bims-medica 2025-04-27 papers

bims-medica

Biomed News

on Metabolism and diet in cancer

Issue of 2025–04–27
sixteen papers selected by
Brett Chrest, Wake Forest University

Mitochondrial NADPH fuels mitochondrial fatty acid synthesis and lipoylation to power oxidative metabolism.
Combined inhibition of de novo glutathione and nucleotide biosynthesis is synthetically lethal in glioblastoma.
Semaglutide-induced weight loss improves mitochondrial energy efficiency in skeletal muscle.
PPARα regulates ER-lipid droplet protein Calsyntenin-3β to promote ketogenesis in hepatocytes.
The association between plant-based diet indices and the risk of breast cancer: a case-control study.
A parallel reaction monitoring-mass spectrometric method for studying lipid biosynthesis in vitro using 13C16-palmitate as an isotope tracer.
Synergistic effects of BET inhibitors and ferroptosis inducers via targeted inhibition of the BRD4/c-Myc/NRF2 pathway in AML.
Venetoclax Alone or in Combination With Chemotherapy in Paediatric and Adolescent/Young Adult Patients With Relapsed/Refractory Acute Myeloid Leukaemia.
Glutaminase-1 Mediated Glutaminolysis to Glutathione Synthesis Maintains Redox Homeostasis and Modulates Ferroptosis Sensitivity in Cancer Cells.
Nutritional Interventions in Advanced Cancer: Scoping Review.
Ketogenesis mitigates metabolic dysfunction-associated steatotic liver disease through mechanisms that extend beyond fat oxidation.
Metabolomic profiling of a cholesterol lowering plant-based diet from two randomized controlled feeding trials.
The power of trapped ion mobility for isotope tracer experiments.
Restricted Surface Diffusion of Cytochromes on Bioenergetic Membranes with Anionic Lipids.
Low-Carbohydrate (Ketogenic) Diet in Children with Obesity: Part 1-Diet Impact on Anthropometric Indicators and Indicators of Metabolic Syndrome and Insulin Resistance.
Unbiased analysis of NUP98-KDM5A-induced murine leukemia reveals phenotypic heterogeneity recapitulating human disease subtypes.

Nat Cell Biol. 2025 Apr 21.

Mitochondrial NADPH fuels mitochondrial fatty acid synthesis and lipoylation to power oxidative metabolism.

Dohun Kim, Rushendhiran Kesavan, Kevin Ryu, Trishna Dey, Austin Marckx, Cameron Menezes, Prakash P Praharaj, Stewart Morley, Bookyong Ko, Mona H Soflaee, Harrison J Tom, Harrison Brown, Hieu S Vu, Shih-Chia Tso, Chad A Brautigam, Andrew Lemoff, Marcel Mettlen, Prashant Mishra, Feng Cai, Doug K Allen, Gerta Hoxhaj.

Nicotinamide adenine dinucleotide phosphate (NADPH) is a vital electron donor essential for macromolecular biosynthesis and protection against oxidative stress. Although NADPH is compartmentalized within the cytosol and mitochondria, the specific functions of mitochondrial NADPH remain largely unexplored. Here we demonstrate that NAD+ kinase 2 (NADK2), the principal enzyme responsible for mitochondrial NADPH production, is critical for maintaining protein lipoylation, a conserved lipid modification necessary for the optimal activity of multiple mitochondrial enzyme complexes, including the pyruvate dehydrogenase complex. The mitochondrial fatty acid synthesis (mtFAS) pathway utilizes NADPH for generating protein-bound acyl groups, including lipoic acid. By developing a mass-spectrometry-based method to assess mammalian mtFAS, we reveal that NADK2 is crucial for mtFAS activity. NADK2 deficiency impairs mtFAS-associated processes, leading to reduced cellular respiration and mitochondrial translation. Our findings support a model in which mitochondrial NADPH fuels the mtFAS pathway, thereby sustaining protein lipoylation and mitochondrial oxidative metabolism.

DOI: https://doi.org/10.1038/s41556-025-01655-4
Cell Rep. 2025 Apr 19. pii: S2211-1247(25)00367-5. [Epub ahead of print]44(5): 115596

Combined inhibition of de novo glutathione and nucleotide biosynthesis is synthetically lethal in glioblastoma.

Suresh Udutha, Céline Taglang, Georgios Batsios, Anne Marie Gillespie, Meryssa Tran, Johanna Ten Hoeve, Thomas G Graeber, Pavithra Viswanath.

  Understanding the mechanisms by which oncogenic events alter metabolism will help identify metabolic weaknesses that can be targeted for therapy. Telomerase reverse transcriptase (TERT) is essential for telomere maintenance in most cancers. Here, we show that TERT acts via the transcription factor forkhead box O1 (FOXO1) to upregulate glutamate-cysteine ligase (GCLC), the rate-limiting enzyme for de novo biosynthesis of glutathione (GSH, reduced) in multiple cancer models, including glioblastoma (GBM). Genetic ablation of GCLC or pharmacological inhibition using buthionine sulfoximine (BSO) reduces GSH synthesis from [U-13C]-glutamine in GBMs. However, GCLC inhibition drives de novo pyrimidine nucleotide biosynthesis by upregulating the glutamine-utilizing enzymes glutaminase (GLS) and carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotatase (CAD) in an MYC-driven manner. Combining BSO with the glutamine antagonist JHU-083 is synthetically lethal in vitro and in vivo and significantly extends the survival of mice bearing intracranial GBM xenografts. Collectively, our studies advance our understanding of oncogene-induced metabolic vulnerabilities in GBMs.

Keywords:  CP: Cancer; CP: Metabolism; TERT; brain tumors; cancer; glioblastoma; glutamine metabolism; glutathione; in vivo stable isotope tracing; metabolic synthetic lethality; metabolomics; nucleotide biosynthesis; telomerase reverse transcriptase

DOI:  https://doi.org/10.1016/j.celrep.2025.115596
Obesity (Silver Spring). 2025 May;33(5): 974-985

Semaglutide-induced weight loss improves mitochondrial energy efficiency in skeletal muscle.

Ran Hee Choi, Takuya Karasawa, Cesar A Meza, J Alan Maschek, Allison M Manuel, Linda S Nikolova, Kelsey H Fisher-Wellman, James E Cox, Amandine Chaix, Katsuhiko Funai.

OBJECTIVE: Glucagon-like peptide-1 receptor agonists (e.g., semaglutide) potently induce weight loss, thereby reducing obesity-related complications. However, weight regain occurs when treatment is discontinued. An increase in skeletal muscle oxidative phosphorylation (OXPHOS) efficiency upon diet-mediated weight loss has been described, which may contribute to reduced systemic energy expenditure and weight regain. We set out to determine the unknown effect of semaglutide on muscle OXPHOS efficiency.
METHODS: C57BL/6J mice were fed a high-fat diet for 12 weeks before receiving semaglutide or vehicle for 1 or 3 weeks. The rates of ATP production and oxygen (O2) consumption were measured via high-resolution respirometry and fluorometry to determine OXPHOS efficiency in muscle at these two time points.
RESULTS: Semaglutide treatment led to significant reductions in fat and lean mass. Semaglutide improved skeletal muscle OXPHOS efficiency, measured as ATP produced per O2 consumed in permeabilized muscle fibers. Mitochondrial proteomic analysis revealed changes restricted to two proteins linked to complex III assembly (LYRM7 and TTC19; p < 0.05 without multiple corrections) without substantial changes in the abundance of OXPHOS subunits.
CONCLUSIONS: These data indicate that weight loss with semaglutide treatment increases skeletal muscle mitochondrial efficiency. Future studies could test whether it contributes to weight regain.

DOI: https://doi.org/10.1002/oby.24274
Proc Natl Acad Sci U S A. 2025 Apr 29. 122(17): e2426338122

PPARα regulates ER-lipid droplet protein Calsyntenin-3β to promote ketogenesis in hepatocytes.

Lauren F Uchiyama, Alexander Nguyen, Kevin Qian, Liujuan Cui, Khoi T Pham, Xu Xiao, Yajing Gao, Yuta Shimanaka, Marcus J Tol, Laurent Vergnes, Karen Reue, Peter Tontonoz.

  Ketogenesis requires fatty acid flux from intracellular (lipid droplets) and extrahepatic (adipose tissue) lipid stores to hepatocyte mitochondria. However, whether interorganelle contact sites regulate this process is unknown. Recent studies have revealed a role for Calsyntenin-3β (CLSTN3β), an endoplasmic reticulum-lipid droplet contact site protein, in the control of lipid utilization in adipose tissue. Here, we show that Clstn3b expression is induced in the liver by the nuclear receptor PPARα in settings of high lipid utilization, including fasting and ketogenic diet feeding. Hepatocyte-specific loss of CLSTN3β in mice impairs ketogenesis independent of changes in PPARα activation. Conversely, hepatic overexpression of CLSTN3β promotes ketogenesis in mice. Mechanistically, CLSTN3β affects LD-mitochondria crosstalk, as evidenced by changes in fatty acid oxidation, lipid-dependent mitochondrial respiration, and the mitochondrial integrated stress response. These findings define a function for CLSTN3β-dependent membrane contacts in hepatic lipid utilization and ketogenesis.

Keywords:  hepatocyte; ketogenesis; ketogenic diet; lipid metabolism

DOI:  https://doi.org/10.1073/pnas.2426338122
J Health Popul Nutr. 2025 Apr 19. 44(1): 127

The association between plant-based diet indices and the risk of breast cancer: a case-control study.

Fateme Souni, Fatemeh Mansouri, Fatemeh Jafari, Reza Sharifi, Sepideh PourvatanDoust, Zainab Shateri, Mehran Nouri, Bahram Rashidkhani.

   BACKGROUND: Previous studies examining the relationship between plant-based diets and breast cancer (BrC) have provided conflicting evidence. To address these inconsistencies, we aimed to evaluate the association between the plant-based diet index (PDI), healthful PDI (hPDI), and unhealthy PDI (uPDI) with the odds of BrC in Iranian women.
METHODS: The current case-control research was performed on 133 Iranian women with BrC and 265 controls. The study subjects were selected from hospitals in Tehran. PDI, hPDI, and uPDI were categorized into eighteen food groups based on nutrient composition similarity. The relationship between PDIs and BrC was assessed using logistic regression.
RESULTS: After adjusting for confounding factors, the chance of developing BrC was lower in the highest tertile of hPDI compared to the lowest tertile (odds ratio (OR) = 0.495; 95% confidence interval (CI): 0.274-0.891; P = 0.019). In addition, postmenopausal women in the second and last tertiles of hPDI had lower odds of BrC than those in the first tertile (T) (T2: OR = 0.342; 95% CI: 0.141-0.828; P = 0.017- T3: OR = 0.262; 95% CI: 0.107-0.639; P = 0.003) in the adjusted model. Furthermore, in premenopausal women in the highest tertile of uPDI, the odds of BrC were increased compared to the lowest tertile (OR = 2.546; 95% CI: 1.051-6.167; P = 0.038) in the adjusted model.
CONCLUSIONS: Adherence to a healthy plant-based dietary pattern, including vegetables, fruits, whole grains, nuts, and legumes, seems to be beneficial for BrC prevention, particularly in postmenopausal women. Future prospective cohort studies that consider menopausal status and the type of BrC are needed to support these findings.

Keywords:  Breast cancer; Breast cancer prevention; Dietary patterns; Plant-based diet; Risk factors; Tehran

DOI:  https://doi.org/10.1186/s41043-025-00879-2
Anal Chim Acta. 2025 Jun 08. pii: S0003-2670(25)00397-6. [Epub ahead of print]1354 344003

A parallel reaction monitoring-mass spectrometric method for studying lipid biosynthesis in vitro using 13C16-palmitate as an isotope tracer.

Kyeong-Seog Kim, Young Gyun Ko, Woo Seok Yang, Hye Young Kim, Joo-Youn Cho.

   BACKGROUND: Palmitate, which is the end product of fatty acid synthase, is the key fatty acid for understanding of lipid biosynthetic process in mammalian cells. Mass spectrometry (MS) methodology using 13C-palmitate can trace the lipid biosynthesis such as glycerolipids, glycerophospholipids, and sphingolipids. However, due to the interferences of natural heavy isotopes, accurate measurement of 13C-labeled lipid species has been limited. Here we describe a high-throughput isotope tracing experiment to assess lipid biosynthesis using parallel reaction monitoring-MS (PRM-MS) with 13C16-palmitate as an isotope tracer.
RESULTS: The developed method can trace 14 13C16-labeled lipid classes without disturbance from the heavy isotope patterns of natural lipids. Lipid class-based separation was achieved through hydrophilic interaction liquid chromatography (HILIC) which allows facile identification of lipid, and PRM-MS was performed for accurate detection of the 13C16-labeled lipids. A fibroblast (NIH/3T3) cell line was used as an in vitro model, and the NIH/3T3 cells were treated with bovine serum albumin (BSA)-bound 13C16-palmitate. The isotopic disturbance from natural lipid was eliminated using 13C16-palmitate, rather than 13C1-palmitate, as an isotope tracer. After 24 h of incubation with 0.1 mmol/L of BSA-bound 13C16-palmitate in the fibroblasts, NIH/3T3 cells synthesized the 127 13C16-labeled lipid species of glycerolipids, glycerophospholipids, and sphingolipids. Finally, in the NIH/3T3 cells incubated for 1, 6, and 24 h after the treatment of the isotope tracer exhibited an increased profile of 13C16-labeled lipidome, depending on duration of incubation.
SIGNIFICANCE: The HILIC/PRM-MS method using 13C16-palmitate as an isotope tracer enables identification of 13C16-labeled lipid species by annotating 13C16-labeled position, including the 13C16-fatty acyl chain and 13C16-sphingolipid headgroup, without interference of natural heavy isotope patterns. This lipidomic flux analysis using PRM approach is expected to provide insights into assessment of isotope-labeled lipids.

Keywords:  HILIC-MS/MS; Isotope tracing; Lipid biosynthesis; Lipidomics; Parallel reaction monitoring

DOI:  https://doi.org/10.1016/j.aca.2025.344003
Eur J Pharmacol. 2025 Apr 17. pii: S0014-2999(25)00406-6. [Epub ahead of print]998 177652

Synergistic effects of BET inhibitors and ferroptosis inducers via targeted inhibition of the BRD4/c-Myc/NRF2 pathway in AML.

Mengjun Zhong, Shuxin Zhong, Kangjie Qiu, Xueting Peng, Xin Liu, Songnan Sui, Zhangshuai Dai, Xianfeng Wang, Dingrui Nie, Zhi Yu, Quan Yu, Cunte Chen, Yangqiu Li, Chengwu Zeng.

  In acute myeloid leukemia (AML), high expression of BRD4 is associated with poor prognosis. BET inhibitors that mainly inhibit BRD4 can induce AML cell death, but some AML cells are insensitive to BET inhibitors. We found that BET inhibitors could promote the up-regulation of the ferroptosis signaling pathway in AML. In this study, we intend to investigate the synergistic effects of BET inhibitors with ferroptosis inducers in AML cells. The combination of BET inhibitors with ferroptosis inducers (RSL3, FIN56, and Erastin) markedly reduced AML cell viability and increased cell death, as demonstrated by CCK-8 assays and flow cytometry analysis across multiple AML cell lines and primary AML patient samples. Moreover, BET inhibitors combined with ferroptosis inducers elevated the lipid reactive oxygen species (ROS) levels, indicating heightened lipid peroxidation, a hallmark of ferroptosis. Mechanistically, BET inhibitor and ferroptosis inducer co-targeted the BRD4/c-Myc/NRF2 axis, leading to downregulation of NRF2, key regulators of AML cell survival and oxidative stress resistance. NRF2 knockdown amplified the anti-AML effect of this combined treatment, whereas NRF2 overexpression negated this synergy, highlighting its critical role in mediating ferroptosis resistance. Finally, survival analyses of AML patients from the TCGA and GSE71014 datasets revealed that elevated expression of BRD4, NRF2, and its downstream target GPX4, an essential ferroptosis regulator, correlated with poor overall survival, highlighting the clinical relevance of our findings. In all, combining BET inhibition with ferroptosis induction could enhance anti-leukemia effect and represent a novel therapeutic strategy for targeting AML cells.

Keywords:  AML; BET inhibitor; Ferroptosis inducer; NRF2

DOI:  https://doi.org/10.1016/j.ejphar.2025.177652
Pediatr Blood Cancer. 2025 Apr 23. e31714

Venetoclax Alone or in Combination With Chemotherapy in Paediatric and Adolescent/Young Adult Patients With Relapsed/Refractory Acute Myeloid Leukaemia.

Seth E Karol, Seong L Khaw, C Michel Zwaan, Andre Baruchel, Henrique Bittencourt, Todd M Cooper, Christian Flotho, Christopher Fraser, Christopher J Forlenza, Kelly C Goldsmith, Margaret E Macy, Daniel A Morgenstern, Maureen M O'Brien, Arnaud Petit, David S Ziegler, Dirk Reinhardt, Joseph T Opferman, Jeffrey E Rubnitz, Maika Onishi, Diana R Dunshee, Fengjiao Dunbar, Deeksha Vishwamitra, Jeremy A Ross, Xin Chen, Kristina Unnebrink, Maja Kammerlander, Ahmed Hamed Salem, Tammy L Palenski, Gauri Sunkersett, Andrew E Place.

   BACKGROUND: Venetoclax is a potent, oral BCL-2 inhibitor approved as combination therapy for the treatment of adults with newly diagnosed acute myeloid leukaemia (AML) who are ineligible for intensive chemotherapy. This study evaluated the safety and preliminary efficacy of venetoclax alone or combined with chemotherapy in paediatric and adolescent/young adult patients with relapsed/refractory AML.
PROCEDURE: In this phase 1, open-label, two-part, multicentre study, paediatric and adolescent/young adult patients (<25 years of age) with relapsed/refractory AML were treated with venetoclax alone or in combination with hypomethylating agents or cytarabine. The study is registered with ClinicalTrials.gov, NCT03236857.
RESULTS: A total of 37 patients received treatment with either venetoclax as a monotherapy (n = 3) or in combination with decitabine (n = 5), azacitidine (n = 19), low-dose cytarabine (n = 1) or high-dose cytarabine (HDAC; n = 9). Febrile neutropenia (57%), hypokalaemia (38%), and thrombocytopenia (35% [thrombocytopenia, 19%; platelet count decreased, 16%]) were the most common grade 3/4 treatment-emergent adverse events. Across all venetoclax combinations, the overall response rate (ORR) was 24% (9/37), and the median duration of response was 2.6 months (95% CI, 0.5-7.9). Among the combinations, ORR was 44% with venetoclax plus HDAC and 21% with venetoclax plus azacitidine. In biomarker-evaluable patients, responses to venetoclax plus chemotherapy were observed in patients harbouring mutations across a range of functional classifications and heterogeneous BH3 family member dependencies.
CONCLUSIONS: Venetoclax alone or combined with chemotherapy was well tolerated in paediatric and adolescent/young adult patients with relapsed/refractory AML, with promising, although transient, responses with venetoclax plus HDAC or azacitidine.

Keywords:  BCL‐2; acute myeloid leukaemia; paediatric ; phase 1; venetoclax

DOI:  https://doi.org/10.1002/pbc.31714
Cell Prolif. 2025 Apr 21. e70036

Glutaminase-1 Mediated Glutaminolysis to Glutathione Synthesis Maintains Redox Homeostasis and Modulates Ferroptosis Sensitivity in Cancer Cells.

Changsen Bai, Jialei Hua, Donghua Meng, Yue Xu, Benfu Zhong, Miao Liu, Zhaosong Wang, Wei Zhou, Liming Liu, Hailong Wang, Yang Liu, Lifang Li, Xiuju Chen, Yueguo Li.

  Glutaminase-1 (GLS1) has garnered considerable interest as a metabolic target in cancer due to its heightened involvement and activity. However, the precise fate of glutaminolysis catalysed by GLS1 in cancer cells remains elusive. We found that GLS1 knockout led to significant suppression of cancer cell proliferation, which can be reversed or partially restored by supplementation of glutamate or non-essential amino acids that can be converted into glutamate. The addition of spliceosomal KGA or GAC ameliorates cancer cell growth in vitro and in vivo, providing both simultaneously completely reverse the effect. The primary metabolic fate of glutamate produced through glutaminolysis in cancer cells is mainly used to produce glutathione (GSH) for redox homeostasis, not entering the tricarboxylic acid cycle or synthesising nucleotides. GSH monoethyl ester (GSH-MEE) effectively rescues the inhibition of cancer cell proliferation caused by GLS1 knockout. Deletion of GLS1 results in an elevation of reactive oxygen species (ROS) and malondialdehyde (MDA), a reduction of NADPH/NADP+ ratio, and an augmented susceptibility of cells to ferroptosis. Glutathione Peroxidase 4 (GPX4) and GPX1 exhibit complementary roles in redox regulation, with GLS1 knockout promoting GPX4 degradation. Pharmacological inhibition of GLS1 synergises with GPX4 inhibitor to suppress tumour growth. Dual targeting of GPX4 and GPX1 presents a potent anti-cancer strategy. This metabolic mechanism facilitates a deeper comprehension of the abnormal glutamine metabolism in cancer cells, establishing a theoretical basis for the potential clinical utilisation of GLS1 inhibitors and presenting novel perspectives for advancing combinatorial therapeutic approaches.

Keywords:  GLS1; GPX4; GSH; cancer cell; ferroptosis; glutamate

DOI:  https://doi.org/10.1111/cpr.70036
Am J Hosp Palliat Care. 2025 Apr 25. 10499091251335249

Nutritional Interventions in Advanced Cancer: Scoping Review.

Aynur Aktas, Shirley Thomas, Michelle Barrett, Jessica Sui, Jake Waldman, Ciarán Kenny, Jessica Eustice-Cook, Kunal C Kadakia, Declan Walsh.

  Background: It is unclear what evidence supports nutritional advice received by those with advanced cancer. In advanced cancer, the benefits of nutritional interventions are less clear, with no consensus about effectiveness. This uncertainty is compounded by the heterogeneity of nutritional interventions and absence of cohesive, evidence-based approaches. Intervention diversity highlights the need to summarize current dietary and nutritional approaches and their evidence base. Objective: To map and summarize the current evidence base for nutritional interventions in advanced cancer. Methods: A systematic search included studies on nutritional interventions in adults with advanced cancer, excluding enteral/parenteral nutrition. Five databases (CINAHL Ultimate, Embase, Medline, SCOPUS, Web of Science) were searched from inception until 10/20/2023. Four researchers undertook screening and data extraction. Due to the heterogeneous nature of the studies, data synthesis was narrative. Results: The databases search yielded 3290 records. Fifty additional publications were identified through manual searches. Title/abstract screening identified 253 articles for full-text screening, 35 of which met inclusion criteria. Of these, 25 (69%) were randomized controlled trials. The studies were separated into 5 themes: (1) nutraceutical and herbal interventions, (2) ketogenic diet, (3) nutrition advice/support, (4) oral nutrition supplements, (5) other nutritional interventions. Outcome measures reported included anthropometry, biological markers, feasibility, performance status, quality of life, survival, and treatment tolerability. Most provided information about weight and energy intake and a few reported lean body mass. Although some reported positive outcomes, evidence is insufficient for definitive recommendations for any of those interventions. Conclusions: Our scoping review provided limited evidence for various nutritional interventions and dietary approaches. Dietary advice and oral nutritional supplements sometimes appeared to enhance treatment tolerance and improve nutritional status; impact on overall survival was inconsistent. Nutraceutical and herbal interventions showed limited clinical benefits despite apparent biological activity. The variability in outcomes underscores the need for personalized nutritional strategies that consider individual patient factors.

Keywords:  ketogenic diet; neoplasms; nutraceutical and herbal interventions; nutrition support; nutritional advice; supplements

DOI:  https://doi.org/10.1177/10499091251335249
J Clin Invest. 2025 Apr 24. pii: e191021. [Epub ahead of print]

Ketogenesis mitigates metabolic dysfunction-associated steatotic liver disease through mechanisms that extend beyond fat oxidation.

Eric D Queathem, David B Stagg, Alisa B Nelson, Alec B Chaves, Scott B Crown, Kyle Fulghum, D Andre d'Avignon, Justin R Ryder, Patrick J Bolan, Abdirahman Hayir, Jacob R Gillingham, Shannon Jannatpour, Ferrol I Rome, Ashley S Williams, Deborah M Muoio, Sayeed Ikramuddin, Curtis C Hughey, Patrycja Puchalska, Peter A Crawford.

  The progression of metabolic dysfunction-associated steatotic liver disease (MASLD) to metabolic dysfunction-associated steatohepatitis (MASH) involves alterations in both liver-autonomous and systemic metabolism that influence the liver's balance of fat accretion and disposal. Here, we quantify the contributions of hepatic oxidative pathways to liver injury in MASLD-MASH. Using NMR spectroscopy, UHPLC-MS, and GC-MS, we performed stable-isotope tracing and formal flux modeling to quantify hepatic oxidative fluxes in humans across the spectrum of MASLD-MASH, and in mouse models of impaired ketogenesis. In humans with MASH, liver injury correlated positively with ketogenesis and total fat oxidation, but not with turnover of the tricarboxylic acid cycle. Loss-of-function mouse models demonstrated that disruption of mitochondrial HMG-CoA synthase (HMGCS2), the rate-limiting step of ketogenesis, impairs overall hepatic fat oxidation and induces a MASLD-MASH-like phenotype. Disruption of mitochondrial β-hydroxybutyrate dehydrogenase (BDH1), the terminal step of ketogenesis, also impaired fat oxidation, but surprisingly did not exacerbate steatotic liver injury. Taken together, these findings suggest that quantifiable variations in overall hepatic fat oxidation may not be a primary determinant of MASLD-to-MASH progression, but rather, that maintenance of ketogenesis could serve a protective role through additional mechanisms that extend beyond overall rates of fat oxidation.

Keywords:  Fatty acid oxidation; Hepatology; Intermediary metabolism; Metabolism; Obesity

DOI:  https://doi.org/10.1172/JCI191021
Eur J Clin Nutr. 2025 Apr 22.

Metabolomic profiling of a cholesterol lowering plant-based diet from two randomized controlled feeding trials.

Andrea J Glenn, Anne-Julie Tessier, Meaghan E Kavanagh, Gloria A Morgan, Clary B Clish, Jordi Salas-Salvado, Vasanti S Malik, Anthony J Hanley, Richard P Bazinet, Elena M Comelli, Ahmed El-Sohemy, Simin Liu, Beatrice A Boucher, Cyril W C Kendall, David J A Jenkins, Frank B Hu, John L Sievenpiper.

BACKGROUND: Objective biomarkers of diet, such as metabolomics, may improve dietary assessment and provide additional insight into how diet influences disease risk. The portfolio diet, a cholesterol-lowering plant-based diet, is recommended for lowering low-density lipoprotein cholesterol (LDL-C). This diet is low in saturated fat and includes nuts, plant protein (legumes), viscous fiber, and phytosterols.
OBJECTIVE: We examined metabolomic profiles in response to the portfolio diet in two randomized controlled trials (RCTs), where all foods were provided to the participants, compared to a control vegetarian diet and the same control diet with a statin.
METHODS: The first RCT included 34 adults (age 58.4 ± 8.6 y) and the second RCT included 25 adults (age 61.0 ± 9.6 y), all with high LDL-C (>4.1 mmol/L). Plasma samples were obtained at baseline, week 2, and week 4 in both RCTs for metabolomics analysis using liquid chromatography-tandem mass spectrometry. Linear mixed models were used to examine effects of the interventions on the metabolites in each RCT, applying a Bonferroni correction.
RESULTS: Of 496 known metabolites, 145 and 63 metabolites significantly changed within the portfolio diet interventions in the first and second RCT, respectively. The majority were glycerophosphocholines (32%), triacylglycerols (20%), glycerophosphoethanolamines (14%), sphingomyelins (8%), and amino acids and peptides (8%) in the first RCT, and glycerophosphocholines (48%), glycerophosphoethanolamines (17%), and amino acids and peptides (8%) in the second RCT. Fifty-two metabolites were consistently changed in the same direction with the portfolio diet intervention across both RCTs, after Bonferroni correction.
CONCLUSIONS: Many of these metabolites likely reflect the plant-based nature, low saturated fat content, and cholesterol-lowering effects of the diet, such as increased N2-acetylornithine, L-pipecolic acid, lenticin, and decreased C18:0 lipids and cholesteryl esters. Further research is needed to validate these metabolites as biomarkers of a plant-based dietary pattern.

DOI: https://doi.org/10.1038/s41430-025-01625-x
Anal Chim Acta. 2025 Jun 15. pii: S0003-2670(25)00399-X. [Epub ahead of print]1355 344005

The power of trapped ion mobility for isotope tracer experiments.

Karin Preindl, Chuqiao Chen, Supriya Murthy, Florian Gruber, Christian Freystätter, Thomas Weichhart, Thomas Stimpfl, Birgit Reiter, Arvand Haschemi, Gunda Koellensperger.

   BACKGROUND: Isotope tracing experiments in cellular metabolomics are challenged by the multiple isomers and in-source fragments, which need to be considered to obtain unbiased isotopologue ratio measurements. Thus, both, selectivity and sensitivity are key requirements for customized workflows. Trapped ion mobility spectrometry (TIMS) introduces an additional separation dimension to mass spectrometry, separating otherwise co-eluting isomers by measuring the ion mobility of a molecule. This study shows for the first time, the potential of this MS platform for accurate isotopologue assessment as showcased in isotope tracer experiments using mammalian cells.
RESULTS: The validation exercise focused on spectral accuracy, precision, and metabolite detection capabilities and comprised independent measurements on an orbitrap-based platform. Hydrophilic interaction chromatography, in combination with TIMS-TOF-MS delivered excellent results, with a minimum trueness bias and excellent precision (CV%) between 0.3 % and 6.4 %. The ion mobility separation allowed for differentiation of the otherwise co-eluting isomers fructose-6-phosphate (F6P) and glucose-1-phosphate (G1P). Overall, isotopologue distributions were in good agreement upon crossvalidation with the orbitrap platform. Finally, a proof-of-concept tracer study addressed the activity of the glycolysis and the pentose phosphate pathway (PPP) in resting and endotoxin activated macrophages. We confirmed an activation of glycolysis and PPP in LPS activated macrophages, but found a potentially reduced relative contribution of glucose-6-phosphate (G6P) to increased F6P pools. Our findings imply that TIMS is a powerful technology for the reliable measurements of isotope distribution analysis in metabolic tracing experiments.
SIGNIFICANCE: By implementation of ion mobility, it is now possible to generate distinct isotopologue patterns for G1P and F6P in isotope tracer experiments. F6P plays a crucial role in glycolysis and PPP, highlighting the importance of precise analytical measurements. This is particularly true for metabolic studies in immunology and cancer research.

Keywords:  Isotope tracer; Macrophages; TIMS; Trapped ion mobility

DOI:  https://doi.org/10.1016/j.aca.2025.344005
Membranes (Basel). 2025 Apr 13. pii: 124. [Epub ahead of print]15(4):

Restricted Surface Diffusion of Cytochromes on Bioenergetic Membranes with Anionic Lipids.

Aaron Chan, Emad Tajkhorshid.

  Bioenergetic membranes of mitochondria, thylakoids, and chromatophores are primary sites of ATP production in living cells. These membranes contain an electron transport chain (ETC) in which electrons are shuttled between a series of redox proteins during the generation of ATP via oxidative phosphorylation. The phospholipid composition of these membranes, which often include negative lipids, plays a role in determining the electrostatics of their surface owing to the spatial distribution of their charged head groups. Cardiolipin (CDL) is a phospholipid commonly associated with bioenergetic membranes and is also a significant contributor to the negative surface charge. Interactions between cytochromes and phospholipid head groups in the membrane can in principle affect the rate of its travel between ETC components, hence influencing the rate of ATP turnover. Here, we use molecular dynamic (MD) simulations that feature an accelerated membrane model, termed highly mobile membrane mimetic (HMMM), to study protein-lipid interactions during the diffusion of cytochrome c2 between redox partners in a bioenergetic membrane. We observe a "skipping" mode of diffusion for cytochromes along with a bias for binding to anionic lipids, particularly with a strong preference for CDL. During diffusion, cytochrome c2 maintains a relatively fixed tilt with respect to the membrane normal with wider fluctuations in its angle with respect to the plane of the membrane. The obtained results describing the behavior of cytochrome c2 on a representative bioenergetic membrane have direct ramifications in shuttling motions of other similar electron-carrying elements in other bioenergetic membranes, which are composed of a significant amount of anionic lipids. The mode of surface-restricted diffusion reported here would modulate rapid electron transfer between the ETC complexes anchored in bioenergetic membranes by reducing the search space between them.

Keywords:  bioenergetic membranes; cardiolipin; electron transfer; enhanced sampling; molecular dynamics

DOI:  https://doi.org/10.3390/membranes15040124
Diseases. 2025 Mar 25. pii: 94. [Epub ahead of print]13(4):

Low-Carbohydrate (Ketogenic) Diet in Children with Obesity: Part 1-Diet Impact on Anthropometric Indicators and Indicators of Metabolic Syndrome and Insulin Resistance.

Ivanka N Paskaleva, Nartsis N Kaleva, Teodora D Dimcheva, Petya P Markova, Ivan S Ivanov.

   BACKGROUND: The ketogenic diet has been successfully used in the last 100 years in the treatment of epilepsy and other neurological disorders. In recent decades, it gained wider application in the treatment of obesity, metabolic syndrome, and type 2 diabetes. However, there have been only a few studies on its use in children with obesity and associated metabolic disorders.
OBJECTIVES: To determine the clinical and metabolic effects of a well-formulated low-carbohydrate (ketogenic) diet in children with obesity.
METHODS: One hundred children with obesity and metabolic disorders underwent initial anthropometric, laboratory, and ultrasound examinations. They were placed on a well-formulated ketogenic diet and monitored for 4 months. The 58 patients who completed the study underwent follow-up examinations to assess the effects of the diet on anthropometric, clinical, and laboratory markers of metabolic syndrome and insulin resistance, cardiovascular risk factors, and certain hormone levels. Compliance with the diet, common difficulties in adhering to it, side effects, and positive changes in the patients' health were analyzed.
RESULTS: At the end of the study, the average weight loss for the entire group was 6.45 kg, with a reduction in BMI of 3.12 kg/m2. Significant improvements were also observed in insulin resistance indicators, including fasting insulin levels, HOMA-IR index, QUICKI (p < 0.0001), and adiponectin (p = 0.04). The cases of hepatosteatosis decreased twofold, the number of patients with arterial hypertension was significantly reduced, as well as the number of children receiving antihypertensive therapy. Additionally, the number of patients meeting the criteria for metabolic syndrome decreased threefold.
CONCLUSIONS: A well-formulated short-term ketogenic diet is effective in treating obesity, metabolic syndrome, and related comorbidities, and can be part of a comprehensive approach for these patients.

Keywords:  children; insulin resistance; ketogenic diet; metabolic syndrome; obesity

DOI:  https://doi.org/10.3390/diseases13040094
Exp Hematol. 2025 Apr 19. pii: S0301-472X(25)00082-7. [Epub ahead of print] 104791

Unbiased analysis of NUP98-KDM5A-induced murine leukemia reveals phenotypic heterogeneity recapitulating human disease subtypes.

Marilaine Fournier, Marion Dubuissez, Mathieu Neault, Jean-Sébastien Delisle, Frédérick A Mallette, Heather J Melichar.

  NUP98-KDM5A (NK5) is an oncogenic fusion protein implicated in the development of several types of acute myeloid leukemia (AML) in humans, including rare pediatric acute megakaryoblastic leukemia (AMKL). NK5 expression in murine hematopoietic progenitor cells can induce AML in mice. However, the limited number of animals and phenotypic markers used in previous studies preclude the full characterization of the AML subtypes that develop. We used NK5-transduced hematopoietic progenitor cells from murine fetal liver to generate a large cohort of mice, assessed the expression of a panel of myeloid markers to characterize the lineage of leukemic blasts by flow cytometry, and used bioinformatic tools to perform an unbiased analysis assessing the extensive mouse-to-mouse heterogeneity in leukemic cellular phenotypes. We were able to identify phenotypically distinct sub-groups among the NK5 leukemias that segregated predominantly based on expression of the AMKL-associated marker CD41. Our results suggest that NK5 expression in fetal liver cells gives rise to heterogenous types of leukemia similar in proportion to that observed in human pediatric patients. The heterogeneity and mixed phenotypes observed might explain the difficulty in accurately diagnosing leukemia in some patients carrying the NK5 fusion. In addition, this approach may enable identification of the molecular or cellular basis of the diverse NK5-driven AML types. TEASER ABSTRACT: NUP98-KDM5A (NK5) gives rise to a variety of leukemia types in human, including rare pediatric AMKL. The development of curative treatments for NK5+ AMKL is hindered by the lack of animal models that recapitulate human disease. Using unbiased clustering of phenotypic data, we confirm that NK5+ leukemia can be modeled in mice and identify a population of NK5+ AMKL-like leukemias in similar proportion to that observed in human patients. The model will enable identification of the molecular mechanisms driving NK5 leukemias as well as the testing of tailored treatment approaches.

Keywords:  Acute Megakaryoblastic Leukemia; NUP98-KDM5A; Non-biased analysis

DOI:  https://doi.org/10.1016/j.exphem.2025.104791