bims-celmim 2025-03-02 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–03–02
28 papers selected by
Marc Segarra Mondejar

Methionine cycle inhibition disrupts antioxidant metabolism and reduces glioblastoma cell survival.
MiNEApy: Enhancing Enrichment Network Analysis in Metabolic Networks.
Visualization of Subcellular mTOR Complex 1 Activity with a FRET-Based Sensor (TORCAR).
Mitochondrial substrate oxidation regulates distinct cell differentiation outcomes.
How the Topology of the Mitochondrial Inner Membrane Modulates ATP Production.
Dysregulation of mitochondrial α-ketoglutarate dehydrogenase leads to elevated lipid peroxidation in CHCHD2-linked Parkinson's disease models.
Human glycolysis isomerases are inhibited by weak metabolite modulators.
Individual bioenergetic capacity as a potential source of resilience to Alzheimer's disease.
The response of mitochondrial position to glucose stimulation in a model system of the pancreatic beta cell.
Suppression of endothelial ceramide de novo biosynthesis by Nogo-B contributes to cardiometabolic diseases.
S100A2 promotes clear cell renal cell carcinoma tumor metastasis through regulating GLUT2 expression.
The Matrix of Mitochondrial Imaging: Exploring Spatial Dimensions.
Stress exposure in the mdx mouse model of Duchenne muscular dystrophy provokes a widespread metabolic response.
MiR-365-3p inhibits lung cancer proliferation and migration via CPT1A-mediated fatty acid oxidation.
Cholesterol depletion activates trafficking-coupled sphingolipid synthesis.
Comparative metabolomic analysis reveals shared and unique features of COVID-19 cytokine storm and surgical sepsis.
A systems-level, semi-quantitative landscape of metabolic flux in C. elegans.
Heterogeneous metabolic response of endothelial cells from different vascular beds to experimental hyperglycaemia and metformin.
Significance of Malic Enzyme 1 in Cancer: A Review.
Monitoring Cellular Energy Balance in Single Cells Using Fluorescent Biosensors for AMPK.
Mitochondrial targeted therapies in MAFLD.
NOX4 modulates breast cancer progression through cancer cell metabolic reprogramming and CD8+ T cell antitumor activity.
Mitochondrial superoxide regulates pro-inflammatory macrophages.
Tandem metabolic reaction-based sensors unlock in vivo metabolomics.
Sensing of Long-Chain Fatty Acyl-CoA Esters by AMPK.
The MicroMap is a network visualisation resource for microbiome metabolism.
Assays of Different Mechanisms of AMPK Activation, and Use of Cells Expressing Mutant AMPK to Delineate Activation Mechanisms.
Measuring Cellular Adenine Nucleotides by Liquid Chromatography-Coupled Mass Spectrometry.

J Biol Chem. 2025 Feb 25. pii: S0021-9258(25)00198-X. [Epub ahead of print] 108349

Methionine cycle inhibition disrupts antioxidant metabolism and reduces glioblastoma cell survival.

Emma C Rowland, Matthew D'Antuono, Anna Jermakowicz, Nagi G Ayad.

  Glioblastoma (GBM) is a highly aggressive primary malignant adult brain tumor that inevitably recurs with a fatal prognosis. This is due in part to metabolic reprogramming that allows tumors to evade treatment. Therefore, we must uncover the pathways mediating these adaptations to develop novel and effective treatments. We searched for genes that are essential in GBM cells as measured by a whole-genome pan-cancer CRISPR screen available from DepMap and identified the methionine metabolism genes MAT2A and AHCY. We conducted genetic knockdown, evaluated mitochondrial respiration, and performed targeted metabolomics to study the function of these genes in GBM. We demonstrate that MAT2A or AHCY knockdown induces oxidative stress, hinders cellular respiration, and reduces the survival of GBM cells. Furthermore, selective MAT2a or AHCY inhibition reduces GBM cell viability, impairs oxidative metabolism, and shifts the cellular metabolic profile towards oxidative stress and cell death. Mechanistically, MAT2a and AHCY regulate spare respiratory capacity, the redox buffer cystathionine, lipid and amino acid metabolism, and prevent oxidative damage in GBM cells. Our results point to the methionine metabolic pathway as a novel vulnerability point in GBM. Significance We demonstrated that methionine metabolism maintains antioxidant production to facilitate pro-tumorigenic ROS signaling and GBM tumor cell survival. Importantly, targeting this pathway in GBM has the potential to reduce tumor growth and improve survival in patients.

Keywords:  glioblastoma; lipid peroxidation; metabolism; metabolomics; methionine; mitochondria; oxidative stress

DOI:  https://doi.org/10.1016/j.jbc.2025.108349
Bioinformatics. 2025 Feb 22. pii: btaf077. [Epub ahead of print]

MiNEApy: Enhancing Enrichment Network Analysis in Metabolic Networks.

Vikash Pandey.

MOTIVATION: Modeling genome-scale metabolic networks (GEMs) helps understand metabolic fluxes in cells at a specific state under defined environmental conditions or perturbations. Elementary Flux Modes (EFMs) are powerful tools for simplifying complex metabolic networks into smaller, more manageable pathways. However, the enumeration of all EFMs, especially within GEMs, poses significant challenges due to computational complexity. Additionally, traditional EFM approaches often fail to capture essential aspects of metabolism, such as co-factor balancing and by-product generation.The previously developed Minimum Network Enrichment Analysis (MiNEA) method addresses these limitations by enumerating alternative minimal networks for given biomass building blocks and metabolic tasks. MiNEA facilitates a deeper understanding of metabolic task flexibility and context-specific metabolic routes by integrating condition-specific transcriptomics, proteomics, and metabolomics data. This approach offers significant improvements in the analysis of metabolic pathways, providing more comprehensive insights into cellular metabolism.
RESULTS: Here, I present MiNEApy, a Python package reimplementation of MiNEA, which computes minimal networks and performs enrichment analysis. I demonstrate the application of MiNEApy on both a small-scale and a genome-scale model of the bacterium E. coli, showcasing its ability to conduct minimal network enrichment analysis using minimal networks and context-specific data.
AVAILABILITY: MiNEApy can be accessed at: https://github.com/vpandey-om/mineapy.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btaf077
Methods Mol Biol. 2025 ;2882 139-162

Visualization of Subcellular mTOR Complex 1 Activity with a FRET-Based Sensor (TORCAR).

Ayse Z Sahan, Sohum Metha, Jin Zhang.

  The mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient-sensing complex that integrates inputs from several pathways to promote cell growth and proliferation. mTORC1 localizes to many cellular compartments, including the nucleus, lysosomes, and plasma membrane. However, little is known about the spatial regulation of mTORC1 and the specific functions of mTORC1 at these locations. To address these questions, we previously developed a Förster resonance energy transfer (FRET)-based mTORC1 activity reporter (TORCAR) to visualize the dynamic changes in mTORC1 activity within live cells. Here, we describe a detailed protocol for using subcellularly targeted TORCAR constructs to investigate subcellular mTORC1 activities via live-cell fluorescence microscopy.

Keywords:  Biosensor; Compartmentalized signaling; Fluorescence; Location-specific

DOI:  https://doi.org/10.1007/978-1-0716-4284-9_7
Trends Cell Biol. 2025 Feb 25. pii: S0962-8924(25)00038-8. [Epub ahead of print]

Mitochondrial substrate oxidation regulates distinct cell differentiation outcomes.

Woo Yong Park, Claudia Montufar, Elma Zaganjor.

  Mitochondrial metabolism, signaling, and dynamics are key regulators of cell fate. While glycolysis supports stemness, mitochondrial expansion and oxidative phosphorylation (OXPHOS) facilitate differentiation. This forum presents emerging evidence that the type of substrate, whether amino acids, carbohydrates, or fatty acids, oxidized by mitochondria significantly influences differentiation outcomes.

Keywords:  OXPHOS; amino acids; differentiation; fatty acids; glucose; mitochondria

DOI:  https://doi.org/10.1016/j.tcb.2025.02.004
Cells. 2025 Feb 11. pii: 257. [Epub ahead of print]14(4):

How the Topology of the Mitochondrial Inner Membrane Modulates ATP Production.

Raquel Adams, Nasrin Afzal, Mohsin Saleet Jafri, Carmen A Mannella.

  Cells in heart muscle need to generate ATP at or near peak capacity to meet their energy demands. Over 90% of this ATP comes from mitochondria, strategically located near myofibrils and densely packed with cristae to concentrate ATP generation per unit volume. However, a consequence of dense inner membrane (IM) packing is that restricted metabolite diffusion inside mitochondria may limit ATP production. Under physiological conditions, the flux of ATP synthase is set by ADP levels in the matrix, which in turn depends on diffusion-dependent concentration of ADP inside cristae. Computer simulations show how ADP diffusion and consequently rates of ATP synthesis are modulated by IM topology, in particular (i) number, size, and positioning of crista junctions that connect cristae to the IM boundary region, and (ii) branching of cristae. Predictions are compared with the actual IM topology of a cardiomyocyte mitochondrion in which cristae vary systematically in length and morphology. The analysis indicates that this IM topology decreases but does not eliminate the "diffusion penalty" on ATP output. It is proposed that IM topology normally attenuates mitochondrial ATP output under conditions of low workload and can be regulated by the cell to better match ATP supply to demand.

Keywords:  ATP synthesis; cristae; electron tomography; membrane topology; metabolic modeling; metabolite diffusion; mitochondria

DOI:  https://doi.org/10.3390/cells14040257
Nat Commun. 2025 Feb 26. 16(1): 1982

Dysregulation of mitochondrial α-ketoglutarate dehydrogenase leads to elevated lipid peroxidation in CHCHD2-linked Parkinson's disease models.

Ge Gao, Yong Shi, Han-Xiang Deng, Dimitri Krainc.

Dysregulation of mitochondrial function has been implicated in Parkinson's disease (PD), but the role of mitochondrial metabolism in disease pathogenesis remains to be elucidated. Using an unbiased metabolomic analysis of purified mitochondria, we identified alterations in α-ketoglutarate dehydrogenase (KGDH) pathway upon loss of PD-linked CHCHD2 protein. KGDH, a rate-limiting enzyme complex in the tricarboxylic acid cycle, was decreased in CHCHD2-deficient male mouse brains and human dopaminergic neurons. This deficiency of KGDH led to elevated α-ketoglutarate and increased lipid peroxidation. Treatment of CHCHD2-deficient dopaminergic neurons with lipoic acid, a KGDH cofactor and antioxidant agent, resulted in decreased levels of lipid peroxidation and phosphorylated α-synuclein. CHCHD10, a close homolog of CHCHD2 that is primarily linked to amyotrophic lateral sclerosis/frontotemporal dementia, did not affect the KGDH pathway or lipid peroxidation. Together, these results identify KGDH metabolic pathway as a targetable mitochondrial mechanism for correction of increased lipid peroxidation and α-synuclein in Parkinson's disease.

DOI: https://doi.org/10.1038/s41467-025-57142-9
FEBS J. 2025 Feb 27.

Human glycolysis isomerases are inhibited by weak metabolite modulators.

Yiming Yang Jónatansdóttir, Óttar Rolfsson, Jens G Hjörleifsson.

  Modulation of enzyme activity by metabolites represents the most efficient and rapid way of controlling metabolism. Investigating enzyme-metabolite interactions can deepen our understanding of metabolic control and aid in identifying enzyme modulators with potential therapeutic applications. These interactions vary in strength, with dissociation constants (Kd) ranging from strong (nm) to weak (μm-mm). However, weak interactions are often overlooked due to the challenges in studying them. Despite this, weak modulators can reveal unknown binding modes and serve as starting points for compound optimization. In this study, we aimed to identify metabolites that weakly modulate the activity of human glucose-6-phosphate isomerase (GPI) and triosephosphate isomerase (TPI), which are potential therapeutic targets in tumor glycolysis. Through a combination of activity and binding assays, the screening revealed multiple weak inhibitors for the two targets, causing partial attenuation of their activity, with Kd and Ki in the low mm range. X-ray crystallography revealed six orthosteric ligands binding to the active sites - four inhibitors of GPI and two of TPI. Our findings underscore the role of weak interactions in enzyme regulation and may provide structural insights that could aid the design of inhibitors targeting human GPI and TPI in cancer intervention.

Keywords:  cancer metabolism; compound screening; glycolysis; metabolic regulation; weak inhibition

DOI:  https://doi.org/10.1111/febs.70049
Nat Commun. 2025 Feb 24. 16(1): 1910

Individual bioenergetic capacity as a potential source of resilience to Alzheimer's disease.

Alzheimer’s Disease Neuroimaging Initiative

Impaired glucose uptake in the brain is an early presymptomatic manifestation of Alzheimer's disease (AD), with symptom-free periods of varying duration that likely reflect individual differences in metabolic resilience. We propose a systemic "bioenergetic capacity", the individual ability to maintain energy homeostasis under pathological conditions. Using fasting serum acylcarnitine profiles from the AD Neuroimaging Initiative as a blood-based readout for this capacity, we identified subgroups with distinct clinical and biomarker presentations of AD. Our data suggests that improving beta-oxidation efficiency can decelerate bioenergetic aging and disease progression. The estimated treatment effects of targeting the bioenergetic capacity were comparable to those of recently approved anti-amyloid therapies, particularly in individuals with specific mitochondrial genotypes linked to succinylcarnitine metabolism. Taken together, our findings provide evidence that therapeutically enhancing bioenergetic health may reduce the risk of symptomatic AD. Furthermore, monitoring the bioenergetic capacity via blood acylcarnitine measurements can be achieved using existing clinical assays.

DOI: https://doi.org/10.1038/s41467-025-57032-0
bioRxiv. 2025 Feb 16. pii: 2025.02.13.637960. [Epub ahead of print]

The response of mitochondrial position to glucose stimulation in a model system of the pancreatic beta cell.

Luis Perez, Xue Wen Ng, David W Piston, Shankar Mukherji.

The compartmentalization of eukaryotic cells into membrane-bound organelles with specific subcellular positioning enables precise spatial and temporal control of cellular functions. While functionally significant mitochondrial localization has been demonstrated in cells such as neurons, it remains unclear how general these cell principles are. Here, we examine the spatial organization of mitochondria within MIN6 pancreatic beta cells under variable glucose conditions. We observe glucose-dependent redistributions of mitochondria, favoring peripheral localization at elevated glucose levels when insulin secretion is also elevated. Our results suggest that active mitochondrial transport along microtubules and calcium activity, but not ATP synthesis, are critical regulators of this redistribution. We derived a mathematical model that reveals a putative affinity of the mitochondria for cellular membranes competes with mitochondrial microtubule attachment to play an important role in establishing the mitochondrial spatial patterns we observe. These results suggest that mitochondrial positioning may contribute to optimizing energy delivery in response to local demand, potentially representing a general regulatory mechanism across various cell types.

DOI: https://doi.org/10.1101/2025.02.13.637960
Nat Commun. 2025 Feb 25. 16(1): 1968

Suppression of endothelial ceramide de novo biosynthesis by Nogo-B contributes to cardiometabolic diseases.

Luisa Rubinelli, Onorina Laura Manzo, Jin Sungho, Ilaria Del Gaudio, Rohan Bareja, Alice Marino, Sailesh Palikhe, Vittoria Di Mauro, Mariarosaria Bucci, Domenick J Falcone, Olivier Elemento, Baran Ersoy, Sabrina Diano, Linda Sasset, Annarita Di Lorenzo.

Accrual of ceramides, membrane and bioactive sphingolipids, has been implicated in endothelial dysfunction preceding cardiometabolic diseases. Yet, direct in vivo evidence, underlying mechanisms, and pathological implications are lacking. Here we show that suppression of ceramides and sphingosine-1-phosphate (S1P), a product of ceramide degradation, are causally linked to endothelial dysfunction and activation, contributing to vascular and metabolic disorders in high fat diet fed (HFD) male mice. Mechanistically, the upregulation of Nogo-B and ORMDL proteins suppress ceramide de novo biosynthesis in endothelial cells (EC) of HFD mice, resulting in vascular and metabolic dysfunctions. Systemic and endothelial specific deletion of Nogo-B restore sphingolipid signaling and functions, lowers hypertension, and hepatic glucose production in HFD. Our results demonstrate in vivo that ceramide and S1P suppression rather than accrual contributes to endothelial dysfunction and cardiometabolic diseases in HFD mice. Our study also sets a framework for the development of therapeutic strategies to treat these conditions.

DOI: https://doi.org/10.1038/s41467-025-56869-9
Cell Death Dis. 2025 Feb 27. 16(1): 135

S100A2 promotes clear cell renal cell carcinoma tumor metastasis through regulating GLUT2 expression.

Mengli Deng, Shaoxia Liao, Jingwen Deng, Chen Li, Lu Liu, Qizheng Han, Yifeng Huo, Xiao Zhou, Xiaodong Teng, Maode Lai, Honghe Zhang, Chong Lai.

Clear cell renal cell carcinoma (ccRCC) is the predominant subtype of renal cancer and is highly malignant. Despite advances in diagnostics and treatment, the prognosis for ccRCC remains poor. The dual nature (promotion or inhibition) of S100A2 in different cancer types shows the complex involvement of its tumorigenesis, but its effect in ccRCC remains unclear. In this study, we first elucidate the tumor-promoting function of S100A2 in ccRCC by reprogramming glycolysis. Mechanistically, we demonstrate that S100A2 accelerates cancer progression through its interaction with the transcription factor HNF1A, leading to activating GLUT2 transcription. The upregulation of GLUT2 significantly enhances glucose uptake by cancer cells, thereby fueling augmented glucose metabolism and fostering the malignant progression of ccRCC. Collectively, our findings highlight the pivotal role of the S100A2-HNF1A-GLUT2 axis in promoting migration and invasion of ccRCC by amplifying glycolysis and suggest that targeting the S100A2-HNF1A-GLUT2 axis is clinically relevant for the treatment of metastatic ccRCC.

DOI: https://doi.org/10.1038/s41419-025-07418-1
Biomolecules. 2025 Feb 05. pii: 229. [Epub ahead of print]15(2):

The Matrix of Mitochondrial Imaging: Exploring Spatial Dimensions.

Irene M G M Hemel, Ilja C W Arts, Michelle Moerel, Mike Gerards.

  Mitochondria play a crucial role in human biology, affecting cellular processes at the smallest spatial scale as well as those involved in the functionality of the whole system. Imaging is the most important research tool for studying the fundamental role of mitochondria across these diverse spatial scales. A wide array of available imaging techniques have enabled us to visualize mitochondrial structure and behavior, as well as their effect on cells and tissues in a range from micrometers to centimeters. Each of the various imaging techniques that are available offers unique advantages tailored to specific research needs. Selecting an appropriate technique suitable for the scale and application of interest is therefore crucial, but can be challenging due to the large range of possibilities. The aim of this review is two-fold. First, we provide an overview of the available imaging techniques and discuss their strengths and limitations for applications across the sub-mitochondrial, cellular, tissue and organ levels for the imaging of mitochondria. Second, we identify opportunities for novel applications and advancement in the field. We emphasize the importance of integration across scales in mitochondrial imaging studies, particularly to bridge the gap between microscopic and non-invasive techniques. While integrating these diverse scales is challenging, primarily because such multi-scale approaches require expertise that spans different imaging modalities, we argue that integration has the potential to provide groundbreaking insights into mitochondrial biology. By providing a comprehensive overview of imaging techniques, this review paves the way for multi-scale imaging initiatives in mitochondrial research.

Keywords:  MRI; imaging; microscopy; mitochondria

DOI:  https://doi.org/10.3390/biom15020229
FEBS J. 2025 Feb 22.

Stress exposure in the mdx mouse model of Duchenne muscular dystrophy provokes a widespread metabolic response.

Erynn E Johnson, James M Ervasti.

  Duchenne muscular dystrophy is a severe neuromuscular wasting disease that is caused by a primary defect in dystrophin protein and involves organism-wide comorbidities such as cardiomyopathy, metabolic and mitochondrial dysfunction, and nonprogressive cognitive impairments. Physiological stress exposure in the mdx mouse model of Duchenne muscular dystrophy results in phenotypic abnormalities that include locomotor inactivity, hypotension, and increased morbidity. Severe and lethal stress susceptibility in mdx mice corresponds to metabolic dysfunction in several coordinated metabolic pathways within dystrophin-deficient skeletal muscle, as well as prolonged elevation in mdx plasma corticosterone levels that extends beyond the wild-type (WT) stress response. Here, we performed a targeted mass spectrometry-based plasma metabolomics screen focused on biological stress pathways in healthy and dystrophin-deficient mdx mice exposed to mild scruff stress. One-third of the stress-relevant metabolites interrogated displayed significant elevation or depletion in mdx plasma after scruff stress and were restored to WT levels by skeletal muscle-specific dystrophin expression. The metabolic pathways of mdx mice altered by scruff stress are associated with regulation of the hypothalamic-pituitary-adrenal axis, locomotor tone, neurocognitive function, redox metabolism, cellular bioenergetics, and protein catabolism. Our data suggest that a mild stress triggers an exaggerated, multi-system metabolic response in mdx mice.

Keywords:  Duchenne muscular dystrophy; biological stress; metabolism; metabolomics; skeletal muscle

DOI:  https://doi.org/10.1111/febs.70029
Sci Rep. 2025 Feb 27. 15(1): 7076

MiR-365-3p inhibits lung cancer proliferation and migration via CPT1A-mediated fatty acid oxidation.

Dan Xu, Bohong Liu, Lingling Wang.

  The relationship between abnormal lipid acid metabolism and the progression of lung cancer is increasingly evident. Carnitine palmitoyltransferase 1A (CPT1A), a rate-limiting enzyme in fatty acid oxidation, has been implicated in the advancement of various cancers. However, the role of CPT1A in lung cancer and the regulatory mechanisms of microRNAs on CPT1A-mediated fatty acid oxidation remain largely unknown. In our study, we demonstrate that miR-365-3p inhibits CPT1A expression by targeting its 3'-untranslated region in lung cancer cells. The inhibition of CPT1A by miR-365-3p leads to increased lipid droplet accumulation, diminished ATP production, and a decrease in fatty acid oxidation levels. Furthermore, the disruption of fatty acid oxidation attenuates the ability of the miR-365-3p/CPT1A axis to modulate lung cancer cell proliferation and migration both in vitro and in vivo. Clinical data reveal that CPT1A expression is significantly upregulated while miR-365-3p is markedly downregulated. Additionally, there exists a negative correlation between miR-365-3p and CPT1A expression, and both are predictive of clinical outcome in lung cancer patients. Collectively, our findings shed light on the function and mechanistic pathway of the miR-365-3p/CPT1A axis in lung cancer, which might provide a potential therapeutic target for lung cancer.

Keywords:  CPT1A; Fatty acid oxidation; Lung cancer; Migration; Proliferation; miR-365-3p

DOI:  https://doi.org/10.1038/s41598-025-91665-x
bioRxiv. 2025 Feb 16. pii: 2025.02.12.637879. [Epub ahead of print]

Cholesterol depletion activates trafficking-coupled sphingolipid synthesis.

Yeongho Kim, Jan Parolek, Christopher G Burd.

Within cellular membranes, sphingomyelin is associated with cholesterol and this complex facilitates homeostatic regulation of membrane viscosity. Acute cholesterol depletion increases the synthesis of very-long-chain (VLC) sphingomyelin, but a link between lipid sensing and sphingolipid synthesis is lacking. Using sphingolipid metabolic flux analysis, we observed that VLC-ceramide, the precursor to VLC complex sphingolipids that are produced in the Golgi apparatus, was rapidly consumed after cholesterol depletion, while synthesis of long-chain sphingolipids was unaffected. Sphingolipid trafficking assays showed that cholesterol depletion enhances VLC-Ceramide trafficking from the endoplasmic reticulum to the Golgi apparatus. Changes in the sizes of coatomer II ER exit sites were correlated with increased VLC-Ceramide trafficking and concomitant increase in sphingomyelin. Depletion of Sec16A, a component of the COPII network, abolished VLC-SM synthesis. This study reveals ER-to-Golgi trafficking of VLC-Ceramide as a key regulatory node in organelle membrane homeostasis pathways.
Summary: In cellular membranes, sphingomyelin is associated with cholesterol. Metabolic flux analysis of sphingolipid metabolism showed that synthesis rate of sphingomyelin, but not ceramide, was increased after depletion of cholesterol due increased rate of COPII-dependent ER-to-Golgi transport of ceramide.

DOI: https://doi.org/10.1101/2025.02.12.637879
Sci Rep. 2025 Feb 24. 15(1): 6622

Comparative metabolomic analysis reveals shared and unique features of COVID-19 cytokine storm and surgical sepsis.

Iana V Russkikh, Oleg S Popov, Tatiana G Klochkova, Natalia N Sushentseva, Svetlana V Apalko, Anna Yu Asinovskaya, Sergey V Mosenko, Andrey M Sarana, Sergey G Shcherbak.

  The clinical manifestations of the cytokine storm (CS) associated with COVID-19 resemble the acute phase of sepsis. Metabolomics may contribute to understanding the specific pathobiology of these two syndromes. The aim of this study was to compare serum metabolomic profiles in CS associated with COVID-19 vs. septic surgery patients. In a retrospective cross-sectional study, serum samples from patients with CS associated with COVID-19, with and without comorbidity, as well as serum samples from patients with surgical sepsis were investigated. Targeted metabolomic analysis was performed on all samples using LC-MS/MS. Analysis revealed that similar alterations in the serum metabolome of patients with COVID-19 and surgical septic patients were associated with amino acid metabolism, nitrogen metabolism, inflammatory status, methionine cycle and glycolysis. The most significant difference was found for serum levels of metabolites of kynurenine synthesis, tricarboxylic acid cycle, gamma-aminobutyric acid and niacinamide. The metabolic pathway of cysteine and methionine metabolism was significantly disturbed in COVID-19 and surgical septic patients. For the first time, the similarities and differences between the serum metabolomic profiles of patients with CS associated with COVID-19 and patients with surgical sepsis were investigated for patients from the Northwest of the Russian Federation.

Keywords:  COVID-19; Cytokine storm; LC–MS/MS; Metabolic pathways; Sepsis; Targeted metabolomic analysis

DOI:  https://doi.org/10.1038/s41598-025-90426-0
Nature. 2025 Feb 26.

A systems-level, semi-quantitative landscape of metabolic flux in C. elegans.

Hefei Zhang, Xuhang Li, L Tenzin Tseyang, Gabrielle E Giese, Hui Wang, Bo Yao, Jingyan Zhang, Rachel L Neve, Elizabeth A Shank, Jessica B Spinelli, L Safak Yilmaz, Albertha J M Walhout.

Metabolic flux, or the rate of metabolic reactions, is one of the most fundamental metrics describing the status of metabolism in living organisms. However, measuring fluxes across the entire metabolic network remains nearly impossible, especially in multicellular organisms. Computational methods based on flux balance analysis have been used with genome-scale metabolic network models to predict network-level flux wiring1-6. However, such approaches have limited power because of the lack of experimental constraints. Here, we introduce a strategy that infers whole-animal metabolic flux wiring from transcriptional phenotypes in the nematode Caenorhabditis elegans. Using a large-scale Worm Perturb-Seq (WPS) dataset for roughly 900 metabolic genes7, we show that the transcriptional response to metabolic gene perturbations can be integrated with the metabolic network model to infer a highly constrained, semi-quantitative flux distribution. We discover several features of adult C. elegans metabolism, including cyclic flux through the pentose phosphate pathway, lack of de novo purine synthesis flux and the primary use of amino acids and bacterial RNA as a tricarboxylic acid cycle carbon source, all of which we validate by stable isotope tracing. Our strategy for inferring metabolic wiring based on transcriptional phenotypes should be applicable to a variety of systems, including human cells.

DOI: https://doi.org/10.1038/s41586-025-08635-6
J Physiol. 2025 Feb 25.

Heterogeneous metabolic response of endothelial cells from different vascular beds to experimental hyperglycaemia and metformin.

C McAleese, G Joudah, I P Salt, J R Petrie, J M Leiper, Laura B Dowsett.

  Endothelial cells (ECs) are highly glycolytic, with mitochondria primarily serving a signalling function. Metabolic disruptions are early contributors to endothelial dysfunction, a primary feature of diabetic vascular complications, such as retinopathy, impaired wound healing and cerebral small vessel disease. The degree to which metabolism varies amongst such different vascular beds is unknown. Mitochondrial function was therefore characterised in human aortic, dermal, retinal and cerebral ECs in vitro, aiming to determine whether basal metabolism influences the response and susceptibility of vascular beds experimental hyperglycaemia (HG). Furthermore, the potential of metformin to maintain endothelial function independent of glycaemic control was assessed. Using a Seahorse analyser, metabolic function of human primary ECs from different vascular beds was compared under basal conditions, as well as HG and metformin treatment. ECs differed significantly in respiratory profile and glycolytic function. For example aortic ECs were preferentially aerobic, whereas dermal ECs were glycolytic. HG significantly lowered mitochondrial network area but elicited modest effects upon respiratory function at the same time as influencing glycolytic function in a manner that was possibly conditional upon basal utilisation. Metformin inhibited basal respiratory function at the same time as significantly enhancing glycolysis in retinal and brain ECs. These data suggest that EC responses to HG and metformin are influenced by the basal metabolic profile, highlighting the potential of targeting EC metabolism to preserve function in a diabetic condition. A nuanced approach is needed to address diabetic vascular complications and endothelial metabolic health in diabetes, both in the investigation of pathophysiology and in prospective therapeutics. KEY POINTS: Endothelial dysfunction is an early feature of diabetes-associated cardiovascular complications Endothelial cells (ECs) are highly glycolytic, with mitochondria serving a signalling function ECs are known to be heterogeneous in function, but how this is reflected in metabolism is not fully understood, in addition to how this influences their response to hyperglycaemia Using experimental hyperglycaemia (HG) in vitro, we demonstrate that ECs differed significantly in respiratory profile and glycolytic function. Their response to HG is possibly contingent upon this basal utilisation. These results suggest a nuanced approach is needed when investigating diabetic vascular complications, both in the investigation of pathophysiology and in prospective therapeutics.

Keywords:  diabetes mellitus; endothelial cell; metabolism; mitochondria

DOI:  https://doi.org/10.1113/JP288006
Curr Issues Mol Biol. 2025 Jan 29. pii: 83. [Epub ahead of print]47(2):

Significance of Malic Enzyme 1 in Cancer: A Review.

Rina Fujiwara-Tani, Chie Nakashima, Hitoshi Ohmori, Kiyomu Fujii, Yi Luo, Takamitsu Sasaki, Ruiko Ogata, Hiroki Kuniyasu.

  Malic enzyme 1 (ME1) plays a key role in promoting malignant phenotypes in various types of cancer. ME1 promotes epithelial-mesenchymal transition (EMT) and enhances stemness via glutaminolysis, energy metabolism reprogramming from oxidative phosphorylation to glycolysis. As a result, ME1 promotes the malignant phenotypes of cancer cells and poor patient prognosis. In particular, ME1 expression is promoted in hypoxic environments associated with hypoxia-inducible factor (HIF1) α. ME1 is overexpressed in budding cells at the cancer invasive front, promoting cancer invasion and metastasis. ME1 also generates nicotinamide adenine dinucleotide (NADPH), which, together with glucose-6-phosphate dehydrogenase (G6PD) and isocitrate dehydrogenase (IDH1), expands the NADPH pool, maintaining the redox balance in cancer cells, suppressing cell death by neutralizing mitochondrial reactive oxygen species (ROS), and promoting stemness. This review summarizes the latest research insights into the mechanisms by which ME1 contributes to cancer progression. Because ME1 is involved in various aspects of cancer and promotes many of its malignant phenotypes, it is expected that ME1 will become a novel drug target in the near future.

Keywords:  cancer stem cells; energy metabolism; epithelial–mesenchymal transition; hypoxia; malic enzyme 1

DOI:  https://doi.org/10.3390/cimb47020083
Methods Mol Biol. 2025 ;2882 47-79

Monitoring Cellular Energy Balance in Single Cells Using Fluorescent Biosensors for AMPK.

Nicholaus DeCuzzi, Nont Kosaisawe, Michael Pargett, Markhus Cabel, John G Albeck.

  5'-Adenosine monophosphate-activated protein kinase (AMPK) senses cellular metabolic status and reflects the balance between ATP production and ATP usage. This balance varies from cell to cell and changes over time, creating a need for methods that can capture cellular heterogeneity and temporal dynamics. Fluorescent biosensors for AMPK activity offer a unique approach to measure metabolic status nondestructively in single cells in real time. In this chapter, we provide a brief rationale for using live-cell biosensors to measure AMPK activity, survey the current AMPK biosensors, and discuss considerations for using this approach. We provide methodology for introducing AMPK biosensors into a cell line of choice, setting up experiments for live-cell fluorescent microscopy of AMPK activity, and calibrating the biosensors using immunoblot data.

Keywords:  AMPKAR; Biosensors; Fluorescent protein reporters; Forster resonance energy transfer (FRET); Live-cell microscopy; Metabolic signaling; Single cell

DOI:  https://doi.org/10.1007/978-1-0716-4284-9_3
Biochem Biophys Res Commun. 2025 Feb 17. pii: S0006-291X(25)00212-8. [Epub ahead of print]753 151498

Mitochondrial targeted therapies in MAFLD.

Sien Lai, Dongsheng Tang, Juan Feng.

  Metabolic dysfunction-associated fatty liver disease (MAFLD) is a clinical-pathological syndrome primarily characterized by excessive accumulation of fat in hepatocytes, independent of alcohol consumption and other well-established hepatotoxic agents. Mitochondrial dysfunction is widely acknowledged as a pivotal factor in the pathogenesis of various diseases, including cardiovascular diseases, cancer, neurodegenerative disorders, and metabolic diseases such as obesity and obesity-associated MAFLD. Mitochondria are dynamic cellular organelles capable of modifying their functions and structures to accommodate the metabolic demands of cells. In the context of MAFLD, the excess production of reactive oxygen species induces oxidative stress, leading to mitochondrial dysfunction, which subsequently promotes metabolic disorders, fat accumulation, and the infiltration of inflammatory cells in liver and adipose tissue. This review aims to systematically analyze the role of mitochondria-targeted therapies in MAFLD, evaluate current therapeutic strategies, and explore future directions in this rapidly evolving field. We specifically focus on the molecular mechanisms underlying mitochondrial dysfunction, emerging therapeutic approaches, and their clinical implications. This is of significant importance for the development of new therapeutic approaches for these metabolic disorders.

Keywords:  MAFLD; Mitochondria; Targeted therapy

DOI:  https://doi.org/10.1016/j.bbrc.2025.151498
Front Immunol. 2025 ;16 1534936

NOX4 modulates breast cancer progression through cancer cell metabolic reprogramming and CD8+ T cell antitumor activity.

Yingying Xiong, Yiming Weng, Shan Zhu, Jian Qin, Jia Feng, Xiaopeng Jing, Chao Luo, Wei Gong, Rui Sun, Min Peng.

   Introduction: Breast cancer is the most frequently diagnosed malignancy and a leading cause of cancer-related mortality among women worldwide. Although NADPH oxidase 4 (NOX4) has been implicated in various oncogenic processes, its exact function in breast cancer progression, metabolic reprogramming, and immune modulation remains unclear.
Methods: We used murine 4T1 and EO771 breast cancer models to generate NOX4 knockout (KO) cell lines via CRISPR/Cas9. In vitro assays (cell proliferation, colony formation, wound healing, and Seahorse metabolic analyses) and in vivo orthotopic tumor studies assessed the impact of NOX4 loss. Transcriptomic changes were identified through RNA sequencing and gene set enrichment analysis. We performed MYC knockdown in NOX4 KO cells to investigate its mechanistic role. Flow cytometry characterized tumor-infiltrating immune cells. Finally, NOX4-overexpressing cells were tested for survival benefit and response to dual-checkpoint immunotherapy (anti-PD-1/anti-CTLA-4).
Results: NOX4 deletion accelerated tumor growth in vivo and enhanced proliferation, colony formation, and migratory capacity in vitro. Metabolic profiling showed that NOX4 KO cells had elevated glycolysis and fatty acid oxidation, along with increased mitochondrial mass. Transcriptomic and enrichment analyses revealed MYC pathway activation in NOX4 KO cells; suppressing MYC reversed these hyperproliferative and metabolic changes. Immunologically, NOX4 KO reduced CD8+ T cell infiltration and function, partially due to lowered CCL11/CCL5 levels, while PD-L1 expression was upregulated. In contrast, NOX4 overexpression improved survival in mice and synergized with checkpoint blockade, demonstrating a positive effect on anti-tumor immunity.
Discussion: These findings show that NOX4 constrains breast cancer aggressiveness by limiting MYC-driven metabolic adaptations and supporting CD8+ T cell-mediated immunity. Loss of NOX4 promotes a more malignant phenotype and dampens T cell responses, whereas its overexpression prolongs survival and enhances checkpoint inhibitor efficacy. Therapeutically targeting the NOX4-MYC axis and leveraging NOX4's immunomodulatory capacity could offer promising strategies for breast cancer management.

Keywords:  MYC; NOX4; breast cancer; fatty acid oxidation; metabolic reprogramming

DOI:  https://doi.org/10.3389/fimmu.2025.1534936
Nat Metab. 2025 Feb 24.

Mitochondrial superoxide regulates pro-inflammatory macrophages.

DOI: https://doi.org/10.1038/s42255-025-01223-y
Proc Natl Acad Sci U S A. 2025 Mar 04. 122(9): e2425526122

Tandem metabolic reaction-based sensors unlock in vivo metabolomics.

Xuanbing Cheng, Zongqi Li, Jialun Zhu, Jingyu Wang, Ruyi Huang, Lewis W Yu, Shuyu Lin, Sarah Forman, Evelina Gromilina, Sameera Puri, Pritesh Patel, Mohammadreza Bahramian, Jiawei Tan, Hannaneh Hojaiji, David Jelinek, Laurent Voisin, Kristie B Yu, Ao Zhang, Connie Ho, Lei Lei, Hilary A Coller, Elaine Y Hsiao, Beck L Reyes, Joyce H Matsumoto, Daniel C Lu, Chong Liu, Carlos Milla, Ronald W Davis, Sam Emaminejad.

  Mimicking metabolic pathways on electrodes enables in vivo metabolite monitoring for decoding metabolism. Conventional in vivo sensors cannot accommodate underlying complex reactions involving multiple enzymes and cofactors, addressing only a fraction of enzymatic reactions for few metabolites. We devised a single-wall-carbon-nanotube-electrode architecture supporting tandem metabolic pathway-like reactions linkable to oxidoreductase-based electrochemical analysis, making a vast majority of metabolites detectable in vivo. This architecture robustly integrates cofactors, self-mediates reactions at maximum enzyme capacity, and facilitates metabolite intermediation/detection and interference inactivation through multifunctional enzymatic use. Accordingly, we developed sensors targeting 12 metabolites, with 100-fold-enhanced signal-to-noise ratio and days-long stability. Leveraging these sensors, we monitored trace endogenous metabolites in sweat/saliva for noninvasive health monitoring, and a bacterial metabolite in the brain, marking a key milestone for unraveling gut microbiota-brain axis dynamics.

Keywords:  cofactor-assisted enzymatic reactions; in vivo metabolomics; microbiome; personalized medicine; wearable and implantable metabolite sensors

DOI:  https://doi.org/10.1073/pnas.2425526122
Methods Mol Biol. 2025 ;2882 121-137

Sensing of Long-Chain Fatty Acyl-CoA Esters by AMPK.

Eric M Desjardins, Emily A Day, John W Scott, Gregory R Steinberg.

  Fatty acids are utilized to maintain cellular energy/adenine nucleotide balance under times of energetic stress such as during endurance exercise or fasting. It has long been recognized that fatty acids stimulate their own oxidation through a mechanism involving allosteric inhibition of acetyl-CoA carboxylase (ACC) and reductions in malonyl-CoA. We have recently described a parallel pathway by which long-chain fatty acid-CoAs bind to and activate the AMP-activated protein kinase (AMPK) at the allosteric drug and metabolic (ADaM) binding site. Increases in AMPK activity lead to the phosphorylation and inhibition of ACC which is essential for fatty acids to stimulate fatty acid oxidation. Here, we describe the methods to detect fatty acyl-CoA-induced activation of AMPK in cell-free assays, primary mouse hepatocytes, and in the liver of mice. These methodologies will be useful to allow further investigations into the importance of this fatty acid sensing axis in regulating metabolism and provide a framework for future studies investigating whether there may be other natural ligands targeting the ADaM binding site of AMPK.

Keywords:  AMPK; Cell-free assay; Fat oxidation; Fatty acid sensing; Fatty acyl-CoA; Hepatocytes; In vitro; In vivo; Intralipid; Liver extraction; Methods; Palmitate; Phosphorylation

DOI:  https://doi.org/10.1007/978-1-0716-4284-9_6
bioRxiv. 2025 Feb 16. pii: 2025.02.13.637616. [Epub ahead of print]

The MicroMap is a network visualisation resource for microbiome metabolism.

Cyrille C Thinnes, Renee Waschkowitz, Eoghan Courtney, Eoghan Culligan, Katie Fahy, Ruby A M Ferrazza, Ciara Ferris, Angeline Lagali, Rebecca Lane, Colm Maye, Olivia Murphy, David Noone, Saoirse Ryan, Mihaela Bet, Maria C Corr, Hannah Cummins, David Hackett, Ellen Healy, Nina Kulczycka, Niall Lang, Luke Madden, Lynne McHugh, Ivana Pyne, Ciara Varley, Niamh Harkin, Ronan Meade, Grace O'Donnell, Bram Nap, Filippo Martinelli, Almut Heinken, Ines Thiele.

The human microbiome plays a crucial role in metabolism and thereby influences health and disease. Constraint-based reconstruction and analysis (COBRA) has proven an attractive framework to generate mechanism-derived hypotheses along the nutrition-host-microbiome-disease axis within the computational systems biology community. Unlike for human, no large-scale visualisation resource for microbiome metabolism has been available to date. To address this gap, we created the MicroMap, a manually curated microbiome metabolic network visualisation, which captures the metabolic content of over a quarter million microbial genome-scale metabolic reconstructions. The MicroMap contains 5,064 unique reactions and 3,499 unique metabolites, including for 98 drugs. The MicroMap allows users to intuitively explore microbiome metabolism, inspect microbial metabolic capabilities, and visualise computational modelling results. Further, the MicroMap shall serve as an educational tool to make microbiome metabolism accessible to broader audiences beyond computational modellers. For example, we utilised the MicroMap to generate a comprehensive collection of 257,429 visualisations, corresponding to the entire scope of our current microbiome reconstruction resources, to enable users to visually compare and contrast the metabolic capabilities for different microbes. The MicroMap seamlessly integrates with the Virtual Metabolic Human (VMH, www.vmh.life) and the COBRA Toolbox (opencobra.github.io), and is freely accessible at the MicroMap dataverse (https://dataverse.harvard.edu/dataverse/micromap), in addition to all the generated reconstruction visualisations.

DOI: https://doi.org/10.1101/2025.02.13.637616
Methods Mol Biol. 2025 ;2882 81-102

Assays of Different Mechanisms of AMPK Activation, and Use of Cells Expressing Mutant AMPK to Delineate Activation Mechanisms.

Fiona A Ross, D Grahame Hardie.

  Eukaryotic cells not only sense carbon nutrients directly, but also sense them indirectly by monitoring the levels of cellular adenine nucleotides produced by their catabolism. Starvation for a key carbon source may cause increases in ADP:ATP ratios that are amplified by the adenylate kinase reaction (2ADP ↔ ATP + AMP) into even larger increases in AMP:ATP ratios. The major cellular sensor of such changes in nucleotide levels is the AMP-activated protein kinase (AMPK) which, once activated, acts to restore energy balance within cells. Increases in the AMP:ATP ratio result in conformational changes in AMPK that: (1) cause allosteric activation; (2) promote phosphorylation at a critical threonine residue (Thr172) in the kinase domain of AMPK-α subunits by the upstream kinase LKB1; (3) protect against Thr172 dephosphorylation by protein phosphatases. Together, these three mechanisms of activation can cause up to a 1000-fold increase in AMPK activity, and this chapter will describe assays to monitor these different activation mechanisms in cell-free assays. Adenine nucleotides (AMP/ADP/ATP) bind to sites formed by sequence repeats termed CBS motifs in the AMPK-γ subunits. Several pathogenic mutations in these motifs have been identified that either reduce or eliminate the sensitivity of AMPK to changes in AMP and other nucleotides. We also describe the use of cells expressing such mutants to determine whether agents that activate AMPK do so by disturbing adenine nucleotide levels.

Keywords:  AMP-activated protein kinase; AMP-insensitive mutants; AMPK; Dephosphorylation; Kinase assays; Phosphorylation

DOI:  https://doi.org/10.1007/978-1-0716-4284-9_4
Methods Mol Biol. 2025 ;2882 3-14

Measuring Cellular Adenine Nucleotides by Liquid Chromatography-Coupled Mass Spectrometry.

Ashley J Ovens, Dingyi Yu, Toby A Dite, Bruce E Kemp, Jonathan S Oakhill.

  Adenine nucleotides (AXPs, also referred to as adenosines or adenylates) are a group of organic molecules including adenosine 5'- mono-, di-, and tri-phosphate (AMP, ADP, and ATP, respectively) that, combined, resembles an electrochemical storage cell to facilitate cellular energy storage and transfer. ATP, generated from ADP by photosynthesis, anaerobic respiration, and oxidative phosphorylation, powers many energy-requiring processes in the cell through hydrolysis of its terminal (γ) phosphate, whereas ADP is equilibrated with AMP and ATP by the adenylate kinase reaction. AXPs are major signaling molecules that regulate a wide range of anabolic and catabolic enzymes including AMP-activated protein kinase (AMPK), phosphofructokinase, and pyruvate dehydrogenase.Methods to determine concentrations of AXPs from cells and biological samples have historically relied on high-performance liquid chromatography (HPLC)/capillary electrophoresis techniques to measure [ATP] and [ADP]. However, due to its low basal concentrations, these techniques lack sufficient sensitivity to directly measure [AMP], which must be extrapolated using assumptions of adenylate kinase equilibrium that neglect AMP degradation and synthesis pathways. Here, we describe a detailed protocol to accurately measure [AXP] from cells by liquid chromatography-coupled mass spectrometry (LC/MS), applicable to a wide range of fields including our specific interest in AMPK-dependent metabolic regulation.

Keywords:  AMPK; Adenine nucleotides; Energy; Enzyme regulation; Mass spectrometry; Metabolism

DOI:  https://doi.org/10.1007/978-1-0716-4284-9_1