bims-medica 2025-11-30 papers

bims-medica

Biomed News

on Metabolism and diet in cancer

Issue of 2025–11–30
23 papers selected by
Brett Chrest, Wake Forest University

Consumption of L-Proline as Energy Substrate by Cultured Primary Rat Astrocytes.
Glycolytic ATP production enables rapid mammalian cell growth.
Impact of ketogenic and fast-mimicking diet in gastrointestinal cancer treatment.
Dietary sulfur amino acid restriction improves glucose homeostasis through hepatic de novo serine synthesis.
Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.
ASAH1-mediated sphingolipid metabolic reprogramming in venetoclax resistance of AML: beyond the monocytic phenotypes.
Cryo-EM reveals how ASX-173 inhibits human asparagine synthetase to activate the integrated stress response.
Fluorescence lifetime imaging to investigate propofol-induced metabolic alterations in MDA-MB-231 cells.
NADH dehydrogenase reverses dietary and clock metabolic syndrome.
The proton motive force maintains mtDNA euploidy by balancing mtDNA replication with cell proliferation.
SILAC-based assessment of S-palmitoylated proteins in mammalian cells by metabolic labeling and click-chemistry.
Adaptive nuclear GTP synthesis promotes glioblastoma treatment resistance and is a targetable vulnerability in patients.
How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity.
TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity.
MTHFD2: A Retrospective and a Glance into the Future.
Propionate metabolism dysregulation promotes drug-tolerant persister cell survival in non-small cell lung cancer.
Visualizing dynamics of membrane rafts on live cells.
Na+/H+ Exchanger 1 Inhibition Overcomes Venetoclax Resistance in Acute Myeloid Leukemia.
Iron addicted colorectal cancers exploit Heme-Complex II axis to resist oxidative cell death.
The Inlet, Outlet, and New Ratchet Element for Proton Transfer of the Acinetobacter baumannii F-ATP Synthase and Their Critical Role for Viability.
A metabolic atlas of mouse aging.
All-optical visualization of specific molecules in the ultrastructural context of brain tissue.
Region-specific human brain organoids reveal synaptic and cell state drivers of glioblastoma invasion.

Neurochem Res. 2025 Nov 26. 51(1): 1

Consumption of L-Proline as Energy Substrate by Cultured Primary Rat Astrocytes.

Paul Spellerberg, Ralf Dringen.

  The catabolism of the proteinogenic amino acid L-proline in mammalian cells is mediated by mitochondrial enzymes that can oxidize proline to provide energy for mitochondrial ATP regeneration. To investigate the potential of astrocytes to consume and metabolize L-proline, we incubated cultured primary rat astrocytes with L-proline in the absence or the presence of other energy substrates and investigated L-proline consumption, cellular ATP content and cell viability. In the absence of glucose, the cells consumed L-proline which allowed the cells to maintain a high cellular ATP level as long as extracellular L-proline was detectable. This L-proline consumption was saturable and followed apparent Michaelis-Menten kinetics with a calculated KM value of around 320 µM and a Vmax value of around 100 nmol/(h x mg). In contrast to L-proline, D-proline was not consumed by the cells and was unable to prevent a cellular ATP loss in starved astrocytes. L-Proline consumption was lowered in a concentration-dependent manner by known inhibitors of proline dehydrogenase. The potential of 1 mM L-proline to maintain a high cellular ATP content in starved astrocytes and to prevent cell death was almost identical to that found for 1 mM glucose and a co-application of both substrates had additive ATP-maintaining effects. The presence of L-proline hardly affected the consumption of glucose, while glucose, glucose-derived lactate as well as other energy substrates severely slowed down the astrocytic L-proline consumption. In addition, application of L-proline prevented the rapid loss in cellular ATP level and the subsequent toxicity induced in glucose-deprived astrocytes in the presence of inhibitors of the mitochondrial uptake of pyruvate and fatty acids. These protective effects of proline were abolished by an inhibitor of proline dehydrogenase. The data presented demonstrate that L-proline is an excellent energy substrate for cultured astrocytes especially for conditions of limited availability of other energy substrates.

Keywords:  ATP; Astrocytes; Energy; Metabolism; Mitochondria; Proline

DOI:  https://doi.org/10.1007/s11064-025-04618-1
bioRxiv. 2025 Oct 31. pii: 2025.10.30.685682. [Epub ahead of print]

Glycolytic ATP production enables rapid mammalian cell growth.

Matthew A Kukurugya, Shuying Zhang, Brandon T Ha, Alex E Ekvik, Denis V Titov.

Proliferating cells must produce ATP rapidly enough to meet the energy demands of growth and maintenance. While microbes show a linear coupling between ATP production rate and growth, whether this principle holds in mammalian cells has remained unclear and it has been suggested that most ATP is allocated to cell maintenance, regardless of growth rate. Here, we quantified lactate production, oxygen consumption, and proliferation across twelve mammalian cell lines and found a strong linear relationship between total ATP production and growth with the majority of ATP allocated to macromolecular synthesis. By inhibiting glycolysis, inhibiting respiration, or reducing translation, cells shift along this ATP-growth line in predictable directions, indicating bidirectional coupling between ATP supply and demand. A genetically encoded ATP hydrolysis sink increased ATP turnover yet slowed proliferation, demonstrating that ATP production capacity can limit growth. Together, these results show that respiration alone cannot generate enough ATP to support the growth rates of rapidly dividing cells, whereas glycolysis can. Our results provide a quantitative rationale for the Warburg Effect, where cells rely on glycolysis to achieve doubling times faster than 30 hours. Our results establish ATP production rate as a quantitative constraint on growth across species.

DOI: https://doi.org/10.1101/2025.10.30.685682
Front Oncol. 2025 ;15 1677509

Impact of ketogenic and fast-mimicking diet in gastrointestinal cancer treatment.

Elisa Colombo, Margherita Righini, Vyshnavy Balendra, Konul Rustamli, Ornella Garrone, Margherita Ratti, Michele Ghidini.

  Growing evidence suggests that both the ketogenic diet (KD) and the fast-mimicking diet (FMD) may have significant therapeutic effects in the treatment of gastrointestinal (GI) cancers. KD, characterized by a high fat intake and low carbohydrate intake, induces a state of ketosis that alters energy metabolism, reducing the availability of energy for cancer cells and slowing their growth. Similarly, FMT, which simulates the effects of fasting without requiring complete food abstention, has been studied for its potential to enhance immune response, reduce inflammation, and stimulate autophagy, contributing to the removal of damaged cells. Preclinical and clinical studies indicate that both dietary strategies may enhance the efficacy of chemotherapy while reducing the side effects associated with conventional treatments. Despite these promising findings, few studies have investigated the potential impact of these diets on anticancer treatment of gastrointestinal cancers, and further studies are necessary to better understand the biological mechanisms and to evaluate the safety and effectiveness of these strategies in broader clinical settings. With our review, we aim to analyze the available literature on KD and FMD and their role in the treatment of GI cancers.

Keywords:  fasting-mimicking diet (FMD); gastrointestinal (GI) cancers; insulin-like growth factor-1 (IGF-1); ketogenic diet (KD); ketone bodies (KBs); oxidative stress (OxS); reactive oxygen species (ROS); β-hydroxybutyrate (β-HB)

DOI:  https://doi.org/10.3389/fonc.2025.1677509
bioRxiv. 2025 Oct 17. pii: 2025.10.16.682938. [Epub ahead of print]

Dietary sulfur amino acid restriction improves glucose homeostasis through hepatic de novo serine synthesis.

Andres F Ortega, Cha Mee Vang, Ferrol I Rome, Kaitlyn M Andreoni, Aiden M Phoebe, Alisa B Nelson, Peter A Crawford, James J Galligan, Stanley Ching-Cheng Huang, Curtis C Hughey.

Dietary sulfur amino acid restriction (SAAR) improves whole-body glucose homeostasis, elevates liver insulin action, and lowers liver triglycerides. These adaptations are associated with an increased expression of hepatic de novo serine synthesis enzymes, phosphoglycerate dehydrogenase (PHGDH) and phosphoserine aminotransferase 1 (PSAT1). This study tested the hypothesis that enhanced hepatic serine synthesis is necessary for glucose and lipid adaptations to SAAR. Hepatocyte-specific PSAT1 knockout (KO) mice and wild type (WT) littermates were fed a high-fat control or SAAR diet. In WT mice, SAAR increased liver PSAT1 protein (~70-fold), serine concentration (~2-fold), and 13C-serine (~20-fold) following an intravenous infusion of [U-13C]glucose. The elevated liver serine and partitioning of circulating glucose to liver serine by SAAR were attenuated in KO mice. This was accompanied by a blunted improvement in glucose tolerance in KO mice fed a SAAR diet. Interestingly, SAAR decreased liver lysine lactoylation, a SAA-supported post-translational modification known to inhibit PHGDH enzymatic activity. This suggests dietary SAAR may increase serine synthesis, in part, by lowering lysine lactoylation. Beyond glucose metabolism, dietary SAAR reduced body weight, adiposity, and liver triglycerides similarly in WT and KO mice. Collectively, these results demonstrate that hepatic PSAT1 is necessary for glucose, but not lipid, adaptations to SAAR.

DOI: https://doi.org/10.1101/2025.10.16.682938
Mol Metab. 2025 Nov 24. pii: S2212-8778(25)00195-4. [Epub ahead of print] 102288

Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.

Orion S Willoughby, Anna S Nichenko, Matthew H Brisendine, Niloufar Amiri, Shelby N Henry, Daniel S Braxton, John R Brown, Braeden J Kraft, Kalyn S Jenkins, Adele K Addington, Alexey V Zaitsev, Steven T Burrows, Ryan P McMillan, Haiyan Zhang, Spencer A Tye, Charles P Najt, Siobhan E Craige, Timothy W Rhoads, Junco S Warren, Joshua C Drake.

Metabolic flexibility, the capacity to adapt fuel utilization in response to nutrient availability, is essential for maintaining energy homeostasis and preventing metabolic disease. Here, we investigate the role of Ulk1 phosphorylation at serine 555 (S555), a site regulated by AMPK, in coordinating metabolic switching following short-term caloric restriction and fasting. Using Ulk1(S555A) global knock-in mice, we show loss of S555 phosphorylation impairs glucose oxidation in skeletal muscle and liver during short-term CR, despite improved glucose tolerance. Metabolomic, transcriptomic, and mitochondrial respiration analyses suggest a compensatory reliance on autophagy-derived amino acids in Ulk1(S555A) mice. These findings suggest Ulk1(S555) phosphorylation as a critical regulatory event linking nutrient stress to substrate switching. This work highlights an underappreciated role of Ulk1 in maintaining metabolic flexibility, with implications for metabolic dysfunction.

DOI: https://doi.org/10.1016/j.molmet.2025.102288
BMC Cancer. 2025 Nov 22.

ASAH1-mediated sphingolipid metabolic reprogramming in venetoclax resistance of AML: beyond the monocytic phenotypes.

Lei Zhao, Xinrong Xiang, Ailing Zhong, Hongbin Yu, Jinjun Yang, Mengran Chen, Hong Ding, Chenlu Yang, Yu Wu.

   BACKGROUND: Venetoclax (VEN) in combination with hypomethylating agents has emerged as a pivotal therapy for elderly acute myeloid leukemia (AML) patients ineligible for intensive chemotherapy. However, monocytic AML exhibit greater resistance to VEN-based regimens compared to non-monocytic AML. Identifying exploitable vulnerabilities will mitigate resistance and relapse.
METHODS: We conducted a comprehensive analysis of VEN resistance mechanisms in monocytic AML by integrating bulk AML datasets, single-cell RNA sequencing (scRNA-seq) of AML patient bone marrow and patient-derived xenograft (PDX) models, as well as lipidomic sequencing of induced VEN-resistant cell lines. Additionally, we examined the monocytic markers in VEN-resistant cell lines and assessed VEN sensitivity after knocking down the key sphingolipid metabolism gene ASAH1.
RESULTS: Analysis of bulk RNA-seq data revealed elevated expression of sphingolipid metabolism genes in the French-American-British (FAB) M5 subtype, which exhibited poor response to VEN-based treatment. Further analysis of scRNA-seq data showed that monocytic AML cells surviving VEN treatment demonstrated the highest sphingolipid metabolism score, particularly in CD14⁺ITGAX⁺ monocytic AML cells. Notably, induced VEN-resistant cell lines exhibited significantly increased monocytic markers and differential sphingolipid metabolism profiles compared to parental cells. Among the key regulators of sphingolipid metabolism, ASAH1 was upregulated, while SPHK1 was downregulated. Knocking down ASAH1 enhanced VEN sensitivity without reducing the expression of monocytic markers CD14/CD64。.
CONCLUSIONS: These findings suggest that aberrant sphingolipid metabolism contribute to AML resistance to VEN.

Keywords:  Acute myeloid leukemia; Drug resistance; Monocytic; Sphingolipid; Venetoclax

DOI:  https://doi.org/10.1186/s12885-025-15272-9
bioRxiv. 2025 Oct 17. pii: 2025.10.16.682859. [Epub ahead of print]

Cryo-EM reveals how ASX-173 inhibits human asparagine synthetase to activate the integrated stress response.

Kirk A Staschke, Nicholas T Walda, Lucciano A Pearce, Ronald C Wek, Wen Zhu, Yuichiro Takagi.

Targeting asparagine metabolism is a promising strategy for treating asparaginase-resistant acute lymphoblastic leukemia (ALL), sarcoma, and potentially other solid tumors. Here, we characterize the molecular mechanism by which a cell-penetrable small molecule, ASX-173, inhibits human asparagine synthetase (ASNS), the enzyme that catalyzes intracellular asparagine biosynthesis. ASX-173 reduces cellular asparagine levels, induces the integrated stress response (ISR), and reduces cell growth in HEK-293A cells. A cryo-EM structure reveals that ASX-173 engages a unique, hydrophobic pocket formed by AMP, Mg 2+ , and pyrophosphate in the C-terminal synthetase domain of ASNS, thereby enabling multivalent, high-affinity binding. Based on in vitro kinetic and thermal shift assays, we find that ASX-173 binds to the ASNS/Mg 2+ /ATP complex and is therefore a rare example of an uncompetitive enzyme inhibitor with potential therapeutic use. These findings provide a structural and mechanistic basis for targeting ASNS with small molecules, which have application in treating cancer and other human diseases.

DOI: https://doi.org/10.1101/2025.10.16.682859
Biomed Opt Express. 2025 Nov 01. 16(11): 4470-4482

Fluorescence lifetime imaging to investigate propofol-induced metabolic alterations in MDA-MB-231 cells.

Tabassum Ahmad Tasmi, Lakhvir Singh, Alex J Walsh.

The metabolic effects of anesthetic agents like propofol on cancer cells remain poorly understood despite the widespread use of anesthesia during cancer diagnosis and treatment. Fluorescence lifetime imaging microscopy (FLIM) was used to analyze propofol-induced metabolic changes in triple-negative breast cancer cells (MDA-MB-231) by monitoring endogenous NAD(P)H and FAD fluorescence lifetimes. FLIM of propofol-treated MDA-MB-231 cells revealed concentration-dependent shifts in metabolic states that were supported by Seahorse extracellular flux analysis. While the flux analysis provided population-averaged metabolic data, FLIM enabled high-resolution, dynamic mapping of metabolism in live cancer cells. Our study highlights FLIM as a label-free tool for investigating anesthetic-induced metabolic alterations in cells, offering insights into the potential metabolic mechanisms of propofol.

DOI: https://doi.org/10.1364/BOE.575969
bioRxiv. 2025 Oct 23. pii: 2025.10.22.684030. [Epub ahead of print]

NADH dehydrogenase reverses dietary and clock metabolic syndrome.

Chelsea Hepler, Nathan J Waldeck, Benjamin J Weidemann, Biliana Marcheva, You-Jia Chen, Jacqueline Hecker, Ziming Zhu, Rino Nozawa, Joseph V Mastroni, Anneke K Thorne, Colleen R Reczek, Jonathan Cedernaes, Kathryn M Ramsey, Clara B Peek, Grant D Barish, Navdeep S Chandel, Joseph Bass.

Circadian clocks are internal timing systems that enable organisms to anticipate and adapt to daily environmental changes. These rhythms arise from a transcription-translation feedback loop in which CLOCK/BMAL1 regulate the expression of thousands of genes, including their repressors PER/CRY 1 . Disruption of circadian rhythms contributes to obesity, metabolic disease, and cancer 2-4 , yet how the clock maintains metabolic homeostasis remains limited. Here we report that the clock regulates oxidative metabolism through diurnal respiration of mitochondrial respiratory chain complex I. Genetic loss of the clock and high fat diet feeding in male mice led to reduced complex I respiration within adipocytes, leading to suppression of PPAR and insulin signaling pathways. In contrast, preserving complex I function maintained adipogenic and metabolic gene networks and protected against diet- and circadian-induced metabolic dysfunction independently of weight gain. These findings reveal that circadian disruption impairs metabolic health through mitochondrial complex I dysfunction, establishing clock control of complex I as a key regulator of transcriptional and metabolic homeostasis.

DOI: https://doi.org/10.1101/2025.10.22.684030
bioRxiv. 2025 Oct 27. pii: 2025.10.27.684790. [Epub ahead of print]

The proton motive force maintains mtDNA euploidy by balancing mtDNA replication with cell proliferation.

Sneha P Rath, Vamsi K Mootha.

Human mitochondrial DNA (mtDNA) encodes 13 essential components of the electron transport chain (ETC) 1 . A typical cell contains ∼1000s of copies of mtDNA, but how this copy number is stably maintained is unclear. Here, we track mtDNA copy number (mtCN) recovery in K562 cells following transient, chemically induced depletion to uncover principles of mtCN stability. Below a critical mtCN, ETC activity fails to sustain the proton motive force (PMF) and de novo pyrimidine synthesis-both required for mtDNA replication. PMF-dependent processes like Fe-S cluster biogenesis are also disrupted and stress responses are activated that impair cell proliferation and limit further mtCN dilution by cell division. Nonetheless, mtDNA replication and recovery remain possible via mtDNA-independent PMF, generated by complex V reversal, and uridine salvage. Once mtCN is restored, the ETC and forward complex V activity re-engage, stress responses subside, and proliferation recommences. Each cell division then dilutes mtDNA, serving as a built- in brake on mtCN. Our findings suggest that mtCN homeostasis emerges from the balance of two opposing PMF-driven processes - mtDNA replication and cell proliferation - revealing a bioenergetic logic that preserves mtDNA euploidy through repeated cell divisions.

DOI: https://doi.org/10.1101/2025.10.27.684790
Methods Cell Biol. 2026 ;pii: S0091-679X(25)00001-9. [Epub ahead of print]200 211-243

SILAC-based assessment of S-palmitoylated proteins in mammalian cells by metabolic labeling and click-chemistry.

Anke Vandekeere, Sarah-Maria Fendt, Salvador Aznar Benitah, Miguel Martin-Perez.

  S-palmitoylation of cysteine residues is the only lipid-based posttranslational modification of proteins that is reversible and therefore has important implications in cellular function. S-palmitoylation has been associated with several cellular processes (e.g., cell signaling, protein transport, cell cycle, immune response, lipid metabolism, host-pathogen interaction) and human diseases, including neurological disorders, cancer, and infectious diseases. However, S-palmitoylation research has been hampered by the cumbersome experimental protocols necessary for its study. Currently, there are two main methodologies that, coupled with mass spectrometry (MS), allow the study of S-palmitoylated proteins proteome-wide. They mainly differ in the way of labeling palmitoylated proteins: one relies on "metabolic labeling" with a palmitic acid analog in living cells, while the other is based on "chemical labeling" of thiol groups derived from palmitoylated sites in extracted proteins. Although metabolic labeling is restricted to cultured cells, we will focus on this technique as it is more sensitive and specific than others. Here, we describe the protocol to measure palmitoylation in cancer cells using metabolic labeling coupled to SILAC-based mass spectrometry quantification, which can be applied to other mammalian cell models. Facilitating the use of this methodology will extend the knowledge of palmitoylation signaling and unravel potential therapeutic avenues for diseases in which this unexplored modification is implicated.

Keywords:  Mass spectrometry (MS); Metabolic labeling; Posttranslational modification; S-palmitoylation; Stable isotope labeling with amino acids in cell culture (SILAC)

DOI:  https://doi.org/10.1016/bs.mcb.2025.01.001
medRxiv. 2025 Nov 13. pii: 2025.11.11.25340023. [Epub ahead of print]

Adaptive nuclear GTP synthesis promotes glioblastoma treatment resistance and is a targetable vulnerability in patients.

Andrew J Scott, Ningning Liang, Wajd N Al-Holou, Jie Xu, Alexandra O'Brien, Angelica Lin, Vidhi Pareek, Zhou Sha, Zitong Zhao, John Z Yang, Annabel Yang, Ayesha U Kothari, Kari Wilder-Romans, Zhe Wu, Jiane Feng, Navyateja Korimerla, Ameer Elaimy, Sravya Palavalasa, Jiali Chen, Lu Wang, Li Zhang, Anthony C Andren, Peter Sajjakulnukit, Bernard Marini, Jason A Heth, Meredith A Morgan, Theodore S Lawrence, Stephen J Benkovic, Deepak Nagrath, Sriram Chandrasekaran, Nathan R Qi, Duxin Sun, Bo Wen, Manjunath P Pai, Nathan Clarke, Krithika Suresh, Yoshie Umemura, Costas A Lyssiotis, Weihua Zhou, Daniel R Wahl.

Glioblastoma (GBM), the most lethal of all brain cancers, resists therapy by rewiring metabolism and relying on GTP signaling to promote DNA repair and radiation therapy (RT) resistance. How GBM modulates GTP levels for this signaling in response to RT-induced DNA damage, and the therapeutic tractability of this metabolic activity in the context of standard-of-care chemoradiation therapy, remain unaddressed. Here, we identify acute changes in glioma metabolism within hours of RT, including an acute post-RT rewiring of guanylate synthesis driven by nuclear translocation of the rate-limiting de novo guanylate synthesis enzyme IMPDH1. This subcellular IMPDH1 re-localization and nuclear GTP accumulation are dependent on the DNA damage signal kinase DNA-PK. Targeting intracranial GTP synthesis with the FDA-approved inhibitor mycophenolate mofetil (MMF) slows repair of DNA damage and extends survival of orthotopic murine models treated with combined RT and temozolomide. Extending our findings to humans, we performed a phase 0 clinical trial revealing that oral MMF administration leads to active intracranial drug concentrations, with target engagement indicated by reversal of IMPDH upstream and downstream metabolites in recurrent GBM tumors. Together, these findings implicate IMPDH as a potential metabolic target in GBM whose pharmacological inhibition is feasible and could complement standard-of-care chemoradiation therapy.

DOI: https://doi.org/10.1101/2025.11.11.25340023
Sci Adv. 2025 Nov 28. 11(48): eady9156

How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity.

Gisele A Andree, Kelsey R Miller-Brown, Zhuangyu Zhao, Ally K Smith, Christopher D Dawson, Daniel J Deredge, Catherine L Drennan.

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2'-deoxyadenosine 5'-triphosphate (dATP)/adenosine 5'-triphosphate (ATP) ratio. To investigate allosteric activity regulation in anaerobic or class III (glycyl radical containing) RNRs, we determine cryo-electron microscopy structures of the class III RNR from Streptococcus thermophilus (StNrdD). We find that StNrdD's regulatory "cone" domains adopt markedly different conformations depending on whether the activator ATP or the inhibitor dATP is bound and that these different conformations alternatively position an "active site flap" toward the active site (ATP-bound) or away (dATP-bound). In contrast, the position of the glycyl radical domain is unaffected by the cone domain conformations, suggesting that StNrdD activity is regulated through control of substrate binding rather than control of radical transfer. Hydrogen-deuterium exchange mass spectrometry and mutagenesis support the structural findings. In addition, our structural data provide insight into the molecular basis by which ATP and dATP binding lead to the observed differential cone domain conformations.

DOI: https://doi.org/10.1126/sciadv.ady9156
bioRxiv. 2025 Nov 13. pii: 2025.11.07.687000. [Epub ahead of print]

TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity.

Jacob Du, Uthpala N Wijayaratna, Xinyue Wang, Jeffrey P Fung, Belinda Huang, Farzin Farzaneh, Donald B Kohn, Alexis J Combes, Karin M L Gaensler.

Acute myeloid leukemia (AML) is the most common acute leukemia in adults and is associated with poor outcomes due to frequent relapse after remission induction. While hematopoietic stem cell transplantation (HSCT) can improve survival, many individuals, especially older patients, are ineligible. Prior immunotherapies have not reliably induced effective anti-leukemic immunity and have been associated with severe and unpredictable toxicities. Thus, there is a need for safe and effective therapies that reduce relapse and increase overall survival (OS). We have developed a universally applicable, patient-specific, lentivirally engineered autologous AML cell vaccine, TriLeukeVax (TLV), designed to stimulate leukemia-specific cytolytic immune responses in AML patients in remission. To generate TLV, AML cells are engineered to express the highly synergistic combination of the co-stimulatory protein CD80 and the IL-15/IL-15-receptor alpha (IL-15Rα) heterodimer. Prior proof-of-concept (POC) studies demonstrated eradication of disease in >80% of leukemic mice with serial administration of TLV. In the current studies, TLV was generated from 59/60 cryopreserved, diagnostic bone marrow-derived patient AML samples. Ex vivo priming of post-remission patient T-cells by ex vivo co-culture with autologous TLV stimulated robust proliferative and cytotoxic responses. In secondary co-cultures, T-cells previously primed by initial co-culture with TLV, showed greater clonal expansion and leukemia-specific cytolytic activity towards de novo autologous AML blasts than did control, unprimed T-cells. The enhanced anti-leukemic activity of TLV-primed T-cells against de novo AML confirms the potential for vaccine administration to effectively target minimal residual disease (MRD) persisting after chemotherapy and reduce relapse.
Key Points: TriLeukeVax induces proliferation, activation, and effective anti-leukemic cytolytic responses in remission T-cells.Primed T-cells show polyclonal expansion and transcription profiles associated with proliferation, memory, and cytotoxicity.
Abstract Figure:

DOI: https://doi.org/10.1101/2025.11.07.687000
Int J Mol Sci. 2025 Nov 14. pii: 11025. [Epub ahead of print]26(22):

MTHFD2: A Retrospective and a Glance into the Future.

Costas Koufaris, Vicky Nicolaidou.

  The 1985 confirmation by Mejia and MacKenzie of mammalian NAD-dependent methylenetetrahydrofolate dehydrogenase activity launched four decades of research on methylenetetrahydrofolate dehydrogenase (NAD+-dependent), methenyltetrahydrofolate cyclohydrolase 2 (MTHFD2). This review provides a retrospective on four decades of advancements on MTHFD2 that have revealed its key roles in the folate pathway, amino acid and redox homeostasis, and the metabolism of cancer and immune cells. We trace the initial biochemical characterization of the enzyme, highlight pivotal discoveries regarding MTHFD2's metabolic and non-canonical roles, and discuss the current state of knowledge and future prospects.

Keywords:  MTHFD2; one-carbon metabolism; retrospective

DOI:  https://doi.org/10.3390/ijms262211025
bioRxiv. 2025 Oct 15. pii: 2025.10.15.682658. [Epub ahead of print]

Propionate metabolism dysregulation promotes drug-tolerant persister cell survival in non-small cell lung cancer.

Bobak Parang, Liron Yoffe, Rabia Khan, Zhongchi Li, Michal J Nagiec, Eric E Gardner, Yiwey Shieh, Rachel S Heise, Ashish Saxena, Nasser Altorki, John Blenis.

Recent studies show that genetic sequencing can not fully explain drug resistance in non-small cell lung cancer (NSCLC), suggesting undiscovered non-genetic mechanisms that can enable cancer cell survival. Propionate metabolism is the pathway by which odd-chain fatty acids, branched chain amino acids, and cholesterol are metabolized. We have previously shown that methylmalonic acid (MMA), a byproduct of propionate metabolism that accumulates when the pathway is disrupted, can activate epithelial-to-mesenchymal transition (EMT) in cell lines. But the clinical significance of propionate metabolism in cancer patients is not known. Here we show, for the first time, that propionate metabolism is dysregulated in patients with non-small cell lung cancer. MMA is elevated in lung tumors and in the serum of patients with metastatic NSCLC. Metabolism of cobalamin associated B (MMAB), a key regulatory gene of propionate metabolism, is downregulated in NSCLC and drug-tolerant persister cells, leading to MMA accumulation and EMT activation. We show that restoring expression of MMAB in NSCLC enhances targeted therapy and suppresses TGFB signaling. These findings reveal propionate metabolism dysregulation as a non-genetic mechanism of drug resistance and highlight propionate metabolism as a potential therapeutic target.

DOI: https://doi.org/10.1101/2025.10.15.682658
Sci Adv. 2025 Nov 28. 11(48): eadv7001

Visualizing dynamics of membrane rafts on live cells.

Hsiang-Ling Chuang, Yu-Chen Fa, Kum-Yi Cheng, Er-Chien Horng, Yi-Te Chou, Richard P Cheng, Li-Chen Wu, Ja-An Annie Ho, Chun-Hsien Chen.

Membrane rafts are cellular portals to external stimuli that trigger signaling cascades for sophisticated yet remarkable biochemical activities. Visualization of the topographic evolution of membrane rafts remains unreported on live cells due to the nanosized and dynamic nature. Here, an imaging strategy involving atomic force microscopy and Hadamard product is developed to unveil membrane-raft features. Michigan Cancer Foundation-7 (MCF-7) cells were subjected to fibrinogen or manganese(II) (Mn2+)/resveratrol, both of which are ligands of integrin αVβ3 embedded within membrane rafts; the former promotes metastasis, and the latter enables apoptosis. MCF-7 cellular membranes responded to the two stimulants markedly different. The size, height, spatiotemporal trajectory, and persistent time of ligand-activated nanodomains are revealed. This approach opens up a visualized platform toward the understanding of activation-associated signaling cascades.

DOI: https://doi.org/10.1126/sciadv.adv7001
Cells. 2025 Nov 10. pii: 1759. [Epub ahead of print]14(22):

Na+/H+ Exchanger 1 Inhibition Overcomes Venetoclax Resistance in Acute Myeloid Leukemia.

Shin Young Hyun, Eun Jung Na, Yu Ri Kim, Yoo Hong Min, June-Won Cheong.

  Despite advances with novel targeted agents (e.g., BCL-2 or IDH inhibitors) combined with chemotherapy for acute myeloid leukemia (AML), drug resistance persists. We investigated whether blocking Na+/H+ exchanger 1 (NHE1) could enhance AML cell sensitivity to the BCL-2 inhibitor venetoclax and sought to determine the molecular mechanisms. Our results demonstrated that co-treatment with venetoclax and the NHE1 inhibitor 5-(N,N-hexamethylene) amiloride (HMA) synergistically induced apoptosis in both venetoclax-sensitive and -resistant leukemic cell lines. Specifically, the combination significantly increased apoptosis in venetoclax-resistant THP-1 cells to 72.28% (17.79% with 100 nM venetoclax and 10.15% with 10 μM HMA alone; p < 0.001). Conversely, another venetoclax-resistant line, U-937, showed no significant apoptotic response to the combination. In THP-1 cells, this synergy was mediated via a caspase-dependent programmed cell death pathway, evidenced by an increased BAX/BCL-2 ratio, mitochondrial cytochrome c release, and subsequent caspase-9 and caspase-3 activation. Furthermore, co-treatment downregulated the anti-apoptotic protein MCL-1 and reduced PI3K and Akt phosphorylation, suggesting that inhibition of these survival pathways also contributed to the synergistic effect. Inhibition of NHE1 may substantially enhance venetoclax sensitivity in certain AML models, particularly in venetoclax-resistant THP-1 cells but not in U-937, highlighting biological diversity and the probable involvement of alternative survival pathways.

Keywords:  Na-H exchanger 1; PI3K/Akt pathway; acute myeloid leukemia; resistance; venetoclax

DOI:  https://doi.org/10.3390/cells14221759
bioRxiv. 2025 Nov 06. pii: 2025.11.05.686813. [Epub ahead of print]

Iron addicted colorectal cancers exploit Heme-Complex II axis to resist oxidative cell death.

Chesta Jain, Muqit Essani, Roshan Kumar, Nupur K Das, Rashi Singhal, Nicholas J Rossiter, Brandon Chen, Wesley Huang, Zheng Hong Lee, Sumeet Solanki, Yuezhong Zhang, Peter Sajjakulnukit, Li Zhang, Prarthana J Dalal, David A Hanna, Shannon McCollum, Elena M Stoffel, Joel K Greenson, L James Maher, Costas A Lyssiotis, Ruma Banerjee, Yatrik M Shah.

Colorectal cancer (CRC) cells are addicted to iron, which fuels nucleotide synthesis, mitochondrial respiration, and rapid proliferation. Yet paradoxically, high intracellular iron is cytotoxic to most other cells, raising the question of how CRC cells tolerate and exploit iron-rich environments. One pathway thought to mediate iron toxicity is ferroptosis, an iron-dependent form of cell death. However, most ferroptosis regulators were identified through synthetic chemical screens or small molecule activators, and it remains unclear whether these canonical pathways explain how iron itself triggers cell death, particularly in vivo . Here, using multi-omics profiling, CRISPR screening, and in vivo models, we uncover a heme-succinate dehydrogenase (SDH)-Coenzyme Q (CoQ) axis that enables CRC cells to buffer iron-induced oxidative stress. Heme-dependent SDH reduces CoQ, which redistributes to mitochondrial and plasma membranes to detoxify lipid ROS as a radical trapping antioxidant. This pathway functions alongside, and in some contexts independently of, canonical ferroptosis regulators. These findings reveal that CRCs co-opt metabolic cofactors not only for growth but also for survival under physiologically toxic iron levels, uncovering new vulnerabilities for therapy.

DOI: https://doi.org/10.1101/2025.11.05.686813
ACS Infect Dis. 2025 Nov 27.

The Inlet, Outlet, and New Ratchet Element for Proton Transfer of the Acinetobacter baumannii F-ATP Synthase and Their Critical Role for Viability.

Khoa Cong Minh Le, Vandana Grover, Amaravadhi Harikishore, Tuck Choy Fong, Jan Kazimierz Marzinek, Alexander Krah, Dang Hai Pham, Peter John Bond, Gerhard Grüber.

  The F1FO-ATP synthase is essential to the aerobe Acinetobacter baumannii. Its FO-domain utilizes the proton motive force to rotate the turbine (c10-ring) inside the stator (a subunit), which generates a torque that is translated to the catalytic F1-domain for adenosine 5'-triphosphate (ATP) synthesis. Here, we investigated key features of the FO-domain, including the proton intake channel, proton donor and acceptor residues, an A. baumannii unique subunit a helix, and the proton exit pathway. By employing a heterologous system, we generated mutants and studied their growth kinetic properties in minimal media, as well as the ATP synthesis activity of their inverted-membrane vesicles. The findings highlight the front entry as the main proton uptake pathway and the key residues involved in proton translocation. Molecular dynamics (MD) simulations confirm the role of these charged residues, which interact with water molecules to facilitate a water-mediated proton transfer in a Grotthuss-like mechanism. Similarly, the exit channel with R224 of subunit a playing a central role is described. Importantly, the sequential flow of proton intake, turbine rotation, and proton release are modulated by the unique a subunit helix, which functions like a molecular ratchet to facilitate effective proton transfer for the final formation of ATP. The importance in function, difference in amino acid content, and uniqueness in regulation by its specific molecular ratchet make the A. baumannii proton pathway an attractive inhibitor target, where a cork-like molecule could prevent proton intake and/or release with the consequence of ATP synthesis and cell growth inhibition.

Keywords:  ATP synthase; Acinetobacter baumannii; antibiotics; bacterial pathogenesis; bioenergetics; membrane protein

DOI:  https://doi.org/10.1021/acsinfecdis.5c00619
Cell Metab. 2025 Nov 25. pii: S1550-4131(25)00476-0. [Epub ahead of print]

A metabolic atlas of mouse aging.

Steven E Pilley, Dominik Awad, Djakim Latumalea, Connie New, Edgar Esparza, Shuo Wang, Xuanyi Shi, Li Zhang, Maximilian Unfried, Jasinda H Lee, Ernst Schmid, Ipsita Mohanty, Jenna L E Blum, Shivaanishaa Raventhiran, Esther Wong, Preeti R Iyengar, Racheal Mulondo, Sriraksha Bharadwaj Kashyap, Darius Moaddeli, Peter Sajjakulnukit, Damien Sutton, Harrison K A Wong, Yaqi Gao, George Wang, Aeowynn J Coakley, Gilberto Garcia, Ryo Higuchi-Sanabria, Anja Karlstaedt, Timothy L Frankel, Marina Pasca di Magliano, Whitaker Cohn, Sophia Liu, Bingfei Yu, Pieter C Dorrestein, Ernest Fraenkel, Shawn M Davidson, William B Tu, Brian K Kennedy, Costas A Lyssiotis, Peter J Mullen.

  Humans are living longer and experiencing more age-related diseases, many of which involve metabolic dysregulation, but how metabolism changes in multiple organs during aging is not known. Answering this could reveal new mechanisms of aging and therapeutics. Here, we profile metabolic changes in 12 organs in male and female mice at 5 different ages. We also develop organ-specific metabolic aging clocks that identify metabolic drivers of aging, including alpha-ketoglutarate, previously shown to extend lifespan in mice. We also use the clocks to uncover that carglumic acid is a potential driver of aging and show that it is synthesized by human cells. Finally, we validate that hydroxyproline decreases with age in the human pancreas, emphasizing that our approach reveals insights across species. This study reveals fundamental insights into the aging process and identifies new therapeutic targets to maintain organ health.

Keywords:  LC-MS/MS; MALDI-MSI; aging; aging clocks; healthspan; human tissue; hydroxyproline; metabolism; scRNA-seq; sex

DOI:  https://doi.org/10.1016/j.cmet.2025.10.016
Nat Biotechnol. 2025 Nov 26.

All-optical visualization of specific molecules in the ultrastructural context of brain tissue.

Ons M'Saad, Allison Cairns, Jonathan Gulcicek, Ravi Kiran Kasula, Jacob Liao, Ilona Kondratiuk, Emma H Bewersdorf, Phylicia Kidd, Hanieh Falahati, Juliana E Gentile, Robert F Niescier, Katherine Watters, Robert C Sterner, Seong-Il Lee, Xiaojia Guo, Xinran Liu, Gary Desir, Pietro De Camilli, James E Rothman, Anthony J Koleske, Thomas Biederer, Aaron T Kuan, Joerg Bewersdorf.

Understanding the molecular anatomy and neural connectivity of the brain requires imaging technologies that can map the three-dimensional nanoscale distribution of specific proteins in the context of brain ultrastructure. Light and electron microscopy visualize either specific labels or anatomical ultrastructure but combining molecular specificity with anatomical context is challenging. Here we present pan-expansion microscopy of tissue (pan-ExM-t), an all-optical imaging method that combines ~16-24-fold linear expansion with fluorescent pan-stainings of proteins and lipids (providing electron microscopy-like ultrastructural context) and immunolabeling (for molecular imaging). We demonstrate the versatility of this approach by imaging synaptic and cell-specific antibodies in the ultrastructural three-dimensional context of presynaptic and postsynaptic densities, neuropil nanoarchitecture and cellular organelles in dissociated neuron cultures, and mouse brain tissue sections. Furthermore, we demonstrate tracing of neuronal circuitry from pan-ExM-t image volumes, suggesting that any laboratory with access to a confocal microscope can now localize specific molecules within nanoscale cellular and circuit contexts.

DOI: https://doi.org/10.1038/s41587-025-02905-4
bioRxiv. 2025 Oct 15. pii: 2025.10.15.682580. [Epub ahead of print]

Region-specific human brain organoids reveal synaptic and cell state drivers of glioblastoma invasion.

Tarun N Bhatia, Saisrinidhi Ganta, Mostafa Meselhe, Caitlin Sojka, Antoni Martija, Lisa Nieland, Uriel Rufen-Blanchette, Anson Sing, Alexia King, Brain Organoid Hub, Aparna Bhaduri, Kimberly Hoang, Edjah Nduom, Renee D Read, Jeffrey Olson, Steven A Sloan.

Glioblastoma (GBM) is a highly heterogenous and malignant brain tumor, in part because it disrupts normal brain circuits to fuel its own growth and invasion. Thus, there is a need to identify the molecular features of invasive GBM cells and their regulators in the neural microenvironment. To address this in a fully human model, we engrafted patient-derived GBM cells (total n= 15 independent samples) from three sources- fresh neurosurgical resections, cell lines, and whole GBM organoids-into human induced pluripotent stem cell-derived organoids patterned to forebrain, midbrain, and spinal cord identities. GBM cells from all sources infiltrated brain organoids within 2 days post-engraftment, reaching maximal invasion by day 14. Across organoids of distinct spatial and maturational milieu, GBM cells showed a consistent reduction in astrocyte-like states and an enrichment in neuron/glia progenitor-like (NPC-like) states. These NPC-like GBM cells expressed neuronal and synaptic machinery, and tumors enriched in this transcriptomic state prior to engraftment achieved greater organoid coverage, suggesting enhanced infiltration and synaptic integration of this GBM cell type. Although GBM cell states converged across organoid types after engraftment, infiltration was greater in the forebrain than spinal cord. This is likely reflective of synaptic input from deep-layer TBR1⁺ excitatory neurons in the forebrain, as demonstrated by a combination of rabies-based monosynaptic tracing and single-cell transcriptomics. In contrast, inhibitory neurons were the predominant synaptic partners of GBM in the spinal cord. Together, this fully human model of the neural-GBM connectome reveals how neuron-like GBM states and regionally distinct synaptic inputs cooperatively shape tumor invasion.

DOI: https://doi.org/10.1101/2025.10.15.682580