bims-medica 2025-09-28 papers

bims-medica

Biomed News

on Metabolism and diet in cancer

Issue of 2025–09–28
twenty-two papers selected by
Brett Chrest, Wake Forest University

Global Profiling of Protein β-hydroxybutyrylome in Porcine Liver.
A consensus guide to preclinical indirect calorimetry experiments.
Mevalonate Biosynthesis is a Metabolic Vulnerability of Gemcitabine-resistant Pancreatic Cancer.
Reprogramming neuroblastoma by diet-enhanced polyamine depletion.
CDK12 regulates cellular metabolism to promote glioblastoma growth.
Mitochondrial ATP Biosynthesis Is Negatively Associated with FFA in Cardiac and Skeletal Muscle During the Development of Obesity in a Rodent Model.
Intracellular pH links energy metabolism to lymphocyte death and proliferation.
A drug-diet combination could improve childhood cancer treatment.
Mitochondria-specific photorelease of ceramide induces apoptosis.
Prevalence of Fms-Like Tyrosine Kinase 3 (FLT3) Mutations in Patients With Acute Myeloid Leukaemia: A Systematic Literature Review and Meta-Analysis.
Targeting hepatocyte-specific SLC2A8 blocks hepatic steatosis and dissociates TCA cycle flux inhibition from glutamine anaplerosis.
The role of succinylation-mediated metabolic reprogramming in tumor progression.
Semaglutide impacts skeletal muscle to a similar extent as caloric restriction in mice with diet-induced obesity.
Gliomas phenocopy an inborn error of metabolism to drive neuronal activity and tumor growth.
Probing the metabolic regulator and candidate tumor suppressor ALDH1L1 as a target for non-small cell lung cancer gene therapy.
Naphthoquinone preferentially pairs with non-proton-pumping NADH dehydrogenase for respiratory electron transport.
Flow cytometry protocol for cell death analysis in glioblastoma organoids: A technical note.
Accumulation of succinate in the blood is a potential early indicator of metabolic dysfunction-associated steatotic liver disease (MASLD).
Selective regulation and cellular metabolism by the lactate transporter MCT4 in GBM.
The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution.
Dietary influences on chemotherapy sensitivity and cardiotoxicity modulated by IRE1 targeting in triple-negative breast cancer in female mice.
Detection of minimal residual disease in circulating cell-free DNA in acute myeloid leukemia.

Biology (Basel). 2025 Sep 02. pii: 1183. [Epub ahead of print]14(9):

Global Profiling of Protein β-hydroxybutyrylome in Porcine Liver.

Shuhao Fan, Jinyu Guan, Fang Tian, Haibo Ye, Qianqian Wang, Lei Lv, Yuanyuan Liu, Xianrui Zheng, Zongjun Yin, Xiaodong Zhang.

  The liver orchestrates metabolic homeostasis through dynamic post-translational modifications. β-hydroxybutyrylation (Kbhb), a ketone body-driven modification, regulates epigenetics and metabolism in humans and mice but remains unexplored in livestock. Here, we characterize the porcine hepatic β-hydroxybutyrylome using high-resolution mass spectrometry, identifying 4982 Kbhb sites on 2122 proteins-the largest dataset to date. β-hydroxybutyrylation predominantly targets non-histone proteins (99.68%), with enrichment in fatty acid β-oxidation, TCA cycle, and oxidative phosphorylation pathways. Subcellular localization revealed cytoplasmic (38.1%), mitochondrial (18.1%), and nuclear (15.3%) dominance, reflecting BHB-CoA synthesis sites. Motif analysis identified conserved leucine, phenylalanine, and valine residues at modified lysines, suggesting enzyme-substrate specificity. β-hydroxybutyrate treatment elevated global Kbhb levels, increasing TCA intermediates (e.g., α-ketoglutarate, +9.56-fold) while reducing acetyl-CoA, indicating enhanced mitochondrial flux. Cross-species comparisons showed tissue-specific Kbhb distribution (nuclear in human cells vs. mitochondrial in mice), highlighting metabolic adaptations. This study establishes pigs as a model for Kbhb research, linking it to energy regulation and providing insights into metabolic reprogramming.

Keywords:  TCA cycle; ketone bodies; metabolic regulation; porcine liver; β-hydroxybutyrylation

DOI:  https://doi.org/10.3390/biology14091183
Nat Metab. 2025 Sep;7(9): 1765-1780

A consensus guide to preclinical indirect calorimetry experiments.

International Indirect Calorimetry Consensus Committee (IICCC)

Understanding the complex factors influencing mammalian metabolism and body weight homeostasis is a long-standing challenge requiring knowledge of energy intake, absorption and expenditure. Using measurements of respiratory gas exchange, indirect calorimetry can provide non-invasive estimates of whole-body energy expenditure. However, inconsistent measurement units and flawed data normalization methods have slowed progress in this field. This guide aims to establish consensus standards to unify indirect calorimetry experiments and their analysis for more consistent, meaningful and reproducible results. By establishing community-driven standards, we hope to facilitate data comparison across research datasets. This advance will allow the creation of an in-depth, machine-readable data repository built on shared standards. This overdue initiative stands to markedly improve the accuracy and depth of efforts to interrogate mammalian metabolism. Data sharing according to established best practices will also accelerate the translation of basic findings into clinical applications for metabolic diseases afflicting global populations.

DOI: https://doi.org/10.1038/s42255-025-01360-4
bioRxiv. 2025 Sep 20. pii: 2025.09.19.675739. [Epub ahead of print]

Mevalonate Biosynthesis is a Metabolic Vulnerability of Gemcitabine-resistant Pancreatic Cancer.

Alica K Beutel, Sabrina Calderon, Ethan Nghiem, Kevin Gulay, Leonor P S Santana, Eleni Zimmer, Rima Singh, Cecily Anaraki, Natalie Yousefian, Chantal Allgöwer, Gregory Tong, Cameron Geller, Alina Chao, Dennis Juarez, Thomas Seufferlein, Alexander Muir, Cholsoon Jang, Aimee L Edinger, Marcus Seldin, Thomas F Martinez, Alexander Kleger, David K Chang, Herve Tiriac, Jennifer B Valerin, David A Fruman, Christopher J Halbrook.

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a devastating prognosis. Gemcitabine, a pyrimidine anti-metabolite, is a cornerstone in PDAC therapy. However, resistance remains a major hurdle in clinical care. Resistance can arise from microenvironmental metabolites or through direct metabolic reprogramming of pancreatic cancer cells. Here, we generated PDAC models of acquired gemcitabine resistance to determine the relationship between these mechanisms. We observed that physiological levels of exogenous pyrimidines have a diminished ability to impact gemcitabine response in PDAC cells with acquired resistance. This occurs as the metabolic reprogramming of PDAC cells in response to gemcitabine treatment forces a suppression of the pyrimidine salvage pathway. Importantly, this metabolic rewiring renders gemcitabine-resistant PDAC cells highly susceptible to inhibition of the rate limiting enzyme of the mevalonate biosynthesis pathway, 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), using statins. Notably, statin treatment inhibits the growth of gemcitabine-resistant tumors in immunocompetent mouse models. Through metabolite rescue experiments, we identified geranylgeranyl pyrophosphate as the critical metabolite lost during statin treatment, resulting in reduced protein geranylation in PDAC cells. Finally, as downregulation of the HMGCR is gradually acquired during gemcitabine resistance, we observed that HMGCR expression predicts patient response to gemcitabine. Collectively, these data demonstrate that the mevalonate biosynthesis pathway represents a promising therapeutic target in gemcitabine resistance and may serve as a biomarker to stratify treatment selection in PDAC patients.

DOI: https://doi.org/10.1101/2025.09.19.675739
Nature. 2025 Sep 24.

Reprogramming neuroblastoma by diet-enhanced polyamine depletion.

Sarah Cherkaoui, Christina S Turn, Yuan Yuan, Wenyun Lu, Lifeng Yang, Matthew J McBride, Caroline Eigenmann, George E Allen, Olesya O Panasenko, Lu Zhang, Annette Vu, Kangning Liu, Yimei Li, Om H Gandhi, Lea F Surrey, Sandra D Kienast, Sebastian A Leidel, Michael Wierer, Eileen White, Joshua D Rabinowitz, Michael D Hogarty, Raphael J Morscher.

Neuroblastoma is a highly lethal childhood tumour derived from differentiation-arrested neural crest cells1,2. Like all cancers, its growth is fuelled by metabolites obtained from either circulation or local biosynthesis3,4. Neuroblastomas depend on local polyamine biosynthesis, and the inhibitor difluoromethylornithine has shown clinical activity5. Here we show that such inhibition can be augmented by dietary restriction of upstream amino acid substrates, leading to disruption of oncogenic protein translation, tumour differentiation and profound survival gains in the Th-MYCN mouse model. Specifically, an arginine- and proline-free diet decreases the amount of the polyamine precursor ornithine and enhances tumour polyamine depletion by difluoromethylornithine. This polyamine depletion causes ribosome stalling, unexpectedly specifically at codons with adenosine in the third position. Such codons are selectively enriched in cell cycle genes and low in neuronal differentiation genes. Thus, impaired translation of these codons, induced by combined dietary and pharmacological intervention, favours a pro-differentiation proteome. These results suggest that the genes of specific cellular programmes have evolved hallmark codon usage preferences that enable coherent translational rewiring in response to metabolic stresses, and that this process can be targeted to activate differentiation of paediatric cancers.

DOI: https://doi.org/10.1038/s41586-025-09564-0
JCI Insight. 2025 Sep 25. pii: e190780. [Epub ahead of print]

CDK12 regulates cellular metabolism to promote glioblastoma growth.

Jeong-Yeon Mun, Chang Shu, Qiuqiang Gao, Zhe Zhu, Hasan O Akman, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D Siegelin.

  Glioblastoma IDH-wildtype is the most common and aggressive primary brain tumor in adults, with poor prognosis despite current therapies. To identify new therapeutic vulnerabilities, we investigated the role of CDK12, a transcription-associated cyclin-dependent kinase, in glioblastoma. Genetic or pharmacologic inactivation of CDK12 impaired tumor growth in patientderived xenograft (PDX) models and enhanced the efficacy of temozolomide. Metabolic profiling using extracellular flux analysis and stable isotope tracing with U-¹³C-glucose and U-¹³Cglutamine showed that CDK12 inhibition disrupted mitochondrial respiration, resulting in energy depletion and apoptotic cell death characterized by caspase activation and Noxa induction. Mechanistically, we identified a direct interaction between CDK12 and GSK3β. CDK12 inhibition activated GSK3β, leading to downregulation of PPARD, a transcriptional regulator of oxidative metabolism. This CDK12-GSK3β-PPARD axis was required for glioblastoma cell proliferation and metabolic homeostasis. In vivo, CDK12 inhibition significantly extended survival without overt toxicity and induced complete tumor regression in a subset of animals. Strikingly, combined CDK12 inhibition and temozolomide treatment led to complete tumor eradication in all animals tested. These findings establish CDK12 as a key regulator of glioblastoma metabolism and survival, and provide strong preclinical rationale for its therapeutic targeting in combination with standard-of-care treatments.

Keywords:  Apoptosis; Brain cancer; Metabolism; Oncogenes; Oncology

DOI:  https://doi.org/10.1172/jci.insight.190780
Int J Mol Sci. 2025 Sep 09. pii: 8768. [Epub ahead of print]26(18):

Mitochondrial ATP Biosynthesis Is Negatively Associated with FFA in Cardiac and Skeletal Muscle During the Development of Obesity in a Rodent Model.

Vianey Nava-Aguilar, Angelica Ruiz-Ramirez, Zeltzin Alejandra Ceja-Galicia, Maria de la Luz Hernandez Esquivel, Magalena Cristobal Garcia, Roxana Carbó Zabala, Guillermo-Celestino Cardoso-Saldaña, Mohammed El-Hafidi.

  Many factors related to obesity can impact how mitochondria produce ATP, such as the uncoupling of oxidative phosphorylation (OXPHOS) caused by proton leaks from built-up free fatty acids (FFA), the increased levels of uncoupling proteins (UCPs), and changes in the levels of ATPase inhibitory protein factors 1 (IF1). Therefore, the present study aimed to assess the rate of ATP synthesis in mitochondria isolated from skeletal and cardiac muscle from animal models of sucrose diet-induced obesity at different time periods. Short periods of sucrose intake (6 and 12 weeks) are sufficient to induce fat accumulation, hypertriglyceridemia, and high plasma FFA. However, a significant decline in the ATP synthesis rate starts to be obvious in mitochondria from skeletal muscle after 24 weeks of sucrose consumption. This impairment of ATP synthesis is associated with increased FFA in skeletal muscle homogenate. ATP synthesis rates in both skeletal and cardiac muscle were found to be sensitive to oleic acid and GDP, a physiological inhibitor of UCPs that has been shown to increase with aging. In addition, a sucrose diet increases the IF1 content in both skeletal and heart muscle, probably to avoid the hydrolytic activity of ATP synthase. In mitochondria from heart muscle, a decrease in the ATP synthesis rate was only observed according to the age in both groups of rats, and it was not affected by sucrose feeding. Our results suggest that the decline of the ATP synthesis rate in mitochondria from skeletal muscle can be due to the accumulation of FFA in skeletal muscle tissue as uncouplers, and the IF1 overexpression induced by the sucrose diet is a response mechanism to avoid the ATP hydrolysis and to save the energy charge reduced by FFA-uncoupling OXPHOS.

Keywords:  ATP synthesis rate; free fatty acid; mitochondria; obesity; sucrose diet

DOI:  https://doi.org/10.3390/ijms26188768
Sci Rep. 2025 Sep 25. 15(1): 32878

Intracellular pH links energy metabolism to lymphocyte death and proliferation.

Wei-Ping Zeng, Shuangshuang Yang, Baohua Zhou.

The role of intracellular pH (pHi) of lymphocytes in the control of the magnitude of immune response is unknown. The central question addressed in this report is whether energy metabolism affects pHi, which in turn regulates the death and proliferation of the lymphocytes and hence the magnitude of the immune response. To this end, we studied lymphocytes in the in vitro model of anti-CD3 activation and the in vivo mouse model of ovalbumin sensitization and challenge. We found that low pHi induces apoptosis of proliferating lymphocytes, whereas high pHi is conducive to their survival. In the in vivo model, treating the mice with the metabolic regulators dichloroacetate or C75 that increase the influx of carbons derived from pyruvate and fatty acid to the TCA cycle, respectively, lowered pHi. Treatments with the metabolic regulators CB-839 or GSK2837808A that inhibit glutaminolysis and aerobic glycolysis, respectively, also lowered pHi. Proliferation powered by high mitochondrial membrane potentials (MMPs) in lymphocytes of low but not high pHi was accompanied by apoptosis. After antigenic challenge, lymphocytes of high pHi increased and assumed a positive relation between pHi and MMPs, while lymphocytes of low pHi and with an inverse relation between pHi and MMPs diminished. These changes were largely dependent on glutaminolysis and aerobic glycolysis. It is therefore concluded that glutaminolysis and aerobic glycolysis are important for counterbalancing the acidic effects of pyruvate and fatty acid energy metabolism to promote a favorable pHi environment for lymphocyte survival and the progression of the immune response.

DOI: https://doi.org/10.1038/s41598-025-16862-0
Nature. 2025 Sep 24.

A drug-diet combination could improve childhood cancer treatment.

Frank Speleman, Louis Delhaye.



Keywords:  Cancer; Medical research; Metabolism

DOI:  https://doi.org/10.1038/d41586-025-02824-z
J Lipid Res. 2025 Sep 19. pii: S0022-2275(25)00169-5. [Epub ahead of print] 100907

Mitochondria-specific photorelease of ceramide induces apoptosis.

Christian Schröer, Matthijs Kol, Anna Koch, Emely Döffinger, Murali Annamalai, Joost C M Holthuis.

  Deciphering the mechanisms by which bioactive intermediates of lipid metabolism influence cell behavior is a challenging task. We previously demonstrated that de novo synthesized ceramides are authentic transducers of apoptosis and that their CERT-mediated diversion to mitochondria is sufficient to initiate BAX-dependent apoptosis. To further unravel the mechanism by which mitochondrial ceramides commit cells to death, we here developed a novel mitochondria-targeted and photocaged short-chain ceramide with a clickable alkyne group for derivatization with a fluorescent reporter. We show that this compound readily and selectively accumulates inside mitochondria in a biologically inert state. Subsequent photorelease of the ceramide moiety triggered apoptosis, as evidenced by proteolytic cleavage of central components of the caspase-dependent cell death pathway. Our findings reinforce the notion that ceramides can initiate apoptotic cell death by acting directly on mitochondria and establish mitochondria-targeted photocaged ceramides as novel tools to elucidate the underlying mechanism with the spatiotemporal precision of light.

Keywords:  caspase-9; chemical synthesis; click chemistry; inner mitochondrial membrane; mitochondrial apoptosis; photocage, sphingolipids

DOI:  https://doi.org/10.1016/j.jlr.2025.100907
Cancer Med. 2025 Sep;14(18): e71205

Prevalence of Fms-Like Tyrosine Kinase 3 (FLT3) Mutations in Patients With Acute Myeloid Leukaemia: A Systematic Literature Review and Meta-Analysis.

Juliana F M Lewis, Naval G Daver, Noah Jamie Robinson, Bhavik J Pandya, Bosny Pierre-Louis, Sayma Monir, Jorge Sierra.

   BACKGROUND: Fms-like tyrosine kinase 3 (FLT3) mutations are associated with poor prognosis in patients with acute myeloid leukaemia (AML).
AIMS: We conducted a systematic literature review and meta-analyses of studies reporting FLT3 mutation prevalence in patients with AML.
MATERIALS & METHODS: We searched all publications through September 2022; the earliest publication we retrieved was published in 1997. Based on these publications, data from the studies were generated between 1985 and 2021. Prevalence was evaluated overall and by study type, geographic location of study, patient age, and gender.
RESULTS: Weighted mean (95% confidence interval) prevalence for FLT3 internal tandem duplication (ITD) and FLT3 tyrosine kinase domain (TKD) mutations were 20% (19%-22%) and 7% (6%-8%), respectively, with wide variability in individual study estimates (FLT3-ITD: 5.1%-41.4%; FLT3-TKD: 2.3%-12.0%). Weighted mean prevalence estimates for FLT3-ITD and FLT3-TKD mutations were higher in populations from interventional (FLT3-ITD: 22%; FLT3-TKD: 8%) than non-interventional studies (FLT3-ITD: 19%; FLT3-TKD: 6%). Weighted mean FLT3 mutation prevalence estimates were higher for Europe (FLT3-ITD: 23%; FLT3-TKD: 8%) and lower for Asia (FLT3-ITD: 18%; FLT3-TKD: 5%). Weighted mean prevalence of FLT3-ITD mutations was higher in younger adults (aged 18-59 years; 23%) than paediatric (aged < 18 years; 12%) or older (aged ≥ 60 years; 18%) populations, and in females (22%) than males (18%).
DISCUSSION: This was the first study to comprehensively assess the reported prevalence of FLT3 mutations worldwide among AML patients.
CONCLUSION: We described the distribution of FLT3 mutations; further work is needed to understand prevalence estimate heterogeneity.

Keywords:   fms‐like tyrosine kinase 3 ; acute myeloid leukaemia; meta‐analyses; mutation; prevalence; systematic literature review

DOI:  https://doi.org/10.1002/cam4.71205
Hepatol Commun. 2025 Oct 01. pii: e0810. [Epub ahead of print]9(10):

Targeting hepatocyte-specific SLC2A8 blocks hepatic steatosis and dissociates TCA cycle flux inhibition from glutamine anaplerosis.

Joshua A Adams, Yiming Zhang, Jiameng Sun, Andrew Tilston-Lunel, Cassandra B Higgins, Monique Heitmeier, Sam Ballentine, Eric Tycksen, Roland E Dolle, Paul W Hruz, Brian J DeBosch.

   BACKGROUND: Excess TCA cycle and glutamine anaplerosis are hallmarks of metabolic dysfunction-associated steatotic liver disease and steatohepatitis. Blocking glutamine metabolism attenuates metabolic dysfunction-associated steatohepatitis. However, inhibiting TCA cycle flux by blocking plasma membrane carbohydrate transport is limited by the ubiquitous tissue distribution, function, and homology among the SLC2A family of facilitative carbohydrate transporters, and the potential for carbohydrate blockade to invoke or exacerbate glutamine anaplerosis. Here, we quantify alterations in hepatocyte carbon flux, define the broader metabolic consequences of hepatocyte-specific GLUT8/SLC2A8 inhibition, and delineate the antisteatotic efficacy of a novel small-molecule GLUT8-selective inhibitor.
METHODS: We generated mice with floxed SLC2A8 alleles and expressed hepatocyte-specific Cre by breeding these mice with albumin-Cre transgenic mice, or by administering AAV8 encoding hepatocyte-specific iCre. We performed stable-isotope glucose, fructose, and glutamine metabolic labeling in isolated GLUT8WT and GLUT8LKO hepatocytes and performed metabolic phenotyping in lean and diet-induced obese GLUT8WT and GLUT8LKO mice. Finally, we performed high-throughput screening to identify a GLUT8-selective inhibitor, which we characterized using in vitro models of triglyceride accumulation.
RESULTS: Hepatocyte-specific SLC2A8 deletion reduced diet-induced hepatic and peripheral fat accumulation and increased thermogenesis during ZT12-24 (eg, the dark phase). It also disrupted TCA cycle flux without inducing compensatory glutamine utilization. High-throughput screening identified a small-molecule, GLUT8-selective inhibitor, P20, which blocked hepatocyte TG accumulation and inflammation in in vitro steatotic and inflammatory models.
CONCLUSIONS: Deleting the hepatocyte carbohydrate transporter GLUT8 suppresses TCA cycle flux without inducing compensatory glutamine anaplerosis. The net effect of this is liver protection against multiple forms of dietary insult. Given that selective pharmacological GLUT8 inhibition is feasible, GLUT8 may be a viable target to abate metabolic dysfunction-associated steatohepatitis and other complications of obesity.

Keywords:  GLUT8; TCA cycle; caloric restriction; energy metabolism; fasting; fructose; glucose transporter; glutamine anaplerosis; metabolic dysfunction–associated steatohepatitis; metabolic dysfunction–associated steatotic liver disease

DOI:  https://doi.org/10.1097/HC9.0000000000000810
Mol Biol Rep. 2025 Sep 26. 52(1): 954

The role of succinylation-mediated metabolic reprogramming in tumor progression.

Siyi He, Chunduo Wang, Ranran Li, Kexin Xu, Wuzhiyi Zhang, Binbin Feng, Shengtao Cheng, Jihua Ren, Juan Chen.

  Metabolic reprogramming is a hallmark of tumors, whereby cancer cells remodel their own metabolism to meet the biosynthetic, energetic, and signaling demands required for rapid proliferation and malignant transformation. Posttranslational modifications (PTMs) serve as dynamic molecular switches that fine-tune cellular metabolic networks by precisely modulating the activity, stability, and subcellular localization of metabolic enzymes. This regulatory plasticity drives context-dependent metabolic reprogramming in tumor cells, enabling them to adapt to fluctuating physiological demands or pathological stressors while establishing tumor-specific metabolic signatures critical for survival and progression. Among PTMs, lysine succinylation-a recently identified modification catalyzed by succinyl-CoA-has emerged as a critical regulator of cancer metabolism. This unique modification involves the transfer of a negatively charged four-carbon succinyl group to lysine residues, inducing conformational and functional changes in target proteins. Notably, succinylation is evolutionarily conserved across eukaryotes and prokaryotes and has a broad influence on central metabolic pathways, including the tricarboxylic acid (TCA) cycle, amino acid metabolism, and lipid homeostasis. Mounting evidence highlights its dual roles in both sustaining tumorigenic metabolism and directly activating oncogenic signaling cascades. This review summarizes current insights into how succinylation rewires tumor metabolism and delineates its mechanistic contributions to cancer progression.

Keywords:  Cancer; Lysine succinylation; Metabolic reprogramming; Posttranslational modification; Succinyl-CoA

DOI:  https://doi.org/10.1007/s11033-025-11061-6
J Physiol. 2025 Sep 22.

Semaglutide impacts skeletal muscle to a similar extent as caloric restriction in mice with diet-induced obesity.

S Jeromson, B Baranowski, M Akcan, B D Waters, K Eisner, A Bellucci, S Trang, A Abolhassani, M A Tello-Palencia, A Schweitzer, B Stefanska, C J Mitchell, David C Wright.

  Semaglutide is a GLP-1 receptor agonist that is highly efficacious in reducing food intake and body weight. While semaglutide reduces adipose tissue, there is also a loss of lean mass including skeletal muscle, though it is unclear whether this translates to a loss of muscle function. The effect of discontinuation of semaglutide on rebound weight gain and shifts in body composition is also not well understood. We investigated the impact of semaglutide and matched caloric restriction on body composition in mice with diet-induced obesity. Mice were treated with semaglutide or fed a calorie-matched diet for 4 weeks. Semaglutide and pair-feeding induced significant weight loss with a concomitant reduction in energy expenditure. Weight loss was greater with semaglutide than caloric restriction, despite matched energy intake. Muscle transcriptomic analyses revealed distinct molecular responses between semaglutide and pair-feeding. In a follow-up experiment, semaglutide and pair-feeding was discontinued after 4 weeks, and body weight and food intake were tracked for 6 weeks. At the end of the withdrawal period there was a loss of treatment effects. Lean and fat mass rebounded to baseline levels at the end of the withdrawal period. Muscle size and strength were also comparable between groups. These findings demonstrate that semaglutide reduces muscle size and strength to the same extent as caloric restriction but may be more effective at promoting fat loss. Interestingly, the loss of lean mass and skeletal muscle recovered following treatment discontinuation. KEY POINTS: Semaglutide results in greater weight loss than caloric restriction. Semaglutide treatment increases fat loss compared with caloric restriction. Muscle mass and strength is reduced to a similar extent by semaglutide and restricted feeding.

Keywords:  obesity; semaglutide; skeletal muscle; weight loss

DOI:  https://doi.org/10.1113/JP289449
bioRxiv. 2025 Sep 18. pii: 2025.09.15.676412. [Epub ahead of print]

Gliomas phenocopy an inborn error of metabolism to drive neuronal activity and tumor growth.

Kalil G Abdullah, Kenji Miki, Charles K Edgar, Shuangcheng Alivia Wu, Yi Xiao, Milan R Savani, Maged T Ghoche, Shawn E Kotermanski, Yuan-Tai Huang, Jeffrey I Traylor, Lei Guo, Kathryn Gunn, William H Hicks, Diana D Shi, Min Tang, Michael M Levitt, Mohamad El-Shami, Skyler Oken, Namya Manoj, Bailey C Smith, Vinesh T Puliyappadamba, Pranita Kaphle, Tracey Shipman, Raymond E West, Chaoying Liang, Toral R Patel, Kimmo J Hatanpaa, Prithvi Raj, Shang Ma, Alexander Ksendzovsky, Thomas D Nolin, Bradley C Lega, Pascal O Zinn, Bianca J Kuhn, Natalie M Clark, C Williams, D R Mani, Michael A Gillette, Marco A Calzado, Lin Xu, Lauren G Zacharias, Feng Cai, Thomas P Mathews, Julie-Aurore Losman, Timothy E Richardson, Benjamin Levi, Michelle Monje, Jay R Gibson, Osaama H Khan, Sameer Agnihotri, Kimberly M Huber, Simon Chamberland, Ralph J DeBerardinis, Samuel K McBrayer.

The metabolic hallmarks of high-grade glioma (HGG) are not fully understood. Human brain tissue metabolomics revealed that the creatine synthesis pathway intermediate guanidinoacetate (GAA) accumulated ∼100-fold in HGGs relative to controls, which was caused by imbalanced activities of enzymes in this pathway. Glioma cells secreted GAA rather than using it to produce creatine, implicating an unexpected function. GAA accumulates in GAMT deficiency, an inborn error of metabolism, and elevates neuronal excitability. Neuronal excitability is also increased in glioma and drives tumor growth through neuron-glioma interactions. We hypothesized that glioma-generated GAA excites surrounding neurons. Indeed, GAA induced neuronal hyperactivity by activating GABA A receptors and causing depolarizing GABA currents in glioma-associated neurons with dysregulated chloride homeostasis. Depleting tumoral GAA decreased electrochemical activity, neuron-glioma interactions, and tumor aggressiveness. Our findings unveil a new mechanism linking cancer metabolism with cancer neuroscience and leverage human genetics to nominate GAA synthesis as a target in gliomas.

DOI: https://doi.org/10.1101/2025.09.15.676412
Mol Ther Oncol. 2025 Sep 18. 33(3): 201038

Probing the metabolic regulator and candidate tumor suppressor ALDH1L1 as a target for non-small cell lung cancer gene therapy.

Amira A Abdellatef, Blake R Rushing, Susan Sumner, Natalia I Krupenko, Sergey A Krupenko.

  ALDH1L1, a major cytosolic folate enzyme and key regulator of one-carbon metabolism, is strongly and ubiquitously downregulated in lung adenocarcinomas (LUADs) and silenced in LUAD cell lines. Analysis of publicly available databases indicates that ALDH1L1 expression is associated with better prognosis and overall survival in LUAD patients. Here we used lentiviral delivery of ALDH1L1 to target metabolism in ALDH1L1-deficient LUAD cell lines A549 and H460. In these cells, ALDH1L1 expression led to strong inhibition of proliferation, colony formation, and migration. Untargeted metabolomic analysis has shown that ALDH1L1 knockin produces a strong effect on the metabotype of A549 cells including alterations in the tricarboxylic acid cycle intermediates and acylcarnitines, indicative of the impairment of cellular energetics. We have further demonstrated that in mice ALDH1L1, lentiviral delivery dramatically inhibits growth of subcutaneous xenograft tumors derived from A549 cells and prevents lung colonization in a tail-vein model. These effects prolonged for the duration of the experiments (6 weeks) with no noticeable decrease in ALDH1L1 protein levels at the endpoint of the study. We did not observe side effects of ALDH1L1 delivery on animal health when compared with the control group. Our study suggests that ALDH1L1 delivery could be a promising gene therapy approach for treating LUAD.

Keywords:  A549; ALDH1L1; H460; MT: Regular Issue; gene therapy; lentiviral delivery; lung adenocarcinoma; mouse xenograft tumors; untargeted metabolomics

DOI:  https://doi.org/10.1016/j.omton.2025.201038
PLoS Genet. 2025 Sep 24. 21(9): e1011877

Naphthoquinone preferentially pairs with non-proton-pumping NADH dehydrogenase for respiratory electron transport.

Snehal V Khairnar, Anjali V Patil, L Karvannan, Amitesh Anand.

Optimal resource allocation is crucial to bacterial physiology and necessitates strategic metabolic decisions. One such evolutionary adaptation was the shift to high-potential respiratory chains following Earth's Great Oxidation Event. Respiratory quinones, key redox-active electron carrier molecules, evolved from naphthoquinones (NQs) to ubiquinones (UQs) in response to oxygen availability. The two quinone types differ in their redox potential, with UQs possessing higher potential. Therefore, NQs are more autooxidizable and electron-leaky than UQs. Using adaptive laboratory evolution of a NQ-dependent Escherichia coli strain, we previously showed the fitness advantage of high-potential quinones. Here, we resolve a paradoxical growth benefit conferred by the loss of function of the pyruvate dehydrogenase complex regulator, revealing that NQs preferentially pair with the non-proton-pumping NADH dehydrogenase, thereby optimizing electron transport in low-potential respiratory chains under aerobic conditions.

DOI: https://doi.org/10.1371/journal.pgen.1011877
PLoS One. 2025 ;20(9): e0327660

Flow cytometry protocol for cell death analysis in glioblastoma organoids: A technical note.

Anna-Laura Potthoff, Meng-Chun Hsieh, Ahmad Melhem, Susanna S Ng, Barbara E F Pregler, Annika Vieregge, Markus Raspe, Lea L Friker, Thomas Zeyen, Julian P Layer, Andreas Dolf, Marieta I Toma, Andreas Waha, Torsten Pietsch, Mike-Andrew Westhoff, Hartmut Vatter, Michael Hölzel, Ulrich Herrlinger, Matthias Schneider.

Tumor organoid models have emerged as a promising tool in cancer research. By preserving intra- and intertumoral heterogeneity and structural integrity they provide a physiologically relevant platform for drug-response studies. However, valid methodological approaches for cell death analyses applying flow cytometry, particularly in complex, large organoids, are lacking. Using glioblastoma organoids (GBOs), we developed a flow cytometry protocol to quantify cell death as an important readout in cancer research. Human GBOs were generated out of tumor material from six patients. Temozolomide (TMZ) and lomustine (CCNU) were used as cytotoxic agents commonly employed in glioblastoma therapy. After treatment for 144 and 288 hours, single cell suspensions from densely-packed GBOs were generated through a combined approach of enzymatic and mechanical dissociation. Cells were permeabilized with Triton X and subsequently stained with propidium iodide (PI). PI staining labels fragmented nuclear DNA, yielding a hypodiploid sub-G1 peak in flow cytometry that markes cell death. After treatment for 288 hours with physiologically-relevant concentrations of TMZ and CCNU cell death rates reached up to 63% in our GBO model. Across three GBO populations, the impact of CCNU at the given concentration was more pronounced compared to that observed with TMZ and the cell death rates of treatment for 288 hours surpassed that of the 144-hour treatment. Both biological and technical replicates showed low variability. Hoechst 33258 staining on the same samples confirmed trends in cell death rates obtained from PI-based analysis. We further validated the treatment-induced effect using a plate-based lactate dehydrogenase release assay and measurements of GBO diameter. Our single-stain flow-cytometry protocol scales to large, dense organoids and provides a practical balance of performance, hands-on time, cost, specificity, and throughput. This protocol could support development and evaluation of subtype-specific therapeutic strategies in translational cancer research.

DOI: https://doi.org/10.1371/journal.pone.0327660
Free Radic Biol Med. 2025 Sep 20. pii: S0891-5849(25)00986-4. [Epub ahead of print]241 220-235

Accumulation of succinate in the blood is a potential early indicator of metabolic dysfunction-associated steatotic liver disease (MASLD).

Olivia Chalifoux, Chloe Dagostino, Meijing Li, Stephanie Trezza, Cathryn Grayson, Mariana De Sa Tavares Russo, Daina Zofija Avizonis, Marek Michalak, Luis B Agellon, Ryan J Mailloux.

There is currently a need to identify new biomarkers to diagnose metabolic dysfunction-associated steatotic liver disease (MASLD). Here, using C57BL6N male mice fed a high-fat diet (HFD), we provide evidence that extracellular succinate buildup is a sex-dependent diagnostic marker for MASLD. Male mice fed the HFD for 2-weeks developed simple steatosis, which was associated with the plasma buildup of succinate to 50 μM. Feeding the mice this diet for up to 7 weeks advanced the condition to MASLD, resulted in cardiac fibrosis, and the further increased plasma succinate to 100 μM. Using Huh-7 hepatoma cells as a model, we found fructose overload increased the concentration of succinate in the culture media, and this was associated with mitochondrial dysfunction and the hyper production of mitochondrial hydrogen peroxide (mtH2O2). HepG2 hepatocellular blastoma cells subjected to fructose overload in culture also accumulated succinate in the media. Treatment of the Huh-7 and HepG2 cells exposed to fructose with ursodeoxycholic acid (UDCA) or its taurine-conjugated form, TUDCA, which are known to elicit protective hepatocellular effects by inducing antioxidant defenses, strongly inhibited succinate build up by preserving mitochondrial function and preventing H2O2 hyper-production. Finally, using our glutaredoxin-2 (Glrx2-/-) gene knockout mouse model on a C57BL6N background, we found deleting the Glrx2 gene in male mice completely abrogated the accumulation of succinate, cis-aconitate, and itaconate in plasma. Importantly, wild-type (Wt) or Glrx2-/-female littermates did not accumulate any of these metabolites in plasma when fed the HFD, which coincided with MASLD resistance. Collectively, our findings show succinate accumulates rapidly in the extracellular milieu in our mouse model for MASLD and cell culture models for hepatic lipotoxicity. These findings suggest the applicability of succinate as a biomarker of early MASLD particularly among males and especially in pediatric populations.

DOI: https://doi.org/10.1016/j.freeradbiomed.2025.09.029
Med Oncol. 2025 Sep 26. 42(11): 497

Selective regulation and cellular metabolism by the lactate transporter MCT4 in GBM.

Sofian Al Shboul, Bingqiao Zhao, Estefania Esposito, Vanessza Fentor, Ashita Singh, Fraser Massie, Ted Hupp, Tessa Moses, Paul M Brennan, Kathryn Ball, Irena Dapic.

  Hypoxia drives adaptive gene expression in glioblastoma (GBM), influencing tumor progression and metabolic reprogramming. This study investigated the hypoxic response of a patient-derived GBM cancer stem cell line, identifying key hypoxia-inducible genes such as SLC16A3, CA9, BNIP3, VEGFA, and NDRG1. SLC16A3 encodes the lactate transporter MCT4, whose expression has been implicated in biology of several cancers, including GBM. To evaluate role of MCT4, its expression was transiently reduced using siRNA resulting in an attenuated hypoxic induction of NDRG1 and SOX2, while sparing CA9 and BNIP3. Immunoblotting of GBM patient tissues revealed heterogeneous co-expression of MCT4 and NDRG1, highlighting a possible metabolic diversity within tumors. Moreover, metabolomic data of the cells showed dysregulated metabolites such as elevated stearic acid and decreased levels of D-( +)-2-phosphoglyceric acid, lactic acid, purine, pyridoxal, N,N,N-trimethyl lysine, and phosphatidylcholine (18:1/18:1) (del9-trans). Decreased intracellular lactate and increased acidity under hypoxic conditions, confirmed important role of MCT4 role in lactate transport and pH regulation. By establishing central role of MCT4 in hypoxia-driven processes, this study provides valuable insights into GBM metabolic plasticity and suggests that MCT4 might be potential therapeutic target.

Keywords:  Glioblastoma; Glioma stem cells; Hypoxia; Lactate transport; MCT4; Metabolic reprogramming; NDRG1

DOI:  https://doi.org/10.1007/s12032-025-03060-1
Nature. 2025 Sep;645(8082): 877-885

The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution.

Biodiversity Cell Atlas meeting participants

Cell types are fundamental functional units that can be traced across the tree of life. Rapid advances in single-cell technologies, coupled with the phylogenetic expansion in genome sequencing, present opportunities for the molecular characterization of cells across a broad range of organisms. Despite these developments, our understanding of eukaryotic cell diversity remains limited and we are far from decoding this diversity from genome sequences. Here we introduce the Biodiversity Cell Atlas initiative, which aims to create comprehensive single-cell molecular atlases across the eukaryotic tree of life. This community effort will be phylogenetically informed, rely on high-quality genomes and use shared standards to facilitate comparisons across species. The Biodiversity Cell Atlas aspires to deepen our understanding of the evolution and diversity of life at the cellular level, encompassing gene regulatory programs, differentiation trajectories, cell-type-specific molecular profiles and inter-organismal interactions.

DOI: https://doi.org/10.1038/s41586-025-09312-4
Physiol Rep. 2025 Sep;13(18): e70400

Dietary influences on chemotherapy sensitivity and cardiotoxicity modulated by IRE1 targeting in triple-negative breast cancer in female mice.

Yismeilin R Feliz-Mosquea, Adam S Wilson, Nildris Cruz-Diaz, Valerie S Payne, Katherine L Cook, David R Soto-Pantoja.

  Triple-negative breast cancer (TNBC) predominantly affects young and minority women, with cytotoxic chemotherapy regimens causing severe side effects, including chronic cardiac dysfunction. Obesity worsens TNBC survival. Inositol-requiring enzyme-1 (IRE1), a key arm of the unfolded protein response (UPR), influences tumor progression. Using a TNBC mouse model with control and Western diets, we tested IRE1-targeting antisense morpholino and doxorubicin. Targeting IRE1 alone reduced tumor growth and, combined with doxorubicin, did not interfere with the oncologic efficacy of this drug. We observed that increased activation of caspase-3 was consistently activated by IRE1 in tumors regardless of diet and combination treatment. Furthermore, the blockade of IRE1 mitigated chemotherapy-induced cardiotoxicity by preserving systolic dysfunction, reducing cardiac fibrosis, and preventing cell death. The potential difference in cell death mechanisms observed between the heart and tumors may be associated with different levels of oxidative stress as measured by 4HNE in our in vivo model. Thus, systemic IRE1 suppression protected cardiac tissue while preserving the oncologic efficacy of anthracyclines.

Keywords:  cardiac damage; doxorubicin; inositol‐requiring enzyme 1 (IRE1); lung metastases; triple‐negative breast cancer

DOI:  https://doi.org/10.14814/phy2.70400
Sci Rep. 2025 Sep 23. 15(1): 32679

Detection of minimal residual disease in circulating cell-free DNA in acute myeloid leukemia.

Charlotte Sommer, Hildegard I D Mack, Madeleine C Killer, Petra Ross, Andrea Nist, Thorsten Stiewe, Andreas Neubauer, Cornelia Brendel, Elisabeth K M Mack.

  Minimal/measurable residual disease (MRD) in Acute Myeloid Leukemia (AML) is defined as persistent leukemic cells below cytomorphological detection threshold. Next generation sequencing (NGS) of circulating cell-free DNA (cfDNA) to profile cancer-associated mutations has been shown to allow for quantification of disease burden in solid tumors and has also been suggested to enable minimally invasive follow-up of AML patients. In this pilot study we investigated the technical sensitivity and potential prognostic implications of cfDNA-based MRD monitoring in AML after allogeneic stem cell transplantation in comparison to donor chimerism analysis or, respectively, after consolidation chemotherapy. 75 cfDNA samples from 29 patients were analyzed by targeted NGS using a commercially available 10- or 37-gene hotspot panel (VariantPlex Core AML or Core Myeloid panel, ArcherDx). Patients' leukemias exhibited 1-7 mutations as determined by routine diagnostics. Only previously identified mutations were considered for MRD evaluation. cfDNA was isolated in sufficient amounts for NGS from all samples (total yield 24 ng-5.2 µg). The sensitivity of variant detection increased with higher overall read count and higher mutation-specific coverage (variant allele frequency [VAF] range 0.08-100%). At least one previously known mutation was identified in 32/55 samples (58%, VAF 0.08-78.04%) which were taken during hematological complete remission (CR) in both patients after allogeneic stem cell transplantation (aHSCT) and patients after consolidation chemotherapy. In patients after aHSCT (n = 25), at least one previously known mutation was detected in 16/29 cfDNA samples (55.1%, VAF 0.08-6.7%) obtained when donor chimerism was ≥ 90% and in 6/6 samples (100%, VAF: 0.88-63.77%) with reduced donor chimerism. Probability of progression-free survival 17 months after aHSCT in patients with donor chimerism ≥ 90% but mutation-positive cfDNA was 64% compared to 100% in patients with undetectable MRD. In patients after consolidation chemotherapy, cfDNA was positive in all samples taken during CR (n = 4; VAF 0.26-29.84%) and non-CR (n = 4; VAF 8.46-100%). Our results indicate that NGS of cfDNA is suitable for MRD monitoring in AML and offers higher sensitivity for detecting residual leukemic cells than chimerism analysis in patients after aHSCT. Further studies are needed to evaluate clinical relevance of MRD status as determined in cfDNA.

Keywords:  Acute myeloid leukemia; Cell-free DNA; Minimal residual disease; Next-generation sequencing

DOI:  https://doi.org/10.1038/s41598-025-20589-3