bims-celmim 2025-02-23 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–02–23
twenty-six papers selected by
Marc Segarra Mondejar

Genetic and functional dissection of the glutamate-proline pathway reveals a shortcut for glutamate catabolism in Leishmania.
Exploring the Regulation of Lipid Droplet Catabolism through Lipophagy.
Anaplerosis by medium-chain fatty acids through complex interplay with glucose and glutamine metabolism.
Insights into metabolic changes during epidermal differentiation as revealed by multiphoton microscopy with fluorescence lifetime imaging.
Lon protease 1-mediated metabolic reprogramming promotes the progression of prostate cancer.
Mitochondrial metabolism is rapidly re-activated in mature neutrophils to support stimulation-induced response.
AIF3 splicing variant elicits mitochondrial malfunction via the concurrent dysregulation of electron transport chain and glutathione-redox homeostasis.
The emerging roles of the endoplasmic reticulum in mechanosensing and mechanotransduction.
An organism-level quantitative flux model of energy metabolism in mice.
Hexokinase detachment from mitochondria drives the Warburg effect to support compartmentalized ATP production.
Investigating intestinal epithelium metabolic dysfunction in celiac disease using personalized genome-scale models.
Tissue-specific and spatially dependent metabolic signatures perturbed by injury in skeletally mature male and female mice.
B cell immunometabolism in health and disease.
CDK6 kinase inhibition unmasks metabolic dependencies in BCR::ABL1+ leukemia.
A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity.
A detailed review on the role of miRNAs in mitochondrial-nuclear cross talk during cancer progression.
Enhanced flux potential analysis links changes in enzyme expression to metabolic flux.
NUAKs facilitate mTOR-mediated NSCLC proliferation and metastasis by modulating glucose metabolism and inhibiting p53 activity.
GMRSP encoded by lncRNA H19 regulates metabolic reprogramming and alleviates aortic dissection.
How are mitochondrial nucleoids trafficked?
Visualizing bulk autophagy in vivo by tagging endogenous LC3B.
Lactylation in cancer: metabolic mechanism and therapeutic strategies.
The endoplasmic reticulum luminal Ca2+ regulates cardiac Ca2+ pump function.
Pyruvate kinase M2 modulates mitochondrial dynamics and EMT in alveolar epithelial cells during sepsis-associated pulmonary fibrosis.
A dual-channel fluorescent probe with mitochondria-immobilization: Detecting polarity and viscosity during mitophagy.
RBM43 controls PGC1α translation and a PGC1α-STING signaling axis.

FEBS J. 2025 Feb 17.

Genetic and functional dissection of the glutamate-proline pathway reveals a shortcut for glutamate catabolism in Leishmania.

Gustavo Daniel Campagnaro, Angela Kaysel Cruz.

  Trypanosomatids are early-divergent eukaryotes that have adapted to parasitism. During their life cycles, these parasites switch between a mammalian and an invertebrate host, and the ability to adapt their metabolism to different nutritional sources is instrumental for their success. In the invertebrate host, these protists have access to high amounts of amino acids and efficiently utilise it for energy production. Proline is a particularly efficient energy source for trypanosomes. Glutamate is also efficiently used by Trypanosoma cruzi and can be converted into proline as part of the glutamate-proline pathway prior to its intramitochondrial catabolism. By employing a series of genetic modifications and functional analysis, we show here that Leishmania parasites, the causative agents of leishmaniases, can utilise proline, glutamate and glutamine as energy sources, and although these parasites possess all the genes necessary for the biosynthesis of proline from glutamate, this pathway has, at best, limited function, with at least one of its components (pyrroline-5-carboxylate reductase) assuming divergent functions in different life cycle stages of the parasite. In fact, we show that the catabolism of glutamate is independent of proline biosynthesis and the former is most likely directly imported into the mitochondrion and catabolised to recover the cellular redox metabolism and increase mitochondrial membrane potential. Moreover, our data suggest a relevant role for glutamate dehydrogenase in nutritional stress response in Leishmania. These findings highlight relevant differences in amino acid metabolism between Trypanosoma and Leishmania and suggest a diversification in amino acid metabolic pathways within Trypanosomatidae.

Keywords:  Leishmania; glutamate–proline pathway; mitochondrial metabolism; moonlight activity; proline–glutamate

DOI:  https://doi.org/10.1111/febs.70030
J Vis Exp. 2025 Jan 31.

Exploring the Regulation of Lipid Droplet Catabolism through Lipophagy.

Carolina Lagos, Diego Tapia, Cristina Silva, Jorge Cancino.

Macroautophagy, commonly referred to as autophagy, is a highly conserved cellular process responsible for the degradation of cellular components. This process is particularly prominent under conditions such as fasting, cellular stress, organelle damage, cellular damage, or aging of cellular components. During autophagy, a segment of the cytoplasm is enclosed within double-membrane vesicles known as autophagosomes, which then fuse with lysosomes. Following this fusion, the contents of autophagosomes undergo non-selective bulk degradation facilitated by lysosomes. However, autophagy also exhibits selective functionality, targeting specific organelles, including mitochondria, peroxisomes, lysosomes, nuclei, and lipid droplets (LDs). Lipid droplets are enclosed by a phospholipid monolayer that isolates neutral lipids from the cytoplasm, protecting cells from the harmful effects of excess sterols and free fatty acids (FFAs). Autophagy is implicated in various conditions, including neurodegenerative diseases, metabolic disorders, and cancer. Specifically, lipophagy -- the autophagy-dependent degradation of lipid droplets -- plays a crucial role in regulating intracellular FFA levels across different metabolic states. This regulation supports essential processes such as membrane synthesis, signaling molecule formation, and energy balance. Consequently, impaired lipophagy increases cellular vulnerability to death stimuli and contributes to the development of diseases such as cancer. Despite its significance, the precise mechanisms governing lipid droplet metabolism regulated by lipophagy in cancer cells remain poorly understood. This article aims to describe confocal imaging acquisition and quantitative imaging analysis protocols that enable the investigation of lipophagy associated with metabolic changes in cancer cells. The results obtained through these protocols may shed light on the intricate interplay between autophagy, lipid metabolism, and cancer progression. By elucidating these mechanisms, novel therapeutic targets may emerge for combating cancer and other metabolic-related diseases.

DOI: https://doi.org/10.3791/67287
J Biol Chem. 2025 Feb 13. pii: S0021-9258(25)00155-3. [Epub ahead of print] 108307

Anaplerosis by medium-chain fatty acids through complex interplay with glucose and glutamine metabolism.

Hannah M German, Jolita Ciapaite, Nanda M Verhoeven-Duif, Judith J M Jans.

  The constant replenishment of tricarboxylic acid (TCA) cycle intermediates, or anaplerosis, is crucial to ensure optimal TCA cycle activity in times of high biosynthetic demand. In inborn metabolic diseases, anaplerosis is often affected, leading to impaired TCA cycle flux and ATP production. In these cases, anaplerotic compounds can be a therapy option. Triheptanoin, a triglyceride containing three heptanoate chains, is thought to be anaplerotic through production of propionyl- and acetyl-CoA. However, the precise mechanism underlying its anaplerotic action remains poorly understood. In this study, we performed a comprehensive in vitro analysis of heptanoate metabolism and compared it to that of octanoate, an even-chain fatty acid which only provides acetyl-CoA. Using stable isotope tracing, we demonstrate that both heptanoate and octanoate contribute carbon to the TCA cycle in HEK293T cells, confirming direct anaplerosis. Furthermore, by using labeled glucose and glutamine, we show that heptanoate and octanoate decrease the contribution of glucose-derived carbon and increase the influx of glutamine-derived carbon into the TCA cycle. Our findings also point towards a change in redox homeostasis, indicated by an increased NAD+/NADH ratio, accompanied by a decreased lactate/pyruvate ratio and increased de novo serine biosynthesis. Taken together, these results highlight the broad metabolic effects of heptanoate and octanoate supplementation, suggesting that therapeutic efficacy may strongly depend on specific disease pathophysiology. Furthermore, they underline the need for careful selection of fatty acid compound and concentration to optimize anaplerotic action.

Keywords:  Anaplerosis; fatty acids; isotopic tracer; mass spectrometry (MS); metabolic disease; metabolomics; redox regulation

DOI:  https://doi.org/10.1016/j.jbc.2025.108307
Sci Rep. 2025 Feb 21. 15(1): 6377

Insights into metabolic changes during epidermal differentiation as revealed by multiphoton microscopy with fluorescence lifetime imaging.

Monika Malak, Chen Qian, Jeemol James, Syam Nair, Julie Grantham, Marica B Ericson.

  Rapid developments in the field of organotypic cultures have generated a growing need for effective and non-invasive methods for quality control during tissue development. In this study, we correlate metabolic changes with epidermal differentiation and demonstrate that multiphoton microscopy with fluorescence lifetime imaging (MPM-FLIM) can be applied to monitor epidermal differentiation of keratinocytes with respect to proliferative and differentiated states. In a 2D keratinocyte tissue culture model, increased expression of differentiation markers keratin-1 and keratin-10 was induced with calcium supplementation. An accompanying shift from glycolysis to mitochondrial respiration was detected in metabolic flux assays. Analysis of MPM-FLIM images acquired at 750 nm and 900 nm excitation revealed a decreased relative fraction of intracellular NADH and FAD after high calcium treatment, consistent with increased oxidative phosphorylation. Epidermal differentiation could be monitored over a 96 h period. Discrimination analysis based on k-means clustering generated clusters that correlated well with the duration of high Ca2+ treatment, suggesting that MPM-FLIM can provide useful parameters for monitoring keratinocyte differentiation.

Keywords:  Epidermal differentiation; Fluorescence lifetime imaging; Label-free imaging; Metabolism; Multiphoton microscopy

DOI:  https://doi.org/10.1038/s41598-025-90101-4
Cell Death Dis. 2025 Feb 19. 16(1): 116

Lon protease 1-mediated metabolic reprogramming promotes the progression of prostate cancer.

Mengfei Yao, Xingming Zhang, Tianqi Wu, Tao Feng, Xiaojie Bian, Mierxiati Abudurexiti, Wenfeng Wang, Guohai Shi, Gong-Hong Wei, Qin Zhang, Xiangyun Li, Gang Feng, Leilei Du, Jianhua Wang.

Lon protease 1 (LONP1) is an ATP-dependent protease located in the mitochondrial matrix and plays a crucial role in regulating mitochondrial proteostasis, metabolism, and cellular stress responses et al. Aberrant LONP1 expression has been found in the progression of various tumors; however, the role and molecular mechanisms of LONP1 in prostate cancer (PCa) remain poorly understood. Here we show that overexpression of LONP1 is closely related to adverse clinic pathological features and poor prognosis in PCa patients. Mechanistically, the findings reveal that LONP1 is implicated in modulating the metabolic switch from oxidative phosphorylation (OXPHOS) to aerobic glycolysis, thereby promoting tumor proliferation, invasion, and metastasis both in vitro and in vivo. Meanwhile, we prove that LONP1 as a protease directly targets mitochondrial pyruvate carrier 1 (MPC1), a key metabolic protein in the process of glycolysis, and enhances its degradation, which in turn suppresses tricarboxylic acid (TCA) cycle and ultimately promotes the progression of PCa. Furthermore, using PCa in cancer-prone mice homozygous for a prostate-targeted conditional Pten knockout and Lonp1 knockin, we integrate transcriptomic and proteomic analyses of prostate tumors, upon which reveals that Lonp1 overexpression results in a significant downregulation of NADH: ubiquinone oxidoreductase activity, consequently impeding the electron transfer process and mitochondrial ATP synthesis, associated with metastasis of PCa. Collectively, our results highlight that metabolic reprogramming induced by LONP1 in PCa is closely coupled with disease progression, suggesting that targeting the LONP1-mediated cascade in the mitochondrial may provide therapeutic potential for PCa disease.

DOI: https://doi.org/10.1038/s41419-025-07449-8
bioRxiv. 2025 Feb 08. pii: 2025.02.03.636312. [Epub ahead of print]

Mitochondrial metabolism is rapidly re-activated in mature neutrophils to support stimulation-induced response.

Jorgo Lika, James A Votava, Rupsa Datta, Aleksandr M Kralovec, Frances M Smith, Anna Huttenlocher, Melissa C Skala, Jing Fan.

Neutrophils are highly abundant innate immune cells that are constantly produced from myeloid progenitors in the bone marrow. Differentiated neutrophils can perform an arsenal of effector functions critical for host defense. This study aims to quantitatively understand neutrophil mitochondrial metabolism throughout differentiation and activation, and to elucidate the impact of mitochondrial metabolism on neutrophil functions. To study metabolic remodeling throughout neutrophil differentiation, murine ER-Hoxb8 myeloid progenitor-derived neutrophils and human induced pluripotent stem cell-derived neutrophils were assessed as models. To study the metabolic remodeling upon neutrophil activation, differentiated ER-Hoxb8 neutrophils and primary human neutrophils were activated with various stimuli, including ionomycin, MSU crystals, and PMA. Characterization of cellular metabolism by isotopic tracing, extracellular flux analysis, metabolomics, and fluorescence-lifetime imaging microscopy revealed dynamic changes in mitochondrial metabolism. As neutrophils mature, mitochondrial metabolism decreases drastically, energy production is fully offloaded from oxidative phosphorylation, and glucose oxidation through TCA cycle is substantially reduced. Nonetheless, mature neutrophils retain the capacity for mitochondrial metabolism. Upon stimulation with certain stimuli, TCA cycle is rapidly activated. Mitochondrial pyruvate carrier inhibitors reduce this re-activation of the TCA cycle and inhibit the release of neutrophil extracellular traps. Mitochondrial metabolism also impacts neutrophil redox status, migration, and apoptosis without significantly changing overall bioenergetics. Together, these results demonstrate that mitochondrial metabolism is dynamically remodeled and plays a significant role in neutrophil function and fate. Furthermore, these findings point to the therapeutic potential of mitochondrial pyruvate carrier inhibitors in a range of conditions where dysregulated neutrophil response drives inflammation and contributes to pathology.

DOI: https://doi.org/10.1101/2025.02.03.636312
Nat Commun. 2025 Feb 20. 16(1): 1804

AIF3 splicing variant elicits mitochondrial malfunction via the concurrent dysregulation of electron transport chain and glutathione-redox homeostasis.

Mi Zhou, Shuiqiao Liu, Yanan Wang, Bo Zhang, Ming Zhu, Jennifer E Wang, Veena Rajaram, Yisheng Fang, Weibo Luo, Yingfei Wang.

Genetic mutations in apoptosis-inducing factor (AIF) have a strong association with mitochondrial disorders; however, little is known about the aberrant splicing variants in affected patients and how these variants contribute to mitochondrial dysfunction and brain development defects. We identified pathologic AIF3/AIF3-like splicing variants in postmortem brain tissues of pediatric individuals with mitochondrial disorders. Mutations in AIFM1 exon-2/3 increase splicing risks. AIF3-splicing disrupts mitochondrial complexes, membrane potential, and respiration, causing brain development defects. Mechanistically, AIF is a mammalian NAD(P)H dehydrogenase and possesses glutathione reductase activity controlling respiratory chain functions and glutathione regeneration. Conversely, AIF3, lacking these activities, disassembles mitochondrial complexes, increases ROS generation, and simultaneously hinders antioxidant defense. Expression of NADH dehydrogenase NDI1 restores mitochondrial functions partially and protects neurons in AIF3-splicing mice. Our findings unveil an underrated role of AIF as a mammalian mitochondrial complex-I alternative NAD(P)H dehydrogenase and provide insights into pathologic AIF-variants in mitochondrial disorders and brain development.

DOI: https://doi.org/10.1038/s41467-025-57081-5
J Cell Sci. 2025 Feb 15. pii: JCS263503. [Epub ahead of print]138(4):

The emerging roles of the endoplasmic reticulum in mechanosensing and mechanotransduction.

Jonathan Townson, Cinzia Progida.

  Cells are continuously subjected to physical and chemical cues from the extracellular environment, and sense and respond to mechanical cues via mechanosensation and mechanotransduction. Although the role of the cytoskeleton in these processes is well known, the contribution of intracellular membranes has been long neglected. Recently, it has become evident that various organelles play active roles in both mechanosensing and mechanotransduction. In this Review, we focus on mechanosensitive roles of the endoplasmic reticulum (ER), the functions of which are crucial for maintaining cell homeostasis. We discuss the effects of mechanical stimuli on interactions between the ER, the cytoskeleton and other organelles; the role of the ER in intracellular Ca2+ signalling via mechanosensitive channels; and how the unfolded protein response and lipid homeostasis contribute to mechanosensing. The expansive structure of the ER positions it as a key intracellular communication hub, and we additionally explore how this may be leveraged to transduce mechanical signals around the cell. By synthesising current knowledge, we aim to shed light on the emerging roles of the ER in cellular mechanosensing and mechanotransduction.

Keywords:  Endoplasmic reticulum; Mechanosensing; Mechanotransduction; Membrane contact sites

DOI:  https://doi.org/10.1242/jcs.263503
Cell Metab. 2025 Feb 13. pii: S1550-4131(25)00008-7. [Epub ahead of print]

An organism-level quantitative flux model of energy metabolism in mice.

Bo Yuan, Will Doxsey, Özlem Tok, Young-Yon Kwon, Yanshan Liang, Karen E Inouye, Gökhan S Hotamışlıgil, Sheng Hui.

  Mammalian tissues feed on nutrients in the blood circulation. At the organism level, mammalian energy metabolism is comprised of the oxidation, storage, interconversion, and release of circulating nutrients. Here, by integrating isotope tracer infusion, mass spectrometry, and isotope gas analyzer measurement, we developed a framework to systematically quantify fluxes through these metabolic processes for 10 major circulating energy nutrients in mice, resulting in an organism-level quantitative flux model of energy metabolism. This model revealed in wild-type mice that circulating nutrients have metabolic cycling fluxes dominant to their oxidation fluxes, with distinct partitions between cycling and oxidation for individual circulating nutrients. Applications of this framework in obese mouse models showed extensive elevation of metabolic cycling fluxes in ob/ob mice but not in diet-induced obese mice on a per-animal or per-lean mass basis. Our framework is a valuable tool to reveal new features of energy metabolism in physiological and disease conditions.

Keywords:  energy metabolism; futile cycle; high-fat diet; isotope tracing; metabolic flux analysis; ob/ob; obesity

DOI:  https://doi.org/10.1016/j.cmet.2025.01.008
bioRxiv. 2025 Feb 08. pii: 2025.02.07.637120. [Epub ahead of print]

Hexokinase detachment from mitochondria drives the Warburg effect to support compartmentalized ATP production.

Kimberly S Huggler, Carlos A Mellado Fritz, Kyle M Flickinger, Gavin R Chang, Meghan F McGuire, Jason R Cantor.

Hexokinase (HK) catalyzes the synthesis of glucose-6-phosphate, marking the first committed step of glucose metabolism. Most cancer cells express two homologous isoforms (HK1 and HK2) that can each bind to the outer mitochondrial membrane (OMM). CRISPR screens across hundreds of cancer cell lines indicate that both are dispensable for cell growth in traditional culture media. By contrast, HK2 deletion impairs cell growth in Human Plasma-Like Medium (HPLM). Here, we find that HK2 is required to maintain sufficient cytosolic (OMM-detached) HK activity under conditions that enhance HK1 binding to the OMM. Notably, OMM-detached rather than OMM-docked HK promotes "aerobic glycolysis" (Warburg effect), an enigmatic phenotype displayed by most proliferating cells. We show that several proposed theories for this phenotype cannot explain the HK2 dependence and instead find that HK2 deletion severely impairs glycolytic ATP production with little impact on total ATP yield for cells in HPLM. Our results reveal a basis for conditional HK2 essentiality and suggest that demand for compartmentalized ATP synthesis underlies the Warburg effect.

DOI: https://doi.org/10.1101/2025.02.07.637120
BMC Med. 2025 Feb 21. 23(1): 95

Investigating intestinal epithelium metabolic dysfunction in celiac disease using personalized genome-scale models.

Chloe V McCreery, Drew Alessi, Katarina Mollo, Alessio Fasano, Ali R Zomorrodi.

   BACKGROUND: Celiac disease (CeD) is an autoimmune condition characterized by an aberrant immune response triggered by the ingestion of gluten, which damages epithelial cells lining the small intestine. Small intestinal epithelial cells (sIECs) play key roles in the enzymatic digestion and absorption of nutrients, maintaining gut barrier integrity, and regulating immune response. Chronic inflammation and tissue damage associated with CeD disrupt the intricate network of metabolic processes in sIECs that support these functions, impairing their ability to perform their essential roles. However, the specific disrupted metabolic processes underlying sIECs dysfunction in CeD remain largely undefined.
METHODS: To address this knowledge gap, personalized, sex-specific genome-scale models of sIECs metabolism were constructed using transcriptional data from intestinal biopsies of 42 subjects with active CeD, CeD in remission (on a gluten-free diet), and non-CeD controls. These models were computationally simulated under relevant dietary conditions for each group of subjects to assess the activity of several metabolic tasks essential for sIECs function and to profile metabolite secretion into the bloodstream and intestinal lumen.
RESULTS: Significant alterations in the activity of 28 essential metabolic tasks were observed in active CeD and remission CeD, impacting critical processes integral to sIECs function such as oxidative stress regulation, nucleotide synthesis and DNA repair, energy production, and polyamine and amino acid metabolism. Additionally, altered secretion profiles of several metabolites, encompassing amino acids, vitamins, polyamines, lipids, and fatty acids, into the bloodstream were detected in active CeD and remission CeD patients. These findings were partially supported by comparisons with independent external datasets and further corroborated through extensive review of existing literature. Furthermore, a drug target analysis was performed, identifying 22 FDA-approved drugs that target genes encoding impaired sIECs metabolic functions in CeD, potentially helping to restore their normal activity.
CONCLUSIONS: This study unveils new insights into the metabolic reprogramming of sIECs in CeD, highlighting specific dysregulated metabolic processes that compromise cellular functions essential for gut health. These findings offer a foundation for developing therapeutic interventions targeting impaired metabolic processes in CeD.

Keywords:  Celiac disease; Genome-scale modeling; Metabolism; Small intestinal epithelial cells

DOI:  https://doi.org/10.1186/s12916-025-03854-0
bioRxiv. 2025 Feb 07. pii: 2024.09.30.615873. [Epub ahead of print]

Tissue-specific and spatially dependent metabolic signatures perturbed by injury in skeletally mature male and female mice.

Hope D Welhaven, Avery H Welfley, Priyanka P Brahmachary, Donald F Smith, Brian Bothner, Ronald K June.

Joint injury is a risk factor for post-traumatic osteoarthritis. However, metabolic and microarchitectural changes within the joint post-injury in both sexes remain unexplored. This study identified tissue-specific and spatially-dependent metabolic signatures in male and female mice using matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) and LC-MS metabolomics. Male and female C57Bl/6J mice were subjected to non-invasive joint injury. Eight days post-injury, serum, synovial fluid, and whole joints were collected for metabolomics. Analyses compared between injured, contralateral, and naïve mice, revealing local and systemic responses. Data indicate sex influences metabolic profiles across all tissues, particularly amino acid, purine, and pyrimidine metabolism. MALDI-MSI generated 2D ion images of bone, the joint interface, and bone marrow, highlighting increased lipid species in injured limbs, suggesting physiological changes across injured joints at metabolic and spatial levels. Together, these findings reveal significant metabolic changes after injury, with notable sex differences.
Significance statement: Osteoarthritis, the leading cause of disability worldwide, disproportionately affects females with sex being one of the strongest predictors of disease. This disparity is partly driven by sex-specific differences in injury susceptibility, increasing the likelihood of traumatic injury to the anterior cruciate ligament (ACL), other ligaments, and menisci. Using a non-invasive injury model, we demonstrate that injury perturbs the local joint environment and has systemic effects in a sex-specific manner. Furthermore, by leveraging matrix-assisted laser desorption ionization-mass spectrometry imaging of the joint, we provide new insight into the composition of osteochondral tissue at the metabolite level. These sexually dimorphic metabolic responses to joint injury advance current understanding of the complex sexual dimorphism in OA pathogenesis providing a foundation for targeted therapeutic strategies and improved patient outcomes for female patients.

DOI: https://doi.org/10.1101/2024.09.30.615873
Nat Immunol. 2025 Feb 21.

B cell immunometabolism in health and disease.

Eleonora Martinis, Silvia Tonon, Alessandra Colamatteo, Antonio La Cava, Giuseppe Matarese, Carlo Ennio Michele Pucillo.

B cells have crucial roles in the initiation and progression of many pathological conditions, and several therapeutic strategies have targeted the function of these cells. The advent of immunometabolism has provided compelling evidence that the metabolic reprogramming of immune cells can dramatically alter physiopathological immune activities. A better knowledge of the metabolic profiles of B cells can provide valuable means for developing therapies tuning defined cell pathways. Here we review the cellular and molecular mechanisms by which immunometabolism controls the physiology and pathophysiology of B cells and discuss the experimental evidence linking B cell metabolism to health, autoimmunity, and cancer. Considering that several metabolic pathways in B cells are involved differently, or even in opposite ways, in health and disease, we discuss how targeted modulation of B cell immunometabolism could be exploited mechanistically to rebalance abnormal B cell functions that have become altered in disease states.

DOI: https://doi.org/10.1038/s41590-025-02102-0
Cell Death Dis. 2025 Feb 18. 16(1): 107

CDK6 kinase inhibition unmasks metabolic dependencies in BCR::ABL1+ leukemia.

Lisa Scheiblecker, Thorsten Klampfl, Eszter Doma, Sofie Nebenfuehr, Omar Torres-Quesada, Sophie Strich, Gerwin Heller, Daniela Werdenich, Waltraud Tschulenk, Markus Zojer, Florian Bellutti, Alessia Schirripa, Sabine Zöchbauer-Müller, Peter Valent, Ingrid Walter, Eduard Stefan, Veronika Sexl, Karoline Kollmann.

Metabolic reprogramming and cell cycle deregulation are hallmarks of cancer cells. The cell cycle kinase CDK6 has recently been implicated in a wide range of hematopoietic malignancies. We here investigate the role of CDK6 in the regulation of cellular metabolism in BCR::ABL1+ leukemic cells. Our study, using gene expression data and ChIP-Seq analysis, highlights the contribution of CDK6 kinase activity in the regulation of oxidative phosphorylation. Our findings imply a competition for promoter interaction of CDK6 with the master regulator of mitochondrial respiration, NRF-1. In line, cells lacking kinase active CDK6 display altered mitochondria morphology with a defective electron transport chain. The enhanced cytoplasm/mitochondria ATP ratio paralleled by high pyruvate and lactate levels indicate a metabolic switch to glycolysis. Accordingly, combinatorial treatment of leukemic cells including imatinib resistant cells with the CDK4/6 inhibitor palbociclib and the glycolysis inhibitor 2-deoxyglucose (2-DG) enhanced apoptosis, while blocking cell proliferation in leukemic cells. These data may open a new therapeutic avenue for hematologic malignancies with high CDK6 expression by exploiting metabolic vulnerabilities unmasked by blocking CDK6 kinase activity that might even be able to overcome imatinib resistance.

DOI: https://doi.org/10.1038/s41419-025-07434-1
bioRxiv. 2025 Feb 08. pii: 2025.02.03.635951. [Epub ahead of print]

A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity.

Anna S Monzel, Jack Devine, Darshana Kapri, Jose Antonio Enriquez, Caroline Trumpff, Martin Picard.

Mitochondria are a diverse family of organelles that specialize to accomplish complimentary functions 1-3 . All mitochondria share general features, but not all mitochondria are created equal 4 .Here we develop a quantitative pipeline to define the degree of molecular specialization among different mitochondrial phenotypes - or mitotypes . By distilling hundreds of validated mitochondrial genes/proteins into 149 biologically interpretable MitoPathway scores (MitoCarta 3.0 5 ) the simple mitotyping pipeline allows investigators to quantify and interpret mitochondrial diversity and plasticity from transcriptomics or proteomics data across a variety of natural and experimental contexts. We show that mouse and human multi-organ mitotypes segregate along two main axes of mitochondrial specialization, contrasting anabolic (liver) and catabolic (brain) tissues. In cultured primary human fibroblasts exhibiting robust time-dependent and treatment-induced metabolic plasticity 6-8 , we demonstrate how the mitotype of a given cell type recalibrates i) over time in parallel with hallmarks of aging, and ii) in response to genetic, pharmacological, and metabolic perturbations. Investigators can now use MitotypeExplorer.org and the associated code to visualize, quantify and interpret the multivariate space of mitochondrial biology.

DOI: https://doi.org/10.1101/2025.02.03.635951
Biochim Biophys Acta Mol Basis Dis. 2025 Feb 18. pii: S0925-4439(25)00076-6. [Epub ahead of print] 167731

A detailed review on the role of miRNAs in mitochondrial-nuclear cross talk during cancer progression.

Amoolya Kandettu, Raviprasad Kuthethur, Sanjiban Chakrabarty.

  MicroRNAs (miRNAs) are a class of small non-coding RNAs that are associated with biochemical pathways through the post-transcriptional regulation of gene expression in different cell types. Based on their expression pattern and function, miRNAs can have oncogenic and tumor suppressor activities in different cancer cells. Altered mitochondrial function and bioenergetics are known hallmarks of cancer cells. Mitochondria play a central role in metabolic reprogramming during cancer progression. Cancer cells exploit mitochondrial function for cell proliferation, invasion, migration and metastasis. Genetic and epigenetic changes in nuclear genome contribute to altered mitochondrial function and metabolic reprogramming in cancer cells. Recent studies have identified the role of miRNAs as major facilitators of anterograde and retrograde signaling between the nucleus and mitochondria in cancer cells. Detailed analysis of the miRNA-mediated regulation of mitochondrial function in cancer cells may provide new avenues for the diagnosis, prognosis, and therapeutic management of the disease. Our review aims to discuss the role of miRNAs in nuclear-mitochondria crosstalk regulating mitochondrial functions in different cancer types. We further discussed the potential application of mitochondrial miRNAs (mitomiRs) targeting mitochondrial biogenesis and metabolism in developing novel cancer therapy.

Keywords:  Cancer; Cancer therapeutics; MicroRNA; MitomiRs; Nuclear-mitochondria communication

DOI:  https://doi.org/10.1016/j.bbadis.2025.167731
Mol Syst Biol. 2025 Feb 17.

Enhanced flux potential analysis links changes in enzyme expression to metabolic flux.

Xuhang Li, Albertha J M Walhout, L Safak Yilmaz.

  Algorithms that constrain metabolic network models with enzyme levels to predict metabolic activity assume that changes in enzyme levels are indicative of flux variations. However, metabolic flux can also be regulated by other mechanisms such as allostery and mass action. To systematically explore the relationship between fluctuations in enzyme expression and flux, we combine available yeast proteomic and fluxomic data to reveal that flux changes can be best predicted from changes in enzyme levels of pathways, rather than the whole network or only cognate reactions. We implement this principle in an 'enhanced flux potential analysis' (eFPA) algorithm that integrates enzyme expression data with metabolic network architecture to predict relative flux levels of reactions including those regulated by other mechanisms. Applied to human data, eFPA consistently predicts tissue metabolic function using either proteomic or transcriptomic data. Additionally, eFPA efficiently handles data sparsity and noisiness, generating robust flux predictions with single-cell gene expression data. Our approach outperforms alternatives by striking an optimal balance, evaluating enzyme expression at pathway level, rather than either single-reaction or whole-network levels.

Keywords:  Enzyme Expression; Flux Potential Analysis; Metabolic Flux; Metabolic Network Model; Single-cell Data

DOI:  https://doi.org/10.1038/s44320-025-00090-9
Biochim Biophys Acta Mol Cell Res. 2025 Feb 17. pii: S0167-4889(25)00027-8. [Epub ahead of print]1872(3): 119922

NUAKs facilitate mTOR-mediated NSCLC proliferation and metastasis by modulating glucose metabolism and inhibiting p53 activity.

Jaithanya Yesupogu Moorthy Babu, Ravi Manoharan.

  Non-small cell lung cancer (NSCLC) cells frequently exhibit aberrant glucose metabolism, characterized by elevated aerobic glycolysis, pentose phosphate pathway (PPP), and reduced oxidative phosphorylation. However, the specific mechanisms underlying the abnormal activation of glucose metabolism and its contribution to NSCLC tumorigenesis remain incompletely elucidated. In this study, we observed that both NUAK1 and NUAK2 mRNA expression levels were significantly elevated in NSCLC tissues compared to non-tumor tissues, and that high NUAK1/2 expression correlated with poor prognosis in NSCLC patients. Furthermore, NUAK1/2 promotes aerobic glycolysis and PPP in NSCLC cells and stimulates cellular proliferation and migration. Depletion or inhibition of NUAK1/2 results in decreased aerobic glycolysis, PPP activity, cell proliferation, and migration, leading to increased apoptosis of NSCLC cells. Mechanistically, NUAK1/2 enhances mTOR activity by suppressing the activity of p53, thereby promoting NSCLC cell growth and metastasis through the promotion of aerobic glycolysis and PPP. Our findings suggest that NUAK1/2 plays a crucial role in glucose reprogramming and tumorigenesis in NSCLC cells, indicating that targeting NUAK1/2 may represent a potential therapeutic strategy for NSCLC metabolism.

Keywords:  Glucose reprogramming; NSCLC; NUAK1; NUAK2; mTOR; p53

DOI:  https://doi.org/10.1016/j.bbamcr.2025.119922
Nat Commun. 2025 Feb 18. 16(1): 1719

GMRSP encoded by lncRNA H19 regulates metabolic reprogramming and alleviates aortic dissection.

Jizhong Wang, Jitao Liu, Fan Yang, Yinghao Sun, Jiaohua Chen, Jie Liu, Tucheng Sun, Ruixin Fan, Fang Pei, Songyuan Luo, Jie Li, Jianfang Luo.

Metabolic disturbances are hallmarks of vascular smooth muscle cell (VSMC) phenotypic transitions, which play a critical role in the pathogenesis of aortic dissection (AD). In this study, we identify and characterize glucose metabolism regulatory protein (GMRSP), a protein encoded by lncRNA H19. Using VSMC-specific GMRSP induction in knock-in mice, adeno-associated virus-mediated GMRSP overexpression, and exosomal GMRSP delivery, we demonstrate significant improvements in AD and mitochondrial dysfunction. Mechanistically, GMRSP inhibits heterogeneous nuclear ribonucleoprotein (hnRNP) A2B1-mediated alternative splicing of pyruvate kinase M (PKM) pre-mRNA, leading to reduced PKM2 production and glycolysis. This reprogramming preserves the contractile phenotype of VSMCs and prevents their transition to a proliferative state. Importantly, pharmacological activation of PKM2 via TEPP-46 abrogates the protective effects of GMRSP in vivo and in vitro. Clinical relevance is shown by elevated plasma PKM2 levels in AD patients, which correlate with poor prognosis. Collectively, these findings indicate GMRSP as a key regulator of VSMC metabolism and phenotypic stability, highlighting its potential as a therapeutic target for AD.

DOI: https://doi.org/10.1038/s41467-025-57011-5
Trends Cell Biol. 2025 Feb 20. pii: S0962-8924(24)00272-1. [Epub ahead of print]

How are mitochondrial nucleoids trafficked?

Josefa Macuada, Isidora Molina-Riquelme, Verónica Eisner.

  Mitochondria harbor their own DNA (mtDNA), which codifies essential proteins of the oxidative phosphorylation (OXPHOS) system and locally feeds them to their surrounding inner mitochondrial membrane (IMM), according to the 'sphere of influence' theory. mtDNA is compacted into nucleoids, which are tethered to the IMM and distributed throughout the mitochondrial network. Some nucleoid subpopulations present distinct intramitochondrial positioning during fission and their correct positioning is associated with mtDNA segregation and selective degradation. This opinion article focuses on different mechanisms that could control nucleoid positioning through intramitochondrial trafficking, either by cristae reshaping or by intercompartment-driven mechanisms involving the mitochondrial membranes and extramitochondrial elements. Understanding nucleoid trafficking promises insights into mitochondrial dysfunction in pathologies with mtDNA distribution and segregation issues.

Keywords:  cristae reshaping; mitochondrial nucleoid; mtDNA inheritance; nucleoid dynamics; sphere of influence

DOI:  https://doi.org/10.1016/j.tcb.2024.12.007
Autophagy. 2025 Feb 14. 1-17

Visualizing bulk autophagy in vivo by tagging endogenous LC3B.

Xiukui Gao, Yue Xiong, Hangbin Ma, Hao Zhou, Wei Liu, Qiming Sun.

  Macroautophagy/autophagy plays a crucial role in maintaining cellular and organismal health, making the measurement of autophagy flux in vivo essential for its study. Current tools often depend on the overexpression of autophagy probes. In this study, we developed a knock-in mouse model, termed tfLC3-KI, by inserting a tandem fluorescent tag coding sequence into the native Map1lc3b gene locus. We found that tfLC3-KI mice exhibit optimal expression of mRFP-eGFP-LC3B, allowing for convenient measurement of autophagic structures and flux at single-cell resolution, both in vivo and in primary cell cultures. Additionally, we compared autophagy in neurons and glial cells across various brain regions between tfLC3-KI mice and CAG-tfLC3 mice, the latter overexpressing the probe under the strong CMV promoter. Finally, we used tfLC3-KI mice to map the spatial and temporal dynamics of basal autophagy activity in the reproductive system. Our findings highlight the value of the tfLC3-KI mouse model for investigating autophagy flux in vivo and demonstrate the feasibility of tagging endogenous proteins to visualize autophagic structures and flux in both bulk and selective autophagy research in vivo.Abbreviation: BafA1: bafilomycin A1; CQ: chloroquine; EBSS: Earle's balanced salt solution; Es: elongating spermatids; HPF: hippocampalformation; HY: hypothalamus; LCs: leydig cells; OLF: olfactory areas; PepA: pepstatin A; Rs: round spermatids; SCs: sertoli cells; Spc: spermatocytes; Spg: spermatogonia; tfLC3: tandem fluorescently tagged mRFP-eGFP-LC3; TH: thalamus.

Keywords:  Autophagy flux; endogenous LC3B; in vivo; knock-in; tandem fluorescence protein

DOI:  https://doi.org/10.1080/15548627.2025.2457910
Cell Death Discov. 2025 Feb 20. 11(1): 68

Lactylation in cancer: metabolic mechanism and therapeutic strategies.

Ying Sui, Ziyang Shen, Zhenling Wang, Jifeng Feng, Guoren Zhou.

Recent progress in cancer metabolism research has identified lactylation as a critical post-translational modification influencing tumor development and progression. The process relies on lactate accumulation and the activation of lactate-sensitive acyltransferases. Beyond its role in epigenetic regulation, lactylation has emerged as a significant factor in tumor metabolism and evolution, offering fresh opportunities for developing targeted therapies that transcend traditional approaches. This review explores the growing importance of lactylation in cancer biology and highlights its potential for advancing diagnostic tools and therapeutic strategies.

DOI: https://doi.org/10.1038/s41420-025-02349-4
PNAS Nexus. 2025 Feb;4(2): pgaf045

The endoplasmic reticulum luminal Ca2+ regulates cardiac Ca2+ pump function.

Elisa Bovo, Roman Nikolaienko, Daniel Kahn, L Michel Espinoza-Fonseca, Aleksey V Zima.

  The type 2a sarcoplasmic/endoplasmic reticulum Ca2+-ATPase (SERCA2a) plays a central role in Ca2+ signaling of cardiomyocytes. The speed at which SERCA2a pumps Ca2+ from the cytosol into the sarcoplasmic reticulum (SR) determines the diastolic relaxation rate. SERCA2a activity also sets SR Ca2+ load, which determines the amplitude of SR Ca2+ release and the systolic contraction strength. While SERCA2a controls the SR luminal [Ca2+] ([Ca2+]SR), less is known about how dynamic changes in [Ca2+]SR affect SERCA2a function. By measuring the endoplasmic reticulum [Ca2+] ([Ca2+]ER) with the Ca2+ sensor R-CEPIA1er, we characterized the function of recombinant human and native mouse SERCA2a. We found that despite low endoplasmic reticulum (ER) Ca2+ gradient, SERCA2a-mediated Ca2+ transport was significantly slower at low [Ca2+]ER than at intermediate [Ca2+]ER. It appears that certain [Ca2+]ER is required for optimal SERCA2a Ca2+ transport. We tested whether negatively charged amino acids within the luminal loop between transmembrane helices M7 and M8 contribute to SERCA2a regulation by [Ca2+]ER. We found that the triple mutation E877L/D878L/E883L in the M7-M8 loop reduces SERCA2a Ca2+ transport particularly at intermediate [Ca2+]ER. Destabilizing the M7-M8 loop by breaking a disulfide bond between cysteines 875 and 887 abolished ER Ca2+ transport. Complementary molecular dynamics simulations showed that the triple mutant E877L/D878L/E883L stabilizes a Ca2+-bound E2 state of the pump, slowing down release of Ca2+ from the transport sites into the ER compared with the wild-type SERCA2a. These results revealed, for the first time, that SERCA2a Ca2+ transport is regulated by the luminal Ca2+ by interacting with the M7-M8 loop.

Keywords:  calcium ATPase; calcium pump; endoplasmic reticulum; fluorescent microscopy; intracellular calcium signaling

DOI:  https://doi.org/10.1093/pnasnexus/pgaf045
J Transl Med. 2025 Feb 19. 23(1): 205

Pyruvate kinase M2 modulates mitochondrial dynamics and EMT in alveolar epithelial cells during sepsis-associated pulmonary fibrosis.

Jinhua Feng, Xi Huang, Yawen Peng, Wenyu Yang, Xinyi Yang, Ri Tang, Qiaoyi Xu, Yuan Gao, Zhengyu He, Shunpeng Xing, Shuya Mei.

   BACKGROUND: Pulmonary fibrosis (PF) severely impacts both the survival and quality of life of patients with acute respiratory distress syndrome (ARDS) and remains a leading cause of late-stage ARDS-related mortality. The role of epithelial-mesenchymal transition (EMT) in alveolar epithelial cells (AECs) is pivotal in the development of PF.
METHODS: This study explored the modulation of mitochondrial dynamics and the induction of EMT by pyruvate kinase M2 (PKM2) in AECs, aiming to identify new strategies for the prevention and treatment of sepsis-associated PF.
RESULTS: The results demonstrated that exposure to LPS increased the levels of PKM2 and the mitochondrial fission marker dynamin-related protein-1 (DRP1), while reducing the levels of the mitochondrial fusion marker mitofusin-2 (MFN2) and the epithelial marker E-cadherin. Moreover, the mesenchymal markers α-SMA and vimentin were upregulated. Treatment with shikonin effectively reversed these alterations, restoring the balance of mitochondrial dynamics, reversing EMT markers, and alleviating the severity of sepsis-associated PF.
CONCLUSIONS: This study identified PKM2 as a crucial regulator of mitochondrial dynamics and EMT in AECs during sepsis-associated PF. Targeting PKM2 activity offers a promising strategy for developing treatments to mitigate the progression of sepsis-associated PF.

Keywords:  Epithelial-mesenchymal transition; Mitochondrial dynamics; Pulmonary fibrosis; Pyruvate kinase M2; Sepsis

DOI:  https://doi.org/10.1186/s12967-025-06199-7
Biosens Bioelectron. 2025 Feb 07. pii: S0956-5663(25)00120-4. [Epub ahead of print]276 117246

A dual-channel fluorescent probe with mitochondria-immobilization: Detecting polarity and viscosity during mitophagy.

Yue Huang, Yang Liu, Chuan Dong, Qi Zan, Feng Feng, Ruibing Wang, Shaomin Shuang.

  Mitophagy is a key pathway for regulating mitochondrial quality and quantity which is essential for the preservation of cellular homeostasis. Mitophagy process may be accompanied by changes of the mitochondrial microenvironments. The multifunctional fluorescent probe is crucial for the precise detection of multiple microenvironments, which is vital for the visualization of mitophagy. Herein, a mitochondria-immobilized fluorescent probe DPP was designed and fabricated to visualize mitophagy by monitoring polarity and viscosity in dual-channel. The DPP is characterized by "D-π-A″ structure, which provides the basis for the intramolecular charge transfer (ICT) and twisted intramolecular charge transfer (TICT) platform, enabling dual-channel responses to polarity and viscosity at emission wavelengths of 487 nm and 656 nm, respectively. The significant wavelength gap (169 nm) between the above channels prevents signal crosstalk. Additionally, the incorporation of 1, 4-dibenzyl chloride grants the probe mitochondrial immobilization capabilities, avoiding the leak of probe due to mitochondrial depolarization during autophagy. The DPP accumulates in mitochondria and monitors polarity and viscosity changes in green and red channels, respectively. Notably, the investigation of the relationship between polarity and viscosity revealed that an increase in viscosity is accompanied by a decrease in polarity. The mitophagy was effectively observed through the induction of DPP by rapamycin, with a particular emphasis on the increase in viscosity and decrease in polarity. Thus, DPP offers a powerful tool for a deeper understanding of the physiological and pathological processes associated with mitophagy and are regulated by various microenvironmental parameters.

Keywords:  Fluorescent probe; Mitochondria; Polarity; Viscosity

DOI:  https://doi.org/10.1016/j.bios.2025.117246
Cell Metab. 2025 Feb 11. pii: S1550-4131(25)00013-0. [Epub ahead of print]

RBM43 controls PGC1α translation and a PGC1α-STING signaling axis.

Phillip A Dumesic, Sarah E Wilensky, Symanthika Bose, Jonathan G Van Vranken, Steven P Gygi, Bruce M Spiegelman.

  Obesity is associated with systemic inflammation that impairs mitochondrial function. This disruption curtails oxidative metabolism, limiting adipocyte lipid metabolism and thermogenesis, a metabolically beneficial program that dissipates chemical energy as heat. Here, we show that PGC1α, a key governor of mitochondrial biogenesis, is negatively regulated at the level of its mRNA translation by the RNA-binding protein RBM43. RBM43 is induced by inflammatory cytokines and suppresses mitochondrial biogenesis in a PGC1α-dependent manner. In mice, adipocyte-selective Rbm43 disruption elevates PGC1α translation and oxidative metabolism. In obesity, Rbm43 loss improves glucose tolerance, reduces adipose inflammation, and suppresses activation of the innate immune sensor cGAS-STING in adipocytes. We further identify a role for PGC1α in safeguarding against cytoplasmic accumulation of mitochondrial DNA, a cGAS ligand. The action of RBM43 defines a translational regulatory axis by which inflammatory signals dictate cellular energy metabolism and contribute to metabolic disease pathogenesis.

Keywords:  PGC1α; adipocyte; adipose thermogenesis; adipose tissue; cGAS-STING; inflammation; mRNA translation; mitochondria; obesity; oxidative metabolism

DOI:  https://doi.org/10.1016/j.cmet.2025.01.013