bims-medica 2025-12-28 papers

bims-medica

Biomed News

on Metabolism and diet in cancer

Issue of 2025–12–28
nineteen papers selected by
Brett Chrest, Wake Forest University

Mitochondrial glutamine import sustains electron transport chain integrity independently of glutaminolysis in cancer.
ATP in Mitochondria: Quantitative Measurement, Regulation, and Physiological Role.
Ultraviolet-treated riboflavin induces ROS-mediated apoptosis via inhibiting mitochondrial complex I in acute myeloid leukemia.
Metabolism of glioblastoma: a review of metabolic adaptations and metabolic therapeutic interventions.
Romaciclib, a CDK8/CDK19 inhibitor, can overcome venetoclax resistance through a combinatorial strategy.
Mitochondrial control of fuel switching via carnitine biosynthesis.
Protocol for isolation of lipid droplets and mitochondria from acute myeloid leukemia cells for lipidomic analysis.
Loss of heterozygosity exposes germline mutations in complex I and drives Warburg metabolism in oncocytic carcinoma of the thyroid.
The role of the flexible loop region in the substrate binding and catalytic activity of malate dehydrogenases.
Measurement of NAD(H) concentration using BCA dye and applications to assays of dehydrogenases.
Succinate Confers Stronger Cytoprotection in Kidney Cells than in Astrocytes Due to Its More Efficient Involvement in Energy Metabolism.
Effect of low-carbohydrate vs low-fat diet intervention on visceral fat estimated from dual energy X-ray absorptiometry in a 12-month randomized controlled trial.
SLC38A3 deficiency reveals a critical role of blood-derived glutamine in brain development.
Mitochondria-derived PEP licenses glycerolipid synthesis via SLC25A35.
Nicotinamide salvage is required for proliferation and sustaining self-renewal in undifferentiated embryonic stem cells.
Exercise-induced β-hydroxybutyrate contributes to cognitive improvement in aging mice.
Flow cytometric detection of leukemic stem cells in Acute Myeloid Leukemia: current status and future directions.
Pan-cancer analysis of pyrimidine metabolism reveals signaling pathways connections with chemoresistance role.
A reversible feedback mechanism regulating mitochondrial heme synthesis.

Mol Cell. 2025 Dec 22. pii: S1097-2765(25)00975-X. [Epub ahead of print]

Mitochondrial glutamine import sustains electron transport chain integrity independently of glutaminolysis in cancer.

Lingzhi Zhu, Kuishen Wu, Jianwei You, Wen Mi, Jie Xu, Liucheng Li, Fang Yang, Xinyi Xia, Haohang Yan, Fei Li, Li Chen, Pingyu Liu, Fuming Li.

  Oxidative phosphorylation (OXPHOS) fulfills energy metabolism and biosynthesis through the tricarboxylic acid (TCA) cycle and an intact electron transport chain (ETC). Mitochondrial glutamine import (MGI) replenishes the TCA cycle through glutaminolysis, but its broader roles in cancer remain unclear. Here, we show that MGI sustains OXPHOS independently of glutaminolysis by maintaining ETC integrity. Exogenous glutamate availability abrogates cellular dependence on glutaminolysis but not SLC1A5var-mediated MGI. Blocking MGI elicits severe mitochondrial defects, reducing mitochondrial glucose oxidation and increasing glutamine reductive carboxylation. MGI, but not glutaminolysis, is essential for mitochondrial translation by enabling biogenesis of Gln-mt-tRNAGln, the most limiting mitochondrial aminoacyl-tRNA in cancer cells. Finally, deleting SLC1A5 in mice and targeting SLC1A5var in xenograft tumors inhibit Gln-mt-tRNAGln biogenesis and mitochondrial translation and blunt tumor growth. Our findings uncover a previously unrecognized role of MGI in safeguarding ETC integrity independently of glutaminolysis and inform a therapeutic option by targeting MGI to abrogate OXPHOS for cancer treatment.

Keywords:  SLC1A5var; glutamine; glutaminolysis; mitochondrial glutamine import; mitochondrial translation

DOI:  https://doi.org/10.1016/j.molcel.2025.12.001
Biochemistry (Mosc). 2025 Dec;90(12): 1929-1943

ATP in Mitochondria: Quantitative Measurement, Regulation, and Physiological Role.

Anna S Lapashina, Danila O Tretyakov, Boris A Feniouk.

  Oxidative phosphorylation in mitochondria is the main source of ATP in most eukaryotic cells. Concentrations of ATP, ADP, and AMP affect numerous cellular processes, including macromolecule biosynthesis, cell division, motor protein activity, ion homeostasis, and metabolic regulation. Variations in ATP levels also influence concentration of free Mg2+, thereby extending the range of affected reactions. In the cytosol, adenine nucleotide concentrations are relatively constant and typically are around 5 mM ATP, 0.5 mM ADP, and 0.05 mM AMP. These concentrations are mutually constrained by adenylate kinases operating in the cytosol and intermembrane space and are further linked to mitochondrial ATP and ADP pools via the adenine nucleotide translocator. Quantitative data on absolute adenine nucleotide concentrations in the mitochondrial matrix are limited. Total adenine nucleotide concentration lies in the millimolar range, but the matrix ATP/ADP ratio is consistently lower than the cytosolic ratio. Estimates of nucleotide fractions show substantial variability (ATP 20-75%, ADP 20-70%, AMP 3-60%), depending on the organism and experimental conditions. These observations suggest that the 'state 4' - inhibition of oxidative phosphorylation in the resting cells due to the low matrix ADP and elevated proton motive force that impedes respiratory chain activity - is highly unlikely in vivo. In this review, we discuss proteins regulating ATP levels in mitochondria and cytosol, consider experimental estimates of adenine nucleotide concentrations across a range of biological systems, and examine the methods used for their quantification, with particular emphasis on the genetically encoded fluorescent ATP sensors such as ATeam, QUEEN, and MaLion.

Keywords:  ADP; ATP; ATP synthase; ATeam; adenine nucleotide translocator (ANT); mitochondria

DOI:  https://doi.org/10.1134/S0006297925603338
J Photochem Photobiol B. 2025 Dec 22. pii: S1011-1344(25)00250-7. [Epub ahead of print]274 113347

Ultraviolet-treated riboflavin induces ROS-mediated apoptosis via inhibiting mitochondrial complex I in acute myeloid leukemia.

Ruining Liu, Shuang Ge, Jinyuan Sun, Yi Liu, Liping Sun, Yang Yu, Deqing Wang.

  Acute myeloid leukemia (AML) remains challenging due to drug resistance and relapse, and novel therapeutic approaches are urgently needed. Here, we demonstrated that ultraviolet-treated riboflavin (RF-UV) elicited strong antileukemia effects in AML cell lines and primary patient samples, while showing minimal toxicity in normal cells. Mechanistically, inhibition of mitochondrial respiratory Complex I by RF-UV elevated reactive oxygen species (ROS) levels and resulted in ROS-mediated apoptosis, endoplasmic reticulum (ER) stress and mitochondrial dysfunction. Crucially, in vivo research showed RF-UV considerably slowed the development of AML and extended the survival time of mice. Our research unveiled the clinical application potential of RF-UV as a complex I inhibitor in leukemia treatment.

Keywords:  Acute myeloid leukemia; Apoptosis; Complex I; Oxidative stress; Riboflavin

DOI:  https://doi.org/10.1016/j.jphotobiol.2025.113347
Front Oncol. 2025 ;15 1712576

Metabolism of glioblastoma: a review of metabolic adaptations and metabolic therapeutic interventions.

James Chung, Jawad Saad, Ahmad Kafri, Julien Rossignol, Maxwell Verbrugge, Jesse Bakke.

  Glioblastoma (GBM) is the most common and aggressive primary malignancy of the central nervous system, marked by profound metabolic reprogramming that promotes growth, invasion, and therapeutic resistance. This review examines metabolic adaptations that sustain GBM progression and summarizes current and emerging strategies that target these pathways. GBM cells display increased aerobic glycolysis, glutaminolysis, lipid and cholesterol synthesis, and mitochondrial remodeling. These processes are regulated by oncogenic alterations such as EGFR amplification, PTEN loss, and HIF-1α stabilization, which allow tumor cells to thrive in hypoxic and nutrient-poor environments. Accumulation of lactate further supports metabolic flexibility and promotes an immunosuppressive microenvironment. Recent studies have focused on exploiting these metabolic vulnerabilities through dietary, pharmacologic, and oxygen-modulating interventions. The ketogenic diet has been explored as an adjuvant therapy to reduce glucose availability and enhance treatment sensitivity. Pharmacologic approaches include inhibition of key metabolic enzymes such as hexokinase 2, pyruvate kinase M2, pyruvate dehydrogenase kinase, and glutaminase. Additional strategies aim to disrupt mitochondrial function through VDAC1 blockade or to reduce tumor hypoxia using hypoxia-activated prodrugs, hyperbaric oxygen therapy, and oxygen-transporting agents. Preclinical findings suggest these approaches can suppress tumor proliferation and improve responsiveness to radiation and chemotherapy, although clinical evidence remains limited. Combining metabolic interventions with standard therapies may help overcome GBM's intrinsic resistance and metabolic plasticity. Overall, the review highlights metabolism as a key determinant of GBM pathophysiology and a promising target for therapeutic innovation, emphasizing the importance of continued translational research to identify and exploit context-specific metabolic vulnerabilities in this highly lethal disease.

Keywords:  brain cancer; cancer; cancer signaling; glioblastoma; metabolic therapeutics; metabolism

DOI:  https://doi.org/10.3389/fonc.2025.1712576
bioRxiv. 2025 Dec 18. pii: 2025.12.16.693978. [Epub ahead of print]

Romaciclib, a CDK8/CDK19 inhibitor, can overcome venetoclax resistance through a combinatorial strategy.

Urszula Pakulska, Marta Obacz, Jerzy Woźnicki, Katarzyna Wiklik, Samarpana Chakraborty, Marta Micek, Vakul Mohanty, Diego Coelho, Elżbieta Adamczyk, Aniela Gołas, Adrianna Moszyńska, Hui Zhang, Magdalena Cybulska-Lubak, Ewelina Kaniuga, Zuzanna Sadowska-Markiewicz, Marina Konopleva, Michał Mikula, Przemysław Juszczyński, Aditi Shastri, Natalia Baran, Tomasz Rzymski, Milena Mazan.

The combination of venetoclax (VEN) and hypomethylating agents (HMA) is the standard of care in acute myeloid leukemia (AML) for elderly patients unfit for intensive chemotherapy. Despite its clinical success, most patients eventually relapse, creating an urgent need for effective therapeutic alternatives. In this study, we aimed to evaluate the potential of romaciclib, a first-in-class CDK8/CDK19 inhibitor, in combination with VEN to overcome stroma-mediated and primary/acquired VEN-resistance. We assessed the efficacy of RVU120+VEN combination in both sensitive and resistant AML cell lines and primary patient-derived models. Our finding demonstrated that romaciclib synergizes with VEN in AML cell lines and in 8 out of 11 patient-derived cell samples. The proteomic and functional studies demonstrated that combination induced apoptosis through caspase-dependent cleavage of MCL-1. In vivo studies confirmed the efficacy of RVU120+VEN, showing eradication of leukemic cells and bone marrow recovery. Importantly, the combination effectively overcame both stroma-mediated and transcriptionally dependent VEN-resistance. Mechanistic studies, focusing on transcriptomic analyses, identified key resistance-associated pathways, including IL6/JAK/STAT3, TGF-β, PI3K/AKT/MTOR, and inflammatory signaling, being suppressed by combination treatment. Furthermore, an in vivo study using a VEN-resistant patient-derived xenograft (PDX) model confirmed the efficacy of the combination, demonstrating a significant reduction in leukemia burden and a decreased proportion of leukemia initiating cells (LIC) following treatment. These findings prove the highly synergistic mechanism of action of RVU120+VEN combination and the potential to overcome primary/acquired VEN resistance in relapse/refractory AML disease. Altogether, the presented results support ongoing clinical studies evaluating romaciclib and VEN in VEN/HMA-refractory patients ( NCT06191263 ) and provide a basis for future exploration as a frontline therapy in VEN-naïve patients.

DOI: https://doi.org/10.64898/2025.12.16.693978
bioRxiv. 2025 Dec 20. pii: 2025.12.16.694762. [Epub ahead of print]

Mitochondrial control of fuel switching via carnitine biosynthesis.

Christopher Auger, Hiroshi Nishida, Bo Yuan, Guilherme Martins Silva, Masanori Fujimoto, Mark Li, Daisuke Katoh, Dandan Wang, Melia Granath-Panelo, Jihoon Shin, Anthony Verkerke, Alexander Banks, Sheng Tony Hui, Lijun Sun, Jin-Seon Yook, Rose Witte, Shingo Kajimura.

Metabolic adaptation to environmental changes, such as fasting and cold exposure, involves a dynamic shift in fuel utilization from glucose to fatty acid oxidation, a process that relies on carnitine-mediated fatty acid oxidation in mitochondria. While dietary sources of animal origin (e.g., red meat) contribute to the carnitine pool, de novo carnitine synthesis from trimethyllysine (TML) is essential, particularly for those whose dietary sources are vegetables and fruits that contain negligible amounts of carnitine. However, the molecular pathway of de novo carnitine synthesis and its physiological significance remain poorly understood. Here, we showed that SLC25A45 is a mitochondrial TML carrier that controls de novo carnitine biosynthesis in vivo. Genetic loss of SLC25A45 results in systemic carnitine and acylcarnitine deficiency, leading to impaired fatty acid oxidation and thermogenesis during cold adaptation, while promoting glucose catabolism. Notably, Slc25a45-deficient mice maintained a high respiratory exchange ratio and impaired lipid mobilization following treatment with a GLP1 receptor agonist (GLP-1RA), rendering them resistant to GLP-1RA-induced adipose tissue loss. Together, the present study identifies SLC25A45 as a regulatory checkpoint in fuel switching during adaptation, with implications for systemic energy balance and response to GLP-1RA-mediated anti-obesity therapy.

DOI: https://doi.org/10.64898/2025.12.16.694762
STAR Protoc. 2025 Dec 15. pii: S2666-1667(25)00663-X. [Epub ahead of print]6(4): 104257

Protocol for isolation of lipid droplets and mitochondria from acute myeloid leukemia cells for lipidomic analysis.

Ran Zhao, Liang Zhang, Shuxin Dong, Kazuharu Kamachi, Saurabh Kumar Gupta, Hiroki Akiyama, Jalen Nguyen, G Lavender Hackman, Michael Andreeff, Alessia Lodi, Jo Ishizawa.

  Lipid droplets (LDs) are dynamic organelles critical for lipid and energy homeostasis. LD dysregulation is implicated in various diseases, including acute myeloid leukemia (AML), which exhibits aberrant lipid metabolism and chemoresistance. Here, we describe an effective protocol for the co-isolation of LDs and mitochondria from lipid-deficient cell types, e.g., AML cells. We detail procedures for the isolation, quality verification, and results from mass spectrometry-based lipidomic analysis. This protocol enables the functional study of organellar lipidomic regulation in AML.

Keywords:  cancer; cell biology; cell isolation; cell separation/fractionation; mass cytometry

DOI:  https://doi.org/10.1016/j.xpro.2025.104257
bioRxiv. 2025 Dec 09. pii: 2025.12.06.692631. [Epub ahead of print]

Loss of heterozygosity exposes germline mutations in complex I and drives Warburg metabolism in oncocytic carcinoma of the thyroid.

Celia de la Calle Arregui, Anderson R Frank, Kelvin Mun, Jiwoong Kim, Kuntal Majmudar, Justin A Bishop, Cheryl Lewis, Yang Xie, David G McFadden.

Oncocytic (Hürthle cell) carcinoma of the thyroid (OCT) is characterized by widespread loss of heterozygosity (LOH), mitochondrial accumulation and recurrent mitochondrial DNA mutations leading to impairment of complex I. Here, we establish and characterize a novel OCT cell line, UT946, which displays severe mitochondrial electron transport chain dysfunction and a Warburg metabolic phenotype. Using a series of cytoplasmic hybrids, we establish that the complex I defect in UT946 stems from a nuclear-encoded loss of function mutation in the complex I subunit NDUFS1. To our surprise, the mutation in NDUFS1 was inherited as a recessive germline allele that underwent LOH in the tumor to expose functional loss of complex I. A re-analysis of 91 OCT tumor genomes revealed that LOH-driven exposure of recessive germline mutations in complex I subunits was a recurrent mechanism underlying complex I inactivation in OCT. These findings unveil a new germline-driven mechanism of complex I loss and metabolic reprogramming in cancer, and provide further evidence of the strong selective pressure for complex I impairment in OCT.
Teaser: Germline mutations in complex I induce aerobic glycolysis in oncocytic carcinoma of the thyroid through somatic loss of heterozygosity.

DOI: https://doi.org/10.64898/2025.12.06.692631
Protein Sci. 2026 Jan;35(1): e70418

The role of the flexible loop region in the substrate binding and catalytic activity of malate dehydrogenases.

Varuni K Jamburuthugoda, Christopher E Berndsen, Jing Zhang, Jessica K Bell, Wai Cheung-Tung, Daniel Maskovsky, Kayla Kester, Tina Abelson, Ethan Huynh, John Ellis Bell.

  Malate dehydrogenase (MDH) is a ubiquitous enzyme found across all organisms, playing a central role in cellular metabolism. It catalyzes the interconversion between malate and oxaloacetate (OAA), utilizing NAD(H) or NADP(H) as a cofactor. In this study, we investigated the roles of several amino acid residues within the conserved "flexible loop" region of glyoxysomal MDH from Citrullus lanatus (wgMDH). Specifically, we examined how mutations in this region affect structure, substrate binding, catalysis, and substrate inhibition by OAA. We used kinetic experiments and molecular dynamics simulations to explore these effects. Our results demonstrated the importance of the flexible loop region in positioning the substrate for optimal catalysis, specifically for OAA binding. Several mutants exhibited a significant reduction in affinity for OAA binding while showing minimal effects on NADH binding and little or no decrease in overall catalytic activity. Further, two of the mutations showed decreased Ki for OAA, supporting the impact on OAA binding. Modeling of the effects of the loop on the structure and dynamics of MDH revealed that mutations changed the position of the loop relative to the catalytic histidine, leading to defects in binding and catalysis. These findings suggest that alterations in the dynamics of the flexible loop region influence substrate binding over catalysis.

Keywords:  active site mobile loop; enzyme kinetics; malate dehydrogenase; molecular dynamics; substrate inhibition

DOI:  https://doi.org/10.1002/pro.70418
MicroPubl Biol. 2025 ;2025

Measurement of NAD(H) concentration using BCA dye and applications to assays of dehydrogenases.

Umanga Rupakheti, Derian Andrew, Sara E Scanlan, Jackson Tester, Christopher E Berndsen.

Dehydrogenases are a widespread enzyme family that play essential roles in all metabolic processes. We observe that one of the substrates of many dehydrogenases, the coenzyme NAD(H), reacts with copper in the bicinchoninic acid assay to produce a color change that can be measured spectroscopically. NADH reacts across a lower concentration range in this assay (<1 μM to ~50 μM) compared to NAD + (>100 μM), which allows the bicinchoninic acid (BCA) assay to be used to measure dehydrogenase activity, as demonstrated in assays with human malate dehydrogenase 1.

DOI: https://doi.org/10.17912/micropub.biology.001831
Biochemistry (Mosc). 2025 Dec;90(12): 1985-1998

Succinate Confers Stronger Cytoprotection in Kidney Cells than in Astrocytes Due to Its More Efficient Involvement in Energy Metabolism.

Marina I Buyan, Kseniia S Cherkesova, Anna A Brezgunova, Irina B Pevzner, Nadezda V Andrianova, Egor Y Plotnikov.

  Being among the most metabolically active organs, brain and kidneys critically depend on efficient energy metabolism, which primarily relies on oxidative phosphorylation. Acute pathological conditions associated with a lack of metabolic substrates or their impaired utilization trigger signaling cascades that initiate cell death and lead to poorly reversible organ dysfunction. One of the therapeutic approaches to correct the energy deficit is administration of exogenous metabolites of the tricarboxylic acid cycle, such as succinate. In this study, we investigated the effects of exogenous succinate on astrocytes and renal epithelial cells under normal conditions and in serum deprivation-induced injury. Incubation with succinate increased the viability of both cell types under normal and pathological conditions, but a more pronounced cytoprotective effect was observed in renal cells. In injured renal epithelial cells, succinate increased mitochondrial membrane potential, a critical parameter for the maintenance of mitochondrial function and ATP generation. Comparison of respiration and oxidative phosphorylation parameters in astrocytes and renal epithelial cells in the presence of exogenous succinate revealed that epithelial cells exhibited a significantly higher respiratory control and lower proton leak compared to astrocytes, which correlated with the higher cytoprotective activity of succinate for kidney cells. Therefore, succinate showed a noticeable positive effect in the renal epithelium both under normal conditions and after serum deprivation; however, in astrocytes, its effect was less pronounced. This discrepancy might be related to a more efficient succinate utilization by the mitochondria in renal cells and intrinsic bioenergetic differences between astrocytes and epithelial cells. Despite the clinical use of succinate-containing drugs, the determination of optimal dosages and development of effective therapeutic regimens require further investigation. Our results demonstrate cell type-dependent differences in the efficacy of succinate, suggesting that its therapeutic potential may differ significantly depending on the organ-specific bioenergetic and metabolic properties.

Keywords:  apoptosis; astrocytes; brain; energy substrates; kidneys; mitochondria; oxidative phosphorylation; succinate

DOI:  https://doi.org/10.1134/S0006297925602539
Int J Obes (Lond). 2025 Dec 23.

Effect of low-carbohydrate vs low-fat diet intervention on visceral fat estimated from dual energy X-ray absorptiometry in a 12-month randomized controlled trial.

Shawna Follis, Matthew J Landry, Kristen May Cunanan, Marcia L Stefanick, Catherine P Ward, Christopher D Gardner.

BACKGROUND: A healthy low-fat (HLF) and healthy low-carbohydrate (HLC) diet are common strategies for weight loss that vary in their effects on adiposity and metabolism. Visceral adipose tissue (VAT) is the major contributor to metabolism deregulation, beyond subcutaneous adipose tissue (SAT). Despite strong biological evidence that a HLC diet preferentially decreases VAT, the difficulty measuring it has impeded diet trials. We estimated VAT and SAT in the Diet Intervention Examining The Factors Interacting with Treatment Success (DIETFITS) weight loss trial to compare the effects of HLF and HLC diets and effect modification by sex and insulin resistance.
METHODS: In a 1-year weight loss trial, DIETFITS, we compared VAT loss between HLF and HLC diets by randomizing N = 609 adults to either diet. VAT was estimated using dual-energy x-ray absorptiometry at baseline, 6 months, and 12 months. Linear mixed models analyzed associations between diet and VAT. We built separate models to evaluate effect modification by sex and insulin resistance.
RESULTS: Among 449 participants (60% women; mean age 39 years), VAT loss was significantly greater for those eating the HLC diet compared to the HLF diet at 6 months [10.6 cm2; 95% confidence interval (CI): 5,16.2] and 12 months (6.3 cm2; 95% CI: 0.6,12). VAT relative to SAT loss estimates were greater in the HLC diet at 6 months only. Men experienced greater HLC diet-induced VAT loss than did women. Insulin secretion status did not modify VAT loss.
CONCLUSIONS: The HLC diet was associated with greater VAT loss compared to the HLF diet over 12 months. The loss of metabolically harmful VAT was independent from SAT over 6 months. Direct estimation of adipose sub-types provides strong evidence that insulin resistance does not modulate diet response. Sex differences should be considered in effective dietary interventions targeting VAT reduction and metabolic health.

DOI: https://doi.org/10.1038/s41366-025-01989-x
Brain. 2025 Dec 24. pii: awaf473. [Epub ahead of print]

SLC38A3 deficiency reveals a critical role of blood-derived glutamine in brain development.

Inna Radzishevsky, Lama Harb, Maali Odeh, Inon Maoz, Aseel Saeed, Ankita Lahkar, Bella Agranovich, Ifat Abramovich, Farrukh A Chaudhry, Avi Avital, Daniel J Liebl, Herman Wolosker.

  Biallelic mutations in SLC38A3 lead to postnatal progressive microcephaly, epilepsy, and intellectual disability. However, the underlying pathophysiology remains unknown. Here, we identified Slc38a3 expressed at the vascular endothelium as a critical glutamine transporter that mediates blood-to-brain influx of glutamine through the blood-brain barrier (BBB). Endothelial selective deletion of Slc38a3 (Slc38a3-cKO) lowered the influx of glutamine across the BBB and decreased brain glutamine levels in mouse pups. This was associated with lower transfer of glutamine carbons to glutamate and GABA, suggesting impairment of the glutamine-glutamate/GABA metabolic cycle. Like individuals with mutations in SLC38A3, Slc38a3-cKO pups developed postnatal progressive microcephaly as well as behavioural impairments and morphological alterations in synapses. Approximately 30% of Slc38a3-cKO pups fail to thrive, exhibiting motor dysfunction and preweaning lethality. Glutamine deficiency in the Slc38a3-cKO hippocampus was associated with a slower TCA cycle and a seemingly adaptive increase in glycolysis rate. Glutamine supplementation replenished brain glutamine, prevented microcephaly, and normalized motor behavior in Slc38a3-cKO pups, indicating that brain glutamine deficiency is the primary cause of the phenotype. In contrast to the dogma that all glutamine is produced locally in the brain, our data show that Slc38a3 provides blood-derived glutamine for neurotransmitter synthesis, energy metabolism, and synaptogenesis. Our findings suggest that SLC38A3 mutations cause a glutamine-related BBB aminoacidopathy and developmental disorder, which may be amenable to glutamine supplementation therapy.

Keywords:  SN1; SNAT3; amino acid transporters; glutamatergic transmission; glutamine-glutamate/GABA cycle; microcephaly

DOI:  https://doi.org/10.1093/brain/awaf473
bioRxiv. 2025 Dec 16. pii: 2025.12.12.693842. [Epub ahead of print]

Mitochondria-derived PEP licenses glycerolipid synthesis via SLC25A35.

Tadashi Yamamuro, Daisuke Katoh, Guilherme Martins Silva, Hiroshi Nishida, Satoshi Oikawa, Yusuke Higuchi, Dandan Wang, Masanori Fujimoto, Naofumi Yoshida, Mark Li, Jihoon Shin, Zezhou Zhao, Jin-Seon Yook, Lijun Sun, Shingo Kajimura.

Mitochondria provide a variety of metabolites, in addition to ATP, to meet cell-specific needs. One such metabolite is phosphoenolpyruvate (PEP), which contains the highest energy phosphate bond above ATP, and has diverse biological functions, including glycolysis, gluconeogenesis, and glyceroneogenesis. Although PEP is generally considered a cytosolic intermediate, it can also be synthesized within mitochondria by the mitochondria-localized carboxykinase (PCK2, also known as M-PEPCK). However, the mechanism by which mitochondrial PEP is delivered to the cytosolic compartment and caters to cell-specific requirements remains elusive. Here, we identify SLC25A35, a previously uncharacterized mitochondrial inner-membrane protein, as the long-sought carrier responsible for mitochondrial PEP efflux. SLC25A35 is highly expressed in lipogenic cells, such as adipocytes, which employ the mitochondrial pyruvate-to-PEP bypass, and is upregulated by lipogenic stimuli. Reconstitution studies by proteo-liposomes, together with structural analyses, demonstrated specific PEP transport by SLC25A35 in a pH gradient-dependent manner. Importantly, loss of SLC25A35 in adipocytes impaired the conversion of mitochondrial PEP into glycerol-3-phosphate, the glycerol backbone in triglyceride, resulting in reduced glycerolipid synthesis while preserving substrate oxidation in the TCA cycle. Furthermore, blockade of SLC25A35 in the liver of obese mice markedly decreased glycerolipid accumulation, ameliorated hepatic steatosis, and improved systemic glucose homeostasis. Together, the present study identifies mitochondrial PEP transport via SLC25A35 as a metabolic checkpoint of fatty acid esterification, offering a selective target for "lipogenic mitochondria" to limit glycerolipid synthesis, a pivotal step in the pathogenesis of hepatic steatosis and Type 2 diabetes.

DOI: https://doi.org/10.64898/2025.12.12.693842
Stem Cells. 2025 Dec 24. pii: sxaf081. [Epub ahead of print]

Nicotinamide salvage is required for proliferation and sustaining self-renewal in undifferentiated embryonic stem cells.

Mu-Jie Lu, Hsin-Ru Chan, Samiksha Deme, Paul A Oliphint, Jonghwan Kim, Patrick Allard, Xiaolu A Cambronne.

  Stem cells use oxidized nicotinamide adenine dinucleotide (NAD+) in distinct subcellular compartments to support self-renewal and to regulate chromatin. There is limited information, however, about the biosynthetic pathways that replenish intracellular NAD+, which is continuously turned over in undifferentiated mouse embryonic stem cells. Establishing specific metabolic inputs for maintaining self-renewal can help direct reprogramming efforts. We used single fluorescent protein biosensors for in situ NAD+ measurements in J1 mouse embryonic stem cells. Sensors and controls were localized to the nucleus, cytoplasm, and mitochondrial compartments. Using a specific inhibitor for nicotinamide salvage, we found that loss of this pathway depleted NAD+ concentrations in all three subcellular compartments in undifferentiated culture conditions. We determined that loss of nicotinamide salvage reduced colony size, extended cell cycle, and resulted in diminished expression of self-renewal markers. Supplementation with precursors in the nicotinamide salvage pathway bypassed the pharmacological block, replenished cytosolic NAD+ levels, and reversed the effects on colony size. Notably, supplementation with deaminated precursors did not replenish intracellular NAD+ levels, suggesting minimal contribution from this pathway at this stage. In support, expression data from multiple mouse and human lines showed that nicotinamide salvage pathway enzyme NAMPT was predominantly expressed at the embryonic stem cell stage compared to the enzymes in other NAD+ biosynthesis pathways. Collectively, the data showed that undifferentiated embryonic stem cells heavily rely on nicotinamide salvage, indicating that this dependency is conserved.

Keywords:  Biosensor; Embryonic stem cell Nicotinamide salvage; NAD+; self-renewal

DOI:  https://doi.org/10.1093/stmcls/sxaf081
J Sport Health Sci. 2025 Dec 18. pii: S2095-2546(25)00121-8. [Epub ahead of print] 101113

Exercise-induced β-hydroxybutyrate contributes to cognitive improvement in aging mice.

Lian Wang, Liwei Mao, Danlin Zhu, Ke Li, Haoyang Gao, Muge Zhou, Jiabin Wu, Dan Yang, Ze Wang, Wenhong Wang, Yifan Guo, Yingying Xu, Peijie Chen, Weihua Xiao.

   BACKGROUND: Aging is a major contributor to cognitive decline and neurodegeneration, yet effective interventions to counteract aging-related neuronal dysfunction remain limited. β-hydroxybutyrate (β-HB), a ketone body elevated during fasting or aerobic exercise, functions as both an energy substrate and a signaling metabolite.
METHODS: We assessed the effects of exercise-induced and exogenously supplemented β-HB on cognitive performance in aging mice. To examine the role of endogenous β-HB metabolism, we used 3-hydroxybutyrate dehydrogenase 1 (BDH1) knockout mice. In vitro, we investigated the impact of G protein-coupled receptor 109A (GPR109A) knockdown on β-HB-mediated activation of peroxisome proliferator-activated receptor gamma (PPARγ) and downstream pathways.
RESULTS: Exercise elevated circulating β-HB levels and improved cognitive outcomes in aging mice. Exogenous β-HB supplementation mimicked these benefits. Loss of BDH1 impaired endogenous β-HB production and attenuated both exercise- and β-HB-induced cognitive improvements. In vitro, GPR109A knockdown suppressed β-HB-driven activation of PPARγ and downstream neuroprotective pathways linked to inflammation and oxidative stress.
CONCLUSION: These findings identify the β-HB/GPR109A-PPARγ axis as a key mediator of exercise-induced cognitive enhancement in aging. β-HB emerges as a potential therapeutic candidate to mitigate brain aging and cognitive decline.

Keywords:  BDH1; Exercise; GPR109A; PPARγ; β-hydroxybutyrate

DOI:  https://doi.org/10.1016/j.jshs.2025.101113
Front Pharmacol. 2025 ;16 1724473

Flow cytometric detection of leukemic stem cells in Acute Myeloid Leukemia: current status and future directions.

Mariam M Youssef, Christopher Y Park.

  The assessment of measurable residual disease (MRD) plays a critical role in acute myeloid leukemia (AML) treatment response evaluation and prognosis. However, current AML MRD detection by flow cytometry (FC) is limited in sensitivity due to immunophenotypic variability, similarities to normal hematopoietic stem/progenitor cells, and the lack of stable leukemia-associated immunophenotypes. A significant proportion of AML patients classified as MRD-negative by FC eventually relapse, likely due to the persistence of therapy-resistant leukemic stem cells (LSCs) that are not sensitively detected by routine clinical flow panels. Flow cytometry panels designed to detect LSC antigens, while promising, face challenges like immunophenotypic heterogeneity across AML subtypes, lack of standardized marker panels across laboratories, and limited validation. Here, we summarize the current state of FC-based LSC detection in AML, discussing commonly used markers, immunophenotypic variability, assay setup challenges, and we review recent clinical studies on LSC assessment, outlining their main findings and implications for prognosis and MRD integration. We also consider advances in spectral flow cytometry for improved LSC detection.

Keywords:  AML-acute myeloid leukemia; LSC-leukemic stem cells; MRD-measurable residual disease; flow cytometry; therapeutic targeting biomarkers

DOI:  https://doi.org/10.3389/fphar.2025.1724473
Br J Cancer. 2025 Dec 24.

Pan-cancer analysis of pyrimidine metabolism reveals signaling pathways connections with chemoresistance role.

Vignesh Ramesh, Mert Demirdizen, Luisa Pinna, Thomas Koed Doktor, Federica Benso, Mohammad Aarif Siddiqui, Paolo Ceppi.

BACKGROUND: Deregulated pyrimidine metabolism (PyMet) contributes to various tumorigenic features of cancer, including chemoresistance and epithelial-to-mesenchymal transition. However, cancer often encompasses complex signalling and metabolic pathway cascades for its progression and understanding of these molecular regulatory processes in PyMet is quite limited.
METHODS: A comprehensive pan-cancer analysis of around 10,000 gene expression profiles of 32 cancer types was employed using a pathway-based approach utilising gene-sets of signalling and metabolic pathways. The findings were validated using in vitro inhibitor treatments, genetic perturbations and mouse-derived lung tumour organoids.
RESULTS: Pan-cancer analysis identified several top connections with PyMet, including TERT, MTOR, DAX1, HOXA1, TP53 and TNC, implying an interdependency of regulations, which in turn was linked to the chemoresistance mechanisms. Further, these PyMet-signalling interactions were validated in vitro by inhibiting thymidylate synthase (TS) activity using knockdown approach and by brequinar (BRQ), a DHODH inhibitor. Strikingly, the BRQ treatment profile showed a strong inverse association pattern with doxorubicin chemoresistance in multiple cancer types. Indeed, BRQ synergistically sensitises cells to doxorubicin in both lung cancer cell lines and mouse-derived KrasG12D p53Δ/Δ (KP) lung tumour organoids.
CONCLUSIONS: The study highlights the PyMet-pathway interactions and its role in chemoresistance, providing a strategy for targeting PyMet in cancer.

DOI: https://doi.org/10.1038/s41416-025-03282-0
J Biol Chem. 2025 Dec 22. pii: S0021-9258(25)02941-2. [Epub ahead of print] 111089

A reversible feedback mechanism regulating mitochondrial heme synthesis.

Iva Chitrakar, Alexis B Roberson, Pedro H Ayres-Galhardo, Breann L Brown.

  Proper heme biosynthesis is essential for numerous cellular functions across nearly all life forms. In humans, dysregulated heme metabolism is linked to multiple blood diseases, neurodegeneration, cardiovascular disease, and metabolic disorders. Erythroid heme production begins with the rate-limiting enzyme Aminolevulinic Acid Synthase (ALAS2) in the mitochondrion. Although prior studies discuss the regulation of ALAS2 in the nucleus and cytoplasm, its modulation as a mature mitochondrial matrix enzyme remains poorly understood. We report that heme binds mature human ALAS2 with high affinity, acting as a reversible mixed inhibitor that reduces enzymatic activity. Structural modeling supports the hypothesis that two flexible regions of ALAS2 interact with heme, locking the enzyme in an inactive conformation and occluding the active site. Our work reveals a negative feedback mechanism for heme synthesis, offering insights into the spatial regulation of ALAS2 and the maturation of the essential heme cofactor.

Keywords:  Heme; aminolevulinic acid; enzyme inhibition; enzymology; erythropoiesis; heme regulatory motif; protein structure and function; pyridoxal 5-phosphate

DOI:  https://doi.org/10.1016/j.jbc.2025.111089