, the tricarboxylic acid cycle, the hexosamine biosynthetic pathway, and glutaminolysis using uniformly labeled glucose or glutamine. This method provides a novel and adaptable approach to investigate pointed hypotheses on the utilization of glucose or glutamine in disease states and models.

Keywords:  carbon tracing; stable isotope labeling; tandem mass spectrometry; targeted metabolomics

DOI:  https://doi.org/10.1021/acs.jproteome.5c00514
Methods Mol Biol. 2026 ;2990 127-143

Quantifying Mitochondrial Metabolism and Metabolic Fluxes in Soft Agar Cultures.

Birte Dowerg, Fangfang Chen, Thekla Cordes.

  Anchorage-independent cultures provide insights into cell proliferation, differentiation, and tumorigenesis beyond traditional two-dimensional models by mimicking parts of the extracellular matrix (ECM). The soft agar colony formation assay enables cells to proliferate in a three-dimensional manner resulting in metabolic phenotypes that are distinct from traditional monolayer cultures. Here, we established a soft agar colony formation assay with subsequent cell isolation to analyze mitochondrial metabolism, metabolic fluxes, morphology, and gene expression within the same sample. We applied mass spectrometry and tracing approaches to decipher carbon utilization for tricarboxylic acid (TCA) cycle metabolism. We also quantified the alteration of immune-related genes in response to inflammatory stimuli in soft agar cultures that might be relevant to autoimmune diseases, which are frequently associated with inflammatory environments and may contribute insights into chronic inflammation and immune cell survival that parallel tumorigenic processes. Our methodology offers a robust model to better understand cell metabolism and function of anchorage-independent cultures that may contribute to the development of new treatment strategies.

Keywords:  Anchorage-independent cultures; Extracellular matrix; Mass spectrometry; Metabolic flux; Metabolism; Metabolite extraction; Mitochondria; Soft agar; Stable isotope tracer

DOI:  https://doi.org/10.1007/978-1-0716-4997-8_11
Cancer Res. 2025 Nov 21.

Single-Cell Lineage Tracing Uncovers Resistance Signatures and Sensitizing Strategies to FLT3 Inhibitors in Acute Myeloid Leukemia.

Johanna Eriksson, Shuyu Zheng, Mihaela Popa, Jie Bao, Jun Dai, Wenyu Wang, Emmet McCormack, Anna Vähärautio, Jing Tang.

While FLT3 inhibitors have significantly improved the treatment of aggressive FLT3-mutated acute myeloid leukemia (AML), the emergence of resistance remains as a major challenge. Here, we applied our recently developed single-cell lineage tracing method ReSisTrace to identify cells that are intrinsically resistant or sensitive to the FLT3 inhibitors midostaurin and quizartinib in AML with FLT3-ITD mutations. Comparison of the gene expression profiles of these cells revealed transcriptional resistance signatures, including upregulation of GSPT1. Depletion of GSPT1 with CRISPR-Cas9-mediated knockout resulted in increased sensitivity of AML cells to quizartinib treatment. Further, targeting GSPT1 with the small molecule CC-90009 exhibited strong synergistic effects when combined with FLT3 inhibitors in the FLT3-ITD cell lines and primary AML patient samples. In addition, in an FLT3-ITD-positive AML patient-derived xenograft (PDX) mouse model, the CC-90009 and quizartinib combination showed significantly higher anti-tumor efficacy and prolonged overall survival compared to either treatment alone. Furthermore, compounds that induced transcriptomic changes opposite to the resistance signatures prompted cells to acquire FLT3 inhibitor-sensitive states. Vistusertib (mTOR inhibitor), linsitinib (IGF1R and insulin receptor inhibitor), and meisoindigo (IGF1R and Src family kinase inhibitor), all inhibiting pathways parallel to or downstream of oncogenic FLT3 signaling, were predicted and validated to sensitize FLT3-mutated cell lines and primary cells to FLT3 inhibitors. Collectively, these findings demonstrate the ability of ReSisTrace to unveil pre-existing transcriptional features of treatment vulnerability in hematological cancers and elucidate strategies for enhancing FLT3 inhibitor treatment efficacy in FLT3-ITD-mutated AML.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-3753
bioRxiv. 2025 Oct 02. pii: 2025.10.02.678294. [Epub ahead of print]

Metformin inhibits mitochondrial complex I in intestinal epithelium to promote glycemic control.

Zachary L Sebo, Ram P Chakrabarty, Rogan A Grant, Karis B D'Alessandro, Alec R Koss, Jenna L E Blum, Shawn M Davidson, Colleen R Reczek, Navdeep S Chandel.

Metformin is a therapeutically versatile biguanide drug primarily prescribed for type II diabetes. Despite its extensive use, the mechanisms underlying many of its clinical effects, including attenuated postprandial glucose excursions, elevated intestinal glucose uptake, and increased production of lactate, Lac-Phe and GDF15, remain unclear. Here, we map these and other clinical effects of metformin to intestine-specific mitochondrial complex I inhibition. Using human metabolomic data and an orthogonal genetics approach in male mice, we demonstrate that metformin suppresses citrulline synthesis, a metabolite generated exclusively by small intestine mitochondria, and increases GDF15 by inhibiting the mitochondrial respiratory chain at complex I. This inhibition co-opts the intestines to function as a glucose sink, driving uptake of excess glucose and converting it to lactate and Lac-Phe. Notably, the glucose-lowering effect of another biguanide, phenformin, and berberine, a structurally unrelated nutraceutical, similarly depends on intestine-specific mitochondrial complex I inhibition, underscoring a shared therapeutic mechanism.

DOI: https://doi.org/10.1101/2025.10.02.678294
Structure. 2025 Nov 19. pii: S0969-2126(25)00403-4. [Epub ahead of print]

Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I.

Daniel Wohlwend, Thilo Seifermann, Emmanuel Gnandt, Marta Vranas, Stefan Gerhardt, Thorsten Friedrich.

  Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.

Keywords:  EPR spectroscopy; NADH dehydrogenase; X-ray crystallography; bioenergetics; biological electron transfer; cryo-electron microscopy; iron-sulfur cluster; redox potential; respiratory complex I

DOI:  https://doi.org/10.1016/j.str.2025.10.016
Cell Death Discov. 2025 Nov 17. 11(1): 534

Knockdown of SUCLG2 inhibits glioblastoma proliferation and promotes apoptosis through LMNA acetylation and the mediation of H4K16la lactylation.

Wenshan Li, Qingqing Zhang, Hang Yin, Qiao Li, Shangyu Liu, Juncheng Wang, Guoqiang Yuan, Yawen Pan.

Glioblastoma (GBM) is the most aggressive primary tumour in the central nervous system, and dynamic clonal evolution and interactions within the microenvironment cause its significant spatiotemporal heterogeneity. These interactions primarily manifest as metabolic reprogramming, mitochondrial dynamic imbalance, and epigenetic remodelling. SUCLG2 has been implicated in the progression of GBM; however, the underlying mechanism is unclear. This study aimed to investigate the role of SUCLG2 in the proliferation and apoptosis of GBM cells. SUCLG2 was found to interact with LMNA, leading to acetylation modification of its amino acid residue K470 and affecting limited oxidative phosphorylation levels and mitochondrial damage. SUCLG2 interacted with DLAT, reducing the binding of lactate-regulated protein H4K16la to promoter regions and cis-regulatory elements. This suppressed the expression of BEST1, GRAMD4, and MBD6, affecting the proliferation and apoptosis of GBM cells. These findings reveal a new SUCLG2-mediated mechanism in lactate metabolism and mitochondrial apoptosis in GBM and offer novel therapeutic and preventive targets for GBM.

DOI: https://doi.org/10.1038/s41420-025-02856-4
Br J Pharmacol. 2025 Nov 16.

Activation of the pentose phosphate pathway flux by hydrogen peroxide is not regulated by NADPH-mediated feedback inhibition.

Camila Aburto, Valentina Parada-Goddard, Alejandro San Martín.

   BACKGROUND AND PURPOSE: Oxidative stress induces a rerouting of metabolic flux from glycolysis to the pentose phosphate pathway. One proposed mechanism involves negative feedback via tonic inhibition of glucose-6-phosphate dehydrogenase by NADPH. However, recent evidence shows that NADPH levels do not decrease 5-s after hydrogen peroxide treatment. This finding is inconsistent with the canonical model wherein a feedback inhibition loop is modulated by NADPH depletion. This inconsistency prompted us to test the involvement of feedback inhibition at high temporal resolution.
EXPERIMENTAL APPROACH: We employed genetically encoded fluorescent indicators for hydrogen peroxide (HyPerRed) and NADPH (iNap1) expressed in human embryonic kidney HEK293 cells. These tools enabled simultaneous real-time, single-cell monitoring of NADPH and hydrogen peroxide.
KEY RESULTS: Glucose sustained NADPH levels under acute oxidative stress in the first seconds following hydrogen peroxide exposure. This result contradicts the reported feedback inhibition, which is considered one of the fundamental mechanisms to explain the acute rerouting of glycolysis to the pentose phosphate pathway. Furthermore, pharmacological inhibition of G6PDH suggests that the pentose phosphate pathway is the primary source of cytosolic NADPH under oxidative stress. Monitoring NADPH levels following G6PDH inhibition allowed assessment of the NADPH consumption flux, a parameter that rises markedly under oxidative stress.
CONCLUSION AND IMPLICATIONS: Our results support an anticipatory phenomenon that maintains NADPH levels under acute hydrogen peroxide exposure, thereby discarding the proposed feedback inhibition loop. This work offers a new perspective on the regulatory nuances of a metabolic pathway involved in ageing, cancer and many other pathological conditions.

Keywords:  NADPH; feedforward; hydrogen peroxide; metabolism; pentose phosphate pathway

DOI:  https://doi.org/10.1111/bph.70246
Cancer Res Commun. 2025 Nov 18.

Phase 1a/b Multi-Center Study of BPM31510IV Targeting Mitochondrial Metabolism/Warburg Effect as Monotherapy and Combination Chemotherapy in Solid Tumor Patients.

Vivek Subbiah, Peter P Yu, Rangaprasad Sarangarajan, Michael A Kiebish, Leonardo O Rodrigues, Gregory M Miller, Viatcheslav R Akmaev, Shen Luan, John P McCook, Nikunj Tanna, Tracey Reilly, Emily Chen, Valerie Bussberg, Shobha Ravipaty, Vivek K Vishnudas, Stephane Gesta, David Lucius, Can Bruce, Suwagmani Hazarika, Arianne Lyng, Allison Klotz, Vladimir Tolstikov, Janice Stevens, Victoria S Chua, Elder Granger, Poornima K Tekumalla, Ely Benaim, Vijay Modur, Marc S Rudoltz, Paul Y Song, Scott T Tagawa, Andrew Hendifer, Sant P Chawla, Manish A Shah, David S Hong, Ralph Zinner, Niven R Narain, Madappa N Kundranda.

PURPOSE: BPM31510IV, a highly bioavailable intravenously administered coenzyme Q10 (CoQ10) formulation evaluated in a Phase 1a/1b study as monotherapy and in combination with chemotherapy in patients with advanced solid tumors.
PATIENTS AND METHODS: Using a 3+3 design, patients received twice-weekly intravenous infusions of BPM31510IV monotherapy (Arm 1) or combined with gemcitabine, 5-fluorouracil/leucovorin, or docetaxel (Arm 2); crossover between arms was permitted. Tumor response was assessed by RECIST1.1. Pharmacokinetic and multi-omics pharmacodynamic (PD) analyses were performed on plasma and core biopsy samples.
RESULTS: 97 patients were enrolled, 33 in Arm 1 and 71 in Arm 2 (seven patients crossed from Arm 1 to Arm 2). The maximum-tolerated dose was 171 mg/kg for BPM31510IV monotherapy or with 5-fluorouracil/leucovorin and 110 mg/kg with gemcitabine or docetaxel. Four dose-limiting toxicities occurred (two in monotherapy; two in combination with chemotherapy). Most adverse events were coagulation-related, occurring in 96% of patients (Grade ≥3 in 4%). Pharmacokinetics showed dose-proportional increases in CoQ10 levels to supraphysiologic concentrations (>200×). In Arm 1, there was one (3%) partial response (PR), with stable disease (SD) reported in 8 (24%) patients. In Arm 2, there was one (1%) PR with SD reported in 25 (35%) patients. Fluorodeoxyglucose-positron emission tomography imaging and PD data suggest a change in tumor metabolism from glycolysis to oxidative phosphorylation.
CONCLUSIONS: BPM31510IV monotherapy and in combination with chemotherapy was safe, with preliminary evidence of anti-tumor activity. High plasma CoQ10 levels were achieved, inducing PD responses consistent with mitochondrial metabolic changes. These findings support continued clinical development of BPM31510IV.

DOI: https://doi.org/10.1158/2767-9764.CRC-25-0507
J Am Chem Soc. 2025 Nov 17.

Exploiting Metabolic Vulnerabilities in Cancer with a Dual-Transporter-Targeted 2-Deoxyglucose Analogue for Low-Dose, Potent Antitumor Activity.

Sungjin Jeon, Xianjin Qin, Madeline A Hildebrand, Tyler L Odom, Isabella Zamborini, Rohan Patel, Xiaoyi Liu, Chaeone Seo, Cassandra E Callmann.

Clinical translation of 2-deoxyglucose (2DG) as a cancer therapeutic has been precluded by the need for high systemic concentrations to outcompete circulating glucose, resulting in dose-limiting toxicity. Here, we overcome this barrier by covalently linking 2DG to 1,18-octadecanedioic acid (ODDA) to engage both glucose and long chain fatty acid transport pathways simultaneously. The resulting conjugate (2DG-ODDA) associates with serum albumin and leverages dual-transporter uptake by 4T1 triple-negative breast cancer (TNBC) cells. In vitro, 2DG-ODDA is highly potent as compared to the parent 2DG, with a 16-fold lower IC50 value. Analysis of how 2DG-ODDA exerts its cytotoxic effects revealed that the compound induces apoptosis consistent with glycolytic inhibition, as confirmed by metabolic flux analysis showing a significant decrease in glycolysis-derived ATP production. 2DG-ODDA treatment also significantly reduces the rate of mitochondrial ATP production by cells, indicating that the conjugate disrupts multiple cellular processes in its mechanism of action. Further analysis revealed that 2DG-ODDA is cleaved by α-mannosidases. In vivo, low-dose subcutaneous 2DG-ODDA treatment significantly suppresses tumor growth, whereas equimolar 2DG is inactive. Together, these findings establish dual nutrient-pathway targeting as a strategy to confer anticancer activity to otherwise ineffective glycolytic inhibitors by exploiting metabolic vulnerabilities in cancer.

DOI: https://doi.org/10.1021/jacs.5c18136
BMC Cancer. 2025 Nov 17. 25(1): 1774

Prognostic significance of cytogenetic and molecular features in pediatric acute myeloid leukemia: a meta-analysis.

Qing Huang, Zhijie Ling, Wei Zhang, Minghai Zhang.

   BACKGROUND: Pediatric acute myeloid leukemia (AML) is a clinically and genetically heterogeneous malignancy with variable outcomes. Accurate risk stratification based on cytogenetic and molecular markers is essential for guiding therapy. However, the prognostic impact of several key genomic alterations remains inconsistent across studies. This meta-analysis aims to evaluate the prognostic significance of cytogenetic and molecular abnormalities in pediatric AML and clarify their association with survival outcomes.
METHODS: A systematic search was conducted across PubMed, EMBASE, Scopus, Web of Science, and CENTRAL up to May 5, 2025. Studies were included if they reported survival outcomes in pediatric patients (≤ 18 years) with de novo AML and evaluated cytogenetic or molecular markers. Data were extracted and synthesized using a random-effects model. Hazard ratios (HRs) or risk ratios (RRs) were pooled for overall survival (OS), event-free survival (EFS), disease-free survival (DFS), complete remission (CR), and relapse risk (RR). Heterogeneity was assessed using I² statistics, and risk of bias was evaluated using the Newcastle-Ottawa Scale.
RESULTS: Thirty-nine studies encompassing over 1,645 pediatric patients were included in the meta-analysis. WT1 overexpression was significantly associated with OS (RR = 1.38, 95% CI: 1.17-1.63). KIT mutations were linked to inferior OS (RR = 0.69, 95% CI: 0.57-0.84), but not to CR, DFS, or relapse risk. FLT3-ITD mutations showed no consistent prognostic effect (RR = 0.97, 95% CI: 0.65-1.46), with substantial heterogeneity (I² = 83%). CEBPA mutations did not significantly impact EFS (RR = 1.00, 95% CI: 0.93-1.07), and neither RAS mutations nor EVI1 overexpression demonstrated prognostic relevance. Publication bias was minimal, and sensitivity analyses confirmed the robustness of pooled estimates.
CONCLUSION: WT1 overexpression and KIT mutations (in selected cytogenetic contexts) are validated as adverse prognostic indicators in pediatric AML. Conversely, FLT3-ITD and CEBPA mutations require nuanced interpretation due to variable effects and methodological heterogeneity. These findings support the integration of molecular profiling into pediatric AML risk stratification and underscore the need for harmonized, prospective studies to refine prognostic models in this population.

Keywords:  Cytogenetics; FLT3; KIT; Meta-analysis; Molecular markers; Pediatric AML; Prognosis; WT1

DOI:  https://doi.org/10.1186/s12885-025-14761-1