bims-medica 2025-10-05 papers

bims-medica

Biomed News

on Metabolism and diet in cancer

Issue of 2025–10–05
nineteen papers selected by
Brett Chrest, Wake Forest University

Quantifying endogenous and tracer-derived ketone bodies using a dual-label UHPLC-MS/MS method.
Metabolic reprogramming represents a targetable mechanism to overcome acquired resistance to venetoclax in acute myeloid leukemia.
Regulation of pyruvate dehydrogenase complex: Dancing to different drums in cancer.
Alternatively Spliced Citrate Synthase Supports Colorectal Cancer.
ACSS2-Mediated Metabolic-Epigenetic Crosstalk Drives Fulvestrant Resistance and Represents a Novel Therapeutic Target.
Ketogenic Diet and Thyroid Function: A Delicate Metabolic Balancing Act.
Factors affecting response and resistance to venetoclax in acute myeloid leukemia.
Final Results from a First-in-Human Phase 1 Study of the Dual Isocitrate Dehydrogenase (IDH) 1/2 Inhibitor, LY3410738, in Advanced Solid Tumors Harboring IDH1 or IDH2 Mutations.
MRC2 expression modulates metabolism in acute myeloid leukemia stem cells.
Dietary methionine restriction primes T cell metabolism for activation and tumor inhibition and enhances the efficacy of immune checkpoint blockade.
Absolute quantification of TCA cycle intermediates in mouse ocular tissues reveals distinct tissue- and sex-specific mitochondrial metabolism.
Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22.
Long-term outcomes in FLT3-mutated acute myeloid leukemia after frontline hypomethylating agent, venetoclax and a FLT3 inhibitor.
A live cell biosensor protocol for high-resolution screening of therapy-resistant cancer cells.
Mitochondrial respiratory function in human platelets: Influence of sample preparation, assay buffer, and instrumental platform.
Imaging of mitochondrial matrix pH dynamics reveals a functional interaction between the ADP/ATP carrier and ATP synthase to regulate H+ distribution.
Toward a working definition of ketogenic diet resistance in GLUT1 deficiency syndrome.
Preferential lactate metabolism in the human brain during exogenous and endogenous hyperlactataemia.
An extended network for regulation of heme homeostasis in cells.

Talanta. 2025 Sep 30. pii: S0039-9140(25)01410-9. [Epub ahead of print]298(Pt A): 128919

Quantifying endogenous and tracer-derived ketone bodies using a dual-label UHPLC-MS/MS method.

Sandra Adámez-Rodríguez, Eric D Queathem, Abdirahman Hayir, María Luisa Marina, María Castro-Puyana, Patrycja Puchalska.

  Acetoacetate (AcAc) and β-hydroxybutyrate (βOHB) are ketone bodies involved in energy metabolism, particularly during physiological states of glucose scarcity, such as fasting, exercise, and the implementation of a ketogenic diet. The production (ketogenesis) and utilization (ketolysis) of ketone bodies are dynamic processes that can be quantified using stable isotope-labeled tracers in metabolic tracing studies, necessitating precise and sensitive analytical methods for accurately measuring both labeled and unlabeled pools. Although UHPLC-MS/MS has recently emerged as a reliable tool for quantifying ketone bodies, its dependence on 13C-labeled internal standards limits its utility in 13C-based tracer studies. AcAc, in particular, poses challenges due to its chemical instability and the scarcity of authentic, stable, isotopically labeled internal standards. While the chemical reduction of AcAc to βOHB provides a solution, this necessitates a cumbersome desalting step. To overcome these limitations, we developed a novel approach using deuterated AcAc (d3-AcAc) and [3,4,4,4-d4]βOHB as internal standards for the simultaneous quantification of 13C-labeled and unlabeled ketone bodies in biological samples. We optimized the synthesis of AcAc from ethyl-AcAc via base-catalyzed hydrolysis, achieving 99.2 ± 0.2 % purity at 60 °C for 3 h, as confirmed by 1H NMR. Stability assessments in the extraction buffer and post-extraction serum samples confirmed the robustness of newly synthesized d3-AcAc for at least 5 h. A comparative analysis against the labor-intensive conventional method demonstrated superior precision, accuracy, and ease of application, enabling high-throughput metabolic and clinical studies. The optimized UHPLC-MS/MS method substantially improves metabolic tracing capabilities, enabling rapid and accurate investigation of ketone body tracing studies across various physiological and pathological conditions.

Keywords:  Acetoacetate; Beta-hydroxybutyrate; Flux modeling; Ketone bodies; Quantification; Stable isotopes

DOI:  https://doi.org/10.1016/j.talanta.2025.128919
Biochim Biophys Acta Mol Basis Dis. 2025 Oct 01. pii: S0925-4439(25)00413-2. [Epub ahead of print] 168065

Metabolic reprogramming represents a targetable mechanism to overcome acquired resistance to venetoclax in acute myeloid leukemia.

Gustavo Nery de Queiroz, Keli Lima, Marcella Cipelli, Victoria Tomaz, Luiz Gustavo Ferreira Cortez, Marina de Franca Basto Silva, Rafael Lucas Muniz Guedes, Paulo Vidal Campregher, Eduardo Magalhães Rego, Niels Olsen Saraiva Câmara, Leticia Veras Costa-Lotufo, João Agostinho Machado-Neto.

  Acute myeloid leukemia (AML) often develops resistance to the BCL2 inhibitor venetoclax through metabolic reprogramming. This study established acquired venetoclax-resistant AML models (MV4-11VR and MOLM-13VR) to explore resistance mechanisms and therapeutic strategies. Cell viability and apoptosis assays revealed robust acquired resistance to venetoclax upon intermittent drug exposure. Metabolic profiling revealed distinct adaptations: MV4-11VR cells favored glycolysis, while MOLM-13VR cells increased oxidative phosphorylation. Proteomic analysis supported these findings, showing pathway enrichment for carbohydrate metabolism in MV4-11VR and aerobic energy production in MOLM-13VR. Despite these differences, both models shared hyperactivation of the PI3K/AKT/mTOR pathway, as shown by RPS6 hyperphosphorylation. Apoptotic regulation also diverged between the cellular models in relation to modulated BCL2-related genes and activation of the MAPK signaling pathway. Targeting these metabolic changes with metformin (a mitochondrial complex I inhibitor) or KPT-9274 (a NAMPT inhibitor) re-sensitized resistant cells to venetoclax. Combination treatments showed strong synergy and near-complete cell elimination. These results highlight metabolic reprogramming as a heterogeneous but targetable resistance mechanism and support combining metabolic inhibitors with BCL2 blockade to treat refractory AML.

Keywords:  Acute myeloid leukemia; Glycolysis; Metabolic reprogramming; OXPHOS; Targeted therapy; Venetoclax resistance

DOI:  https://doi.org/10.1016/j.bbadis.2025.168065
Int J Cancer. 2025 Oct 04.

Regulation of pyruvate dehydrogenase complex: Dancing to different drums in cancer.

Mulchand S Patel, Todd C Rideout.

  Mechanisms governing the regulation of pyruvate dehydrogenase complex (PDC) are markedly modified in cancer cells compared to normal cells. PDC activity in normal cells is controlled by the reversible phosphorylation of three serine residues by dedicated kinases and phosphatases. Recent advances in metabolic reprogramming of glucose in cancer cells show that new and expanded mechanisms operate to regulate PDC. This comprehensive review presents several post-translational modifications of PDC proteins such as phosphorylation, acetylation, lactylation, methylation, and others (at least 12). Transcriptional regulation of PDC-specific kinase and phosphatase genes amplifies cancer-specific regulation of PDC. In some cancer cells, to enhance the mitochondrial oxidative metabolism to meet increased energy requirements, PDC is maintained in its active state by employing yet another novel mechanism involving AMPK-mediated phosphorylation of two different serine residues. Interestingly, impairment in PDC function as a major supplier of mitochondrial acetyl-CoA to the nuclear pool of acetyl-CoA is circumvented by the translocation of the PDC to the nucleus for histone acetylation. These cancer-specific PDC regulatory mechanisms represent an incredible advancement in our understanding of the reprogramming of cellular metabolism in cancer cells and could contribute to the development of new therapeutic strategies.

Keywords:  aerobic glycolysis; cancer; nuclear translocation; posttranslational modifications; pyruvate dehydrogenase complex

DOI:  https://doi.org/10.1002/ijc.70189
Cancer Res. 2025 Oct 01. OF1-OF3

Alternatively Spliced Citrate Synthase Supports Colorectal Cancer.

Désirée Schatton, Christian Frezza.

Metabolic changes are a major hallmark of cancer with the mitochondrial tricarboxylic acid (TCA) cycle playing a central role in this process. Remodeling of the TCA cycle occurs in cancer cells to sustain the increased anabolic and energetic demands required to grow, proliferate, and metastasize. Alternative splicing (AS) is increasingly recognized as a key regulator of cancer metabolism, yet its specific impact on TCA cycle enzymes remains unclear. In this issue of Cancer Research, Cheung and colleagues describe a novel splicing isoform of citrate synthase (CS), termed CS-ΔEx4, which is highly expressed in colorectal cancer. This CS-ΔEx4 isoform forms heterocomplexes with full-length CS, enhancing CS activity and promoting the metabolic reprogramming characteristic of malignancy. Overexpression of CS-ΔEx4 increases mitochondrial respiration and drives glycolytic carbon flux toward TCA intermediates, resulting in elevated levels of the metabolite 2-hydroxyglutarate. Mechanistically, this increase in 2-hydroxyglutarate, facilitated by increased activity of phosphoglycerate dehydrogenase, leads to epigenetic alterations that support oncogenic gene expression and tumor progression. Suppression of CS-ΔEx4 or pharmacologic inhibition of its activity reverts these metabolic and epigenetic changes, reducing cancer cell survival and metastatic potential. These findings establish a direct link between AS of a core metabolic enzyme and the emergence of cancer hallmarks, suggesting that targeting AS-derived variants like CS-ΔEx4 may represent a promising therapeutic strategy for colorectal cancer and potentially other malignancies in which such isoforms are expressed. See related article by Cheung et al., p. XX.

DOI: https://doi.org/10.1158/0008-5472.CAN-25-3356
bioRxiv. 2025 Sep 23. pii: 2025.09.23.678089. [Epub ahead of print]

ACSS2-Mediated Metabolic-Epigenetic Crosstalk Drives Fulvestrant Resistance and Represents a Novel Therapeutic Target.

Ayça N Mogol, Jin Young Yoo, Alicia Arredondo Eve, Mahima Goel, David J Dutton, Claire P Schane, Audrey Lam, Debapriya Dutta, Betsy Barnick, Eda D Erdogan, Erik R Nelson, Maria Grosse-Perdekamp, Zeynep Madak Erdogan.

1.Endocrine therapies target hormone-dependent cancer cells, primarily through estrogen receptor alpha (ERα), expressed in ∼70% of breast cancers (ER+). Despite treatment advances, 30-40% of ER+ breast cancer patients experience recurrence and metastasis, with 5-year survival rates of only 31.9%. We validated poor outcomes for liver metastasis patients treated with Fulvestrant (Fulv) using the local Carle Foundation Hospital cohort and examined metabolic pathways in liver metastatic patient-derived xenograft (PDX) models, revealing upregulated lipid and acetyl-CoA production. Our previous work demonstrated that combining Fulv with acetyl-CoA synthase inhibitor (ACSI) targeting Acyl-CoA Synthetase Short Chain Family Member 2 (ACSS2), synergistically reduced ER+ metastatic breast cancer (MBC) cell viability in vitro. Using multiple analytical approaches-isotope tracing, CUT&RUN sequencing, immunofluorescence, western blot, and RNA sequencing-we characterized the effects of acetyl-CoA synthesis inhibition on Fulv-induced alterations. Fulv treatment of MBC cells increased ACSS2 expression and acetate utilization. Isotope tracing revealed that Fulv decreased acetate flux to the TCA cycle while promoting fatty acid synthesis. Importantly, ACSS2 was predominantly nuclear and CUT&RUN sequencing showed that Fulv treatment increased ACSS2 chromatin occupancy and ERα/ACSS2/H3K27ac overlapping sites near genes associated with tumor progression, which was eliminated by combination of ACSI and Fulv. RNA sequencing revealed reduction of Fulv-induced expression of genes involved in cancer cell metabolism and key signaling pathways in cancer with the Fulv+ACSI combination. In a therapy-resistant xenograft model, combining Fulv and ACSI reduced Fulv-dependent increase in metastatic burden. Our findings indicate ACSS2 contributes to endocrine therapy resistance through nuclear acetyl-CoA provision for epigenetic alterations. Targeting these cancer cell adaptations represents a novel therapeutic approach potentially reducing metastasis-related mortality and improving breast cancer treatment outcomes.

DOI: https://doi.org/10.1101/2025.09.23.678089
Curr Issues Mol Biol. 2025 Aug 28. pii: 696. [Epub ahead of print]47(9):

Ketogenic Diet and Thyroid Function: A Delicate Metabolic Balancing Act.

Petar Vranjić, Mladen Vuković, Senka Blažetić, Barbara Viljetić.

  The ketogenic diet (KD), a high-fat, low-carbohydrate diet, causes profound metabolic adaptations that go beyond energy production and affect endocrine function and thyroid hormone regulation. By shifting the body's primary fuel source from glucose to fatty acids and ketones, the KD alters insulin signaling, inflammation levels and deiodinase activity, which together affect thyroid hormone metabolism. While this metabolic shift offers potential benefits such as improved insulin sensitivity and reduced systemic inflammation, it also raises concerns about reduced triiodothyronine (T3) levels and altered hypothalamic-pituitary-thyroid (HPT) axis dynamics. This review explores the mechanisms by which the KD affects thyroid function, highlighting both the potential therapeutic benefits and associated risks. Special attention is given to how genetic predispositions, gut microbiota composition and sex-based hormonal differences influence thyroid adaptation to a KD. In addition, there are indications that the influence of the KD on cell metabolism could have therapeutic potential in conditions such as autoimmune thyroid diseases and thyroid cancer. Understanding the delicate balance between the benefits and risks of KD for thyroid health is essential for optimizing its clinical applications and defining individual nutritional strategies.

Keywords:  inflammation; ketogenic diet; thyroid function; triiodothyronine

DOI:  https://doi.org/10.3390/cimb47090696
Front Oncol. 2025 ;15 1577908

Factors affecting response and resistance to venetoclax in acute myeloid leukemia.

Michael D Diamantidis.

  The use of the BCL2 inhibitor venetoclax in combination with hypomethylating agents (HMA) is a revolution for the treatment of frail and elderly acute myeloid leukemia (AML) patients. This effective treatment strategy is increasingly more and more applicable for other subsets of AML patients and is currently being tested in numerous clinical trials in combination with other drugs in all treatment lines. In particular, venetoclax combinations can also serve as a definitive therapy or as an effective bridge to allogeneic hematopoietic stem cell transplantation (HSCT). However, the factors affecting response to venetoclax in the abovementioned AML patients are not completely clear and understood until today. The aim of this review is to describe the molecular and clinical patterns of response and durable remission of venetoclax-based combinations in AML patients. Hence, mutations in IDH1, IDH2, ASXL1, NPM1, DDX41, chromatin-cohesin complex and splicing-factor genes predict superior response to venetoclax, while inferior response to the drug has been observed for FLT3-ITD, KRAS, NRAS and TP53 gene mutations. Intriguingly, the achievement of measurable residual disease (MRD) negativity in the first four cycles of venetoclax administration characterizes a subgroup of NPM1-mutated AML patients with a more favorable outcome. Even though focus will be given on factors influencing response to the drug in this review, the main mechanisms of resistance to venetoclax in AML patients will also be discussed.

Keywords:  BCL2 (B-cell lymphoma 2) inhibition; MCL1 (myeloid cell leukemia sequence 1) overexpression; acute myeloid leukemia (AML); azacitidine (AZA); hypomethylating agents (HMAs); resistance; response; venetoclax (VEN)

DOI:  https://doi.org/10.3389/fonc.2025.1577908
Clin Cancer Res. 2025 Sep 30.

Final Results from a First-in-Human Phase 1 Study of the Dual Isocitrate Dehydrogenase (IDH) 1/2 Inhibitor, LY3410738, in Advanced Solid Tumors Harboring IDH1 or IDH2 Mutations.

James J Harding, Do-Youn Oh, Teresa Macarulla Mercade, Lipika Goyal, Andreas Varkaris, Lola Jade Palmieri, Masafumi Ikeda, Shunsuke Kondo, Li-Yuan Bai, Makoto Ueno, Li-Tzong Chen, Kyriakos P Papadopoulos, Rachna T Shroff, Sani H Kizilbash, Antoine Hollebecque, Jorge Adeva, Rasha Cosman, Tomoya Yokota, Joon Oh Park, Anita Turk, Chih-Yi Liao, Taroh Satoh, Mitesh J Borad, Anthony El-Khoueiry, Nilofer Azad, Kurt A Jaeckle, Herbert H Loong, Wei-Peng Yong, Mark H Bender, Sunoj Chacko Varughese, Deepa Sachdeva, David B Radtke, Ivelina Gueorguieva, Anna M Szpurka, Hsiao-Rong Chen, Hui Liu, Xiaojian Xu, Jordi Rodon.

BACKGROUND: Isocitrate dehydrogenase (IDH) 1/2-isoform inhibitors have clinical efficacy in IDH1/IDH2-mutated (mIDH1/mIDH2) neoplasms. However, primary and secondary resistance limits their therapeutic potential. LY3410738, an oral, brain penetrant, dual mIDH1/mIDH2 isoform-selective inhibitor was designed to overcome resistance.
METHODS: This global, multicenter, open-label, phase 1 study of patients with IDH-mutant solid tumors evaluated LY3410738 as monotherapy (dose-escalation) for advanced solid tumors in combination with cisplatin-gemcitabine for newly diagnosed cholangiocarcinoma or with durvalumab for relapsed/refractory cholangiocarcinoma (dose-expansion) (NCT04521686). Primary objectives were the maximum tolerated dose (MTD), recommended phase 2 dose, and preliminary antitumor activity. Safety, pharmacokinetics, inhibition of D-2-hydroxyglutarate, and circulating tumor DNA (ctDNA) were assessed.
RESULTS: Overall, 119 patients received LY3410738 alone (N=94) or in combination with cisplatin-gemcitabine (N=19) or durvalumab (N=6). No dose-limiting toxicities (DLTs) were observed; the MTD was not determined. Common adverse events included nausea, vomiting, and decreased appetite. Overall response rates of 5.2% and 11.1%, and disease control rates of 56.9% and 63.0%, were observed for patients with relapsed/refractory IDH1- or IDH2-mutant cholangiocarcinoma or IDH1-mutant glioma, respectively. D-2-hydroxyglutarate normalization was rapid and durable. In dose-expansion cohorts, combination treatments were tolerable, with one DLT in the durvalumab cohort. LY3410738 plus cisplatin-gemcitabine demonstrated a response rate of 42.1%, median DOR of 8.1 months, median PFS of 10.2 months for patients with newly diagnosed IDH-mutant cholangiocarcinoma.
CONCLUSIONS: LY3410738 demonstrated largely cytostatic antitumor activity in IDH1- or IDH2-mutated cholangiocarcinoma and IDH1-mutated gliomas. LY3410738 plus cisplatin-gemcitabine exhibited favorable antitumor activity in patients with treatment-naïve IDH-mutated cholangiocarcinoma, warranting further exploration as a treatment strategy.

DOI: https://doi.org/10.1158/1078-0432.CCR-25-0174
Cancer Lett. 2025 Sep 26. pii: S0304-3835(25)00640-8. [Epub ahead of print] 218068

MRC2 expression modulates metabolism in acute myeloid leukemia stem cells.

Taylor S Mills, Marlon Arnone, Elsa Görsch, Simone Poeschel, Stefan Winter, Jessica Kuebler, Lucca M Kimmich, Florian A Büttner, Jan Weller, Saskia S Rudat, Lucas Mix, Jan C Schroeder, Anna M Paczulla Stanger, Matthias Schwab, Claudia Lengerke.

  Leukemic stem cells (LSC) are well recognized for their essential roles in acute myeloid leukemia (AML) initiation and relapse. LSC can be distinguished from non-LSC AML cells by the expression of specific cell surface markers, but there is considerable phenotypic heterogeneity among LSC in AML. Here, using primary patient samples, we report that mannose receptor C-type 2 (MRC2) can be used to enrich for LSC across various AML subtypes. When compared to MRC2- AML cells isolated from the same patient samples, MRC2+ leukemic subpopulations show increased in vitro clonogenic capacity, a stemness transcriptomic signature, and enhanced leukemic capacity in mouse xenograft models. Further, we find that MRC2 is functional on AML cells, and enables their robust uptake of collagen, which supports their glycolytic metabolism. In sum these data highlight the use of functional surface markers to distinguish LSC in AML, and how they can yield insight into their unique characteristics.

Keywords:  MRC2; acute myeloid leukemia; glycolysis; leukemia stem cells; mannose receptor c-type2; metabolism

DOI:  https://doi.org/10.1016/j.canlet.2025.218068
bioRxiv. 2025 Sep 23. pii: 2025.09.18.676961. [Epub ahead of print]

Dietary methionine restriction primes T cell metabolism for activation and tumor inhibition and enhances the efficacy of immune checkpoint blockade.

Xiaoqing Qing, Binita Chakraborty, Panpan Liu, Sandeep Artham, Patrick K Juras, Dongyin Guan, Kristen E Pauken, Ching-Yi Chang, Xia Gao.

The proliferation of many cancer cells is methionine dependent and dietary methionine restriction (MR) has shown anti-tumor effects in a wide variety of immunodeficiency preclinical models. Yet, whether MR exerts an anti-tumor effect in the presence of an immune-competent background remains inconclusive. Accumulating evidence has shown an essential role of methionine in immune cell differentiation and function. Thus, competition for methionine between tumor cells and immune cells in the tumor microenvironment may drive tumor growth and tumor response to therapy. Here, we aim to define the impact of MR on tumor growth and associated immunity. We first assessed the effect of MR in a series of immunocompetent mouse models of melanoma, colorectal cancer, breast cancer, and lung. MR led to a broad tumor inhibition effect across these models and such tumor inhibition was not sex-or genetic background-dependent but appears to be fully or partially immune-dependent. Through flow cytometry analysis, we found a consistent increase in intratumoral activated CD8 + T cells across different tumor models and depletion of CD8 + T cells partially or completely reversed MR-induced tumor inhibition in a model dependent manner. Interestingly in young healthy non-tumor-bearing mice, MR increased spleen CD3 + and CD8 + T cell populations. Metabolomics and RNAseq analysis of spleen-derived CD8 + T cells revealed significant increase in purine metabolism and amino acid metabolism and that are in line with the metabolic feature of activated T cells. Furthermore, MR improved the efficacy of anti-PD1 immune checkpoint blockade. Together, MR primes T cell metabolism for its anti-tumor effect and improves the efficacy of anti-PD1 checkpoint blockade.

DOI: https://doi.org/10.1101/2025.09.18.676961
bioRxiv. 2025 Sep 27. pii: 2025.09.25.678562. [Epub ahead of print]

Absolute quantification of TCA cycle intermediates in mouse ocular tissues reveals distinct tissue- and sex-specific mitochondrial metabolism.

Cloe Ratliff, David Hansman, Tuan Ngo, Yinxiao Xiang, Artjola Puja, Mark Eminhizer, Jinyu Lu, Isabella Mascari, Diana Alabdallat, Jianhai Du.

Objective: Mitochondrial tricarboxylic acid (TCA) cycle is central to energy production and redox balance in the eye, which must sustain high metabolic activity to support vision. Retinal neurons, the retinal pigment epithelium (RPE), cornea, and lens each have distinct physiological roles and metabolic demands, yet the absolute concentrations of key TCA intermediates and their variation by tissue, sex, and time of day are not well-defined.
Methods: Targeted gas chromatography-mass spectrometry was employed to quantify the absolute concentrations of TCA cycle metabolites in mouse ocular tissues collected at 10 AM and 2 PM to capture diurnal variations. Key metabolite ratios were subsequently calculated to provide insight into TCA cycle dynamics across eye tissues.
Results: The retina showed the highest concentrations of TCA metabolites among all ocular tissues, particularly succinate, citrate, and malate, consistent with its high energy demands. The RPE/choroid demonstrated well-balanced intermediates with the highest α-ketoglutarate (α-KG)/Isocitrate ratio, reflecting its efficient mitochondrial oxidation and reductive carboxylation. Corneal metabolism was featured by dominant malate, especially in females, suggesting a metabolic adaptation for redox regulation and oxidative stress defense. The lens had uniformly low metabolite levels except for succinate, indicating minimal mitochondrial activity under physiologically low oxygen conditions. Notably, both the cornea and lens showed significant sex-dependent and diurnal variations in TCA cycle intermediates.
Conclusion: This study demonstrates distinct tissue-specific mitochondrial metabolism in the eye, reflecting the unique functional and biochemical demands of each tissue. These metabolic signatures may underlie their susceptibility to mitochondrial dysfunction in various ocular diseases.

DOI: https://doi.org/10.1101/2025.09.25.678562
Nature. 2025 Oct 01.

Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22.

Fangtao Chi, Qiming Zhang, Jessica E S Shay, Shixun Han, Johanna Ten Hoeve, Yin Yuan, Zhenning Yang, Heaji Shin, Samuel Block, Sumeet Solanki, Yatrik M Shah, Matthew G Vander Heiden, Judith Agudo, Ömer H Yilmaz.

A fundamental question in physiology is understanding how tissues adapt and alter their cellular composition in response to dietary cues1-8. The mammalian small intestine is maintained by rapidly renewing LGR5+ intestinal stem cells (ISCs) that respond to macronutrient changes such as fasting regimens and obesogenic diets, yet how specific amino acids control ISC function during homeostasis and injury remains unclear. Here we demonstrate that dietary cysteine, a semi-essential amino acid, enhances ISC-mediated intestinal regeneration following injury. Cysteine contributes to coenzyme A (CoA) biosynthesis in intestinal epithelial cells, which promotes expansion of intraepithelial CD8αβ+ T cells and their production of interleukin-22 (IL-22). This enhanced IL-22 signalling directly augments ISC reparative capacity after injury. The mechanistic involvement of the pathway in driving the effects of cysteine is demonstrated by several findings: CoA supplementation recapitulates cysteine effects, epithelial-specific loss of the cystine transporter SLC7A11 blocks the response, and mice with CD8αβ+ T cells lacking IL-22 or a depletion of CD8αβ+ T cells fail to show enhanced regeneration despite cysteine treatment. These findings highlight how coupled cysteine metabolism between ISCs and CD8+ T cells augments intestinal stemness, providing a dietary approach that exploits ISC and immune cell crosstalk for ameliorating intestinal damage.

DOI: https://doi.org/10.1038/s41586-025-09589-5
Haematologica. 2025 Oct 02.

Long-term outcomes in FLT3-mutated acute myeloid leukemia after frontline hypomethylating agent, venetoclax and a FLT3 inhibitor.

Nicholas J Short, Sanam Loghavi, Musa Yilmaz, Omer Karrar, Kunhwa Kim, Courtney D Dinardo, Tapan M Kadia, Manuel Maroun, Gautam Borthakur, Ghayas C Issa, Joseph Jabbour, Betul Oran, Elizabeth J Shpall, Uday Popat, Keyur P Patel, Mark Routbort, Marina Konopleva, Farhad Ravandi, Hagop Kantarjian, Naval Daver.

Triplet regimens with a hypomethylating agent, venetoclax and a FLT3 inhibitor yield high rates of response in newly diagnosed FLT3-mutated AML. However, the long-term outcomes and patterns of relapse with these triplet regimens are not well-established. In this retrospective analysis, 73 patients with newly diagnosed FLT3-mutated AML received a frontline FLT3 inhibitor-containing triplet regimen. The composite complete remission (CR) and CR with incomplete hematologic recovery (CRi) rate was 93%. Next-generation sequencing FLT3-ITD MRD negativity (sensitivity: 0.005%) was achieved in 60% of patients after cycle 2 and 90% after cycle 4. The estimated 3-year relapse-free survival (RFS) for FLT3-ITD-mutated and FLT3 TKD-mutated AML was 38% and 76%, respectively, and the 3-year overall survival (OS) was 45% and 76%, respectively. Neither age, NPM1 co-mutation, ELN 2022 risk, nor allogeneic stem cell transplantation in first remission significantly impacted OS. Baseline RAS pathway mutations were associated with poor long-term survival (3-year OS 22% versus 63% without RAS pathway mutation). FLT3 wild type relapses accounted for 65% of relapses, and new RAS pathway mutations were observed in 24% of relapses. Outcomes were poor after relapse (median OS of 6.1 months), particularly for those with persistently detectable FLT3 mutations. Triplet combinations of an HMA, venetoclax and a FLT3 inhibitor result in durable remission and encouraging long-term OS in older adults with newly diagnosed FLT3-mutated AML. However, better strategies to prevent FLT3 wild type relapses and to overcome RAS pathway-mediated resistance are still needed.

DOI: https://doi.org/10.3324/haematol.2025.288553
bioRxiv. 2025 Sep 25. pii: 2025.09.23.678038. [Epub ahead of print]

A live cell biosensor protocol for high-resolution screening of therapy-resistant cancer cells.

Viral D Oza, Colin Williams, Jessica S Blackburn.

The Genetically Encoded Death Indicator (GEDI) is a ratiometric, dual-fluorescence biosensor that enables real-time detection of cell death through calcium influx. Originally developed for use in neurodegeneration models, GEDI can be applied to cancer cells to quantify therapy-induced death at single-cell resolution. This protocol details how to generate GEDI-expressing cancer cell lines, empirically determine stress-induced GEDI thresholds using radiation or chemotherapeutic agents, and perform time-resolved imaging and image analysis to track cell fate. This workflow is optimized for high-throughput drug and radiation screening in heterogeneous populations and is especially useful for identifying chemo- and radio-resistant subclones. Key limitations include the need for empirical GEDI threshold calibration for each treatment condition and careful standardization of imaging parameters. The protocol outputs include GEDI ratio values, single-cell time-of-death annotations, and whole-cell morphological data in parallel, which can be linked to downstream applications such as FACS-based isolation of live or dying subpopulations, transcriptomic profiling of resistant clones, or in vivo validation using xenografts or organotypic slice culture.
Associated content: io.protocol DOI: dx.doi.org/10.17504/protocols.io.eq2ly4d7qlx9/v1.

DOI: https://doi.org/10.1101/2025.09.23.678038
Physiol Rep. 2025 Oct;13(19): e70555

Mitochondrial respiratory function in human platelets: Influence of sample preparation, assay buffer, and instrumental platform.

Craig Porter, Lillie Treas, Oleksandra Pavliv, Daniel Sadler, Matthew Cotter, Shannon Rose, Elisabet Børsheim, Eva C Diaz Fuentes.

  Circulating blood cells such as platelets represent a readily available sample type to determine mitochondrial function in humans. Here, we set out to determine the influence of sample preparation, assay buffer composition, and instrumental platform on the respiratory function of platelets isolated from human blood. Approximately 50 mL of whole blood was collected from healthy adults (n = 16) following an overnight (>12 h) fast. Platelets were immediately isolated from whole blood by centrifugation for respirometry. Respiratory function was assayed in intact and permeabilized platelets using an Oxygraph-2K (O2K) high-resolution respirometer in either RPMI or MIR05 (containing 5 mM glucose, 1 mM pyruvate, and 2 mM glutamine), or the participant's own plasma. In addition, respiratory function was determined in intact platelets using a Seahorse Extracellular Flux analyzer (XFe96) in RPMI buffer containing 1 mM pyruvate, 2 mM glutamine, and variable glucose concentrations (5, 10, and 10 mM). In assays performed in an O2K, routine and ATP-linked respiration were greater in cells assayed in RPMI compared to MIR05 (p < 0.001). However, compared to cells assayed in RPMI or MIR05, routine and ATP-linked respiration were higher in intact platelets assayed in their own plasma (p < 0.001). In digitonin-permeabilized platelets, state 3 respiration was greater when assayed in MIR05 compared to RPMI (p < 0.05). Across instrumental platforms, routine and leak respiration were lower in intact platelets assayed on an O2K versus an XFe96 (p < 0.05), whereas respiration available for ADP phosphorylation was greater in cells assayed on an O2K versus an XFe96 (p < 0.001), due to a diminished coupling response to oligomycin in cells assayed on the XFe96 (p < 0.001). Platelet respiratory function is influenced by assay buffer composition and instrumental platform. Consideration of these factors should be made by investigators planning to use platelet respiratory function as a readout of cellular energetics.

Keywords:  bioenergetics; mitochondria; platelets; respiration

DOI:  https://doi.org/10.14814/phy2.70555
Pharmacol Res. 2025 Sep 25. pii: S1043-6618(25)00398-6. [Epub ahead of print]221 107973

Imaging of mitochondrial matrix pH dynamics reveals a functional interaction between the ADP/ATP carrier and ATP synthase to regulate H+ distribution.

Bernard Ribalet, Scott John, Madeleine G Milner, Leia Salongo, Ambre M Bertholet.

  In mitochondria, the energy derived from the proton gradient across the mitochondrial inner membrane (IMM) is converted into ATP and heat. For these conversions to occur, H+ is pumped out of the matrix via the electron transport chain (ETC) and then re-enters either via the ATP synthase to produce ATP or via the ADP/ATP carrier (AAC) to release heat. Due to its dual functions of ADP/ATP exchange and H+ transport, AAC may be considered a major regulator of the energy distribution of mitochondria between ATP synthesis and thermogenesis. Using real-time imaging of pH with a fluorescent pH probe targeted to the mitochondrial matrix, we investigated in a myoblast cell model how H+ fluxes across the IMM are regulated by AAC and the ATP synthase. Our data show that activation of AAC-dependent H+ transport by the mitochondrial uncoupler BAM15 causes an acidification of the matrix followed by a re-alkalization phase due to the reversed activity of the ATP synthase. Similar re-alkalization and reversal of ATP synthase activity were observed after acidification caused by inhibition of the electron transport chain. Lastly, the discovery that strong protonophoric activity independent of AAC suppresses the re-alkalization phase and consequently the reverse action of the ATP synthase, suggests the need for strict control of the H+ flux through the IMM by AAC. Thus, real-time imaging of matrix pH reveals a functional interaction between AAC and the ATP synthase for the control of H+ fluxes across the IMM.

Keywords:  ADP/ATP carrier; ATP synthase; BAM15; Electron transport chain; FCCP; Mitochondria; PH sensor; Proton transport; Uncoupling protein

DOI:  https://doi.org/10.1016/j.phrs.2025.107973
Epileptic Disord. 2025 Sep 30.

Toward a working definition of ketogenic diet resistance in GLUT1 deficiency syndrome.

Raffaele Falsaperla, Vincenzo Sortino, Gerhard Josef Kluger, Thomas Herberhold, Andrea Rüegger, Pasquale Striano, Martino Ruggieri, Joerg Klepper, Georgia Ramantani.

   OBJECTIVE: The ketogenic diet (KD) is the standard treatment for glucose transporter type 1 deficiency syndrome (GLUT1-DS), typically yielding seizure reduction and cognitive/motor gains. However, a small subset of patients shows limited or no clinical benefit. This phenomenon, referred to as "KD resistance," remains poorly understood and inconsistently defined. We propose a working definition, outline evaluation domains, summarize candidate mechanisms, and indicate management steps.
METHODS: Narrative review of published evidence and expert opinion across clinical, biochemical, EEG, and adherence domains.
RESULTS: KD resistance may be considered when all are present: (1) confirmed therapeutic ketosis (serial blood β-hydroxybutyrate ≥2.0-2.5 mmol/L on repeated measurements); (2) adequate dietary adherence verified by dietetic assessment and, when available, validated tools; (3) sufficient trial duration (≥3 months; longer for primarily cognitive/motor goals); and (4) lack of meaningful improvement on symptom-relevant standardized measures. EEG interictal epileptiform discharge burden can be used as an adjunct marker but is not required. KD resistance may involve several dimensions: failure to achieve therapeutic ketosis, lack of symptom improvement despite confirmed ketosis, or challenges with adherence that limit efficacy. Possible contributing factors include genotypic variability in SLC2A1, mitochondrial dysfunction, impaired blood-brain barrier transport, hormonal influences, and epigenetic regulation. We outline a multidomain evaluation framework with suggested metrics, summarize candidate mechanisms (ketone transport/utilization, mitochondrial function, neurotransmission, ion channels/neuromodulators, inflammation/oxidative stress, epigenetic regulation), and indicate when to introduce a KD-compatible anti-seizure medication.
SIGNIFICANCE: The proposed definition and framework standardize terminology and reporting, guide decisions for suboptimal responders, and set priorities for multicenter validation.

Keywords:  GLUT1DS; ketogenic diet resistance; metabolic disease

DOI:  https://doi.org/10.1002/epd2.70107
J Physiol. 2025 Oct 02.

Preferential lactate metabolism in the human brain during exogenous and endogenous hyperlactataemia.

Jodie L Koep, Jennifer S Duffy, Jay M J R Carr, Madden L Brewster, Jordan D Bird, Justin A Monteleone, Tenasia D R Monaghan, Hashim Islam, Andrew R Steele, Connor A Howe, David B MacLeod, Philip N Ainslie, Travis D Gibbons.

  At rest, glucose serves as the brain's primary oxidative substrate; however, when circulating lactate is elevated, lactate oxidation increases. Whether this glucose-sparing effect differs when lactate is elevated via passive infusion versus exercise remains unknown. To address this, 13 healthy adults (six females) completed protocols of: (1) intravenous sodium lactate infusion (exogenous hyperlactataemia); and (2) cycling exercise (endogenous hyperlactataemia) to matched elevations in arterial lactate concentration (∼4 and ∼8 mmol/l). Radial arterial and internal jugular venous sampling and measures of cerebral blood flow (CBF) were used to calculate cerebral metabolic rates of glucose (CMRGlc), lactate (CMRiLac), and oxygen ( CMRO2${\mathrm{CM}}{{\mathrm{R}}_{{{\mathrm{O}}_2}}}$ ). The exogenous infusion protocol resulted in a higher CBF compared to exercise (P < 0.001), despite causing systemic alkalosis (P < 0.001). During both protocols CMRO2${\mathrm{CM}}{{\mathrm{R}}_{{{\mathrm{O}}_2}}}$ remained unchanged across increases in lactate concentrations (P = 0.610), while CMRGlc decreased (lactate, P = 0.009; condition, P = 0.373) and CMRiLac increased in a dose-dependent manner (lactate, P < 0.001; condition, P = 0.972). At an arterial concentration of 8 mmol/l, circulating lactate accounted for 24% of total cerebral oxidative metabolism. Elevated circulating lactate leads to preferential lactate oxidation and reduced glucose utilization, irrespective of whether lactate is delivered exogenously or produced endogenously. KEY POINTS: The human brain relies primarily on oxidative glucose metabolism; however, with age and in many pathologies cerebral glucose metabolism declines; therefore, there is interest in investigating alternative fuel sources that can meet the high energetic needs of the brain. The present study investigates whether increased lactate availability exerts a glucose-sparing effect in the healthy human brain, and whether this effect is consistent across physiologically distinct states of exogenous (sodium lactate infusion) and endogenous (exercise-induced) hyperlactataemia. We assessed cerebral uptake and metabolism of glucose and lactate following exercise and lactate infusion, using simultaneous arterial and jugular venous blood samples, and Duplex ultrasound. Despite stark systemic physiological differences between conditions, cerebral glucose metabolism declined in proportion to increased circulating lactate irrespective of whether it is delivered exogenously or produced endogenously. These data provide clear evidence that lactate is preferentially oxidized by the brain when made available, helping preserve glucose for non-energetic roles.

Keywords:  cerebral lactate metabolism; cerebral substrate switch; endogenous lactate; exogenous lactate

DOI:  https://doi.org/10.1113/JP289216
Proc Natl Acad Sci U S A. 2025 Oct 07. 122(40): e2508237122

An extended network for regulation of heme homeostasis in cells.

Andrea E Gallio, Noa A Marson, Kate J Heesom, Philip A Lewis, Dominic Alibhai, Celyn A Dugdale, Andrew Herman, Jaswir Basran, Andrew J Hudson, Emma L Raven.

  Iron-bound tetrapyrroles (hemes) are essential for the regulation of cellular functions and bioenergetics. The processes of heme biosynthesis, transport, and degradation are responsible for the supply of heme in mitochondria and its insertion into other downstream proteins. What remains unresolved is how these processes interconnect and the wider implications for the cell in the restoration of homeostasis when heme concentrations change. We demonstrate a wide-ranging and coordinated response to changes in intracellular heme in HEK293 cells through a network of complementary mechanisms that extend well beyond the direct regulation of heme biosynthesis and degradation. These responses connect changes in heme homeostasis to mitochondrial function, including core metabolic processes such as the tricarboxylic acid cycle and oxidative phosphorylation, as well as to enzymes involved in the control and storage of iron. Our findings demonstrate far-reaching consequences to perturbations of heme homeostasis and provide insights into the complexity of the cellular hemome.

Keywords:  biosensing; heme; heme biosynthesis; proteomics; tetrapyrroles

DOI:  https://doi.org/10.1073/pnas.2508237122