bims-celmim Biomed News
on Cellular and mitochondrial metabolism
Issue of 2025–12–14
twenty-one papers selected by
Marc Segarra Mondejar, AINA
  1. FLIM intensity-based image segmentation reveals upregulated energy metabolism and chemotherapy sensitivity in MCF-7 cells.
  2. The sour regulation of metabolism: acidity challenges tumor cells while fueling their metabolic survival.
  3. Reprogramming mitochondrial homeostasis in renal ischemia-reperfusion injury.
  4. Neuronal fatty acid oxidation fuels memory after intensive learning in Drosophila.
  5. Ubiquitin signaling in PINK1/Parkin-dependent mitophagy.
  6. A step-by-step guide to performing cancer metabolism research using custom-made media.
  7. The role of lipid metabolism in neuronal senescence.
  8. Emerging dimensions of mitochondrial specialization.
  9. Dihydroorotate Dehydrogenase in Mitochondrial Ferroptosis and Cancer Therapy.
  10. Mitochondria are absent from microglial processes performing surveillance, chemotaxis, and phagocytic engulfment.
  11. Multiple weak brakes act in concert to control STIM1 and store-operated calcium entry.
  12. Metabolic costs and trade-offs of hypermetabolism in human motor neurons with ATP synthase deficiency.
  13. Rapid mitochondrial repolarization upon reperfusion after cardiac ischemia.
  14. GLP-1R associates with VAPB and SPHKAP at ERMCSs to regulate β-cell mitochondrial remodelling and function.
  15. Protein succinylation in tumors-from biology to clinical therapy.
  16. Three mammalian VDAC isoforms distinctly regulate mitochondrial function and proteome to maintain cell metabolism.
  17. PeriTox-M, a Cell-Based Assay for Peripheral Neurotoxicity with Improved Sensitivity to Mitochondrial Inhibitors.
  18. Dysregulated mitochondrial dynamics in cancer: Unlocking new strategies to combat drug resistance.
  19. A metabolic cell death program downstream of SARM1 couples NAD+ depletion to BAX activation and APAF1 degradation.
  20. Molecular mechanisms underlying p62-dependent secretion of the Alzheimer-associated ubiquitin variant UBB+1.
  21. Modeling Hypoxia/Reoxygenation Injury in Proximal Tubular Epithelial Cells.
  1. J Cell Sci. 2025 Dec 01. pii: jcs263702. [Epub ahead of print]138(23):
    FLIM intensity-based image segmentation reveals upregulated energy metabolism and chemotherapy sensitivity in MCF-7 cells.
    Yu-Kai Huang, Mary Zhuang, Michelle A Digman.
      Mitochondrial transfer to recipient cells triggers a respiratory burst by increasing ATP production and cellular energy metabolism. However, its impact on intracellular metabolic shifts remains unclear. This study introduces a novel methodological approach and new biological insights into mitochondrial dynamics in cancer cells. We developed fluorescence-lifetime imaging microscopy (FLIM) intensity-based image segmentation (FIBIS), an algorithm optimized for single-mitochondrion analysis. FIBIS utilizes NADH autofluorescence, eliminating the need for biomarker staining, and improves mitochondrial detection accuracy by 35% compared to raw intensity thresholding. This method is particularly effective for analyzing dynamic mitochondria in live cells. Using FIBIS, we show that normal epithelial mitochondria uptake alters the free NADH-to-bound NADH ratio, increasing bound NADH in both estrogen- and progesterone receptor-positive and triple-negative breast cancer cells. Additionally, mitochondrial transfer enhances cancer cell sensitivity to oxidative stress-inducing anti-cancer drugs, suggesting a potential restoration of normal reactive oxygen species tolerance. Overall, FIBIS is a robust methodological approach that uses the phasor-FLIM technique to analyze NADH levels (free and bound) at the single-mitochondrion level, providing new biological insights into transferred mitochondrial dynamics in cancer cells.
    Keywords:  Cancer; Fluorescence lifetime; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1242/jcs.263702
  2. Cancer Res. 2025 Dec 11.
    The sour regulation of metabolism: acidity challenges tumor cells while fueling their metabolic survival.
    Bruna Martins Garcia, Patricia Altea-Manzano.
      The tumor microenvironment imposes diverse metabolic challenges to cancer cells. Overcoming these challenges is essential for survival, proliferation, and dissemination. However, how cancer cells cope with the harsh environment and how the different coexisting stresses affect the tumor in vivo is unknown. Recently, Groessl, Kalis and colleagues published their findings in Science showing that acidosis outweighs all other stresses and plays a major role in the adaptation to them. Mechanistically, acidosis inhibits the ERK-DRP1 pathway, resulting in mitochondria elongation, which triggers a metabolic shift from glycolysis to oxidative phosphorylation. These findings highlight the plasticity of cancer cell mitochondria and refute the previous belief that cancer mitochondria are inherently dysfunctional. Indeed, inhibition of mitochondrial fusion or oxidative phosphorylation in acidic tumors is sufficient to promote cell death. Thus, enhancing respiration under acidosis comes to light as an essential metabolic adaptation to cancer survival and proliferation and targeting how cancer cells adapt to acidosis emerges as a new avenue for therapy.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-5633
  3. Cell Signal. 2025 Dec 06. pii: S0898-6568(25)00709-0. [Epub ahead of print]139 112294
    Reprogramming mitochondrial homeostasis in renal ischemia-reperfusion injury.
    Kangyu Wang, Hao Wang, Yalong Zhang, Zijian Zhang, Li Wang, Jianwei Yang, Jiangwei Man, Li Yang.
      Acute kidney injury (AKI) caused by renal ischemia-reperfusion injury (RIRI) is primarily a mitochondrial disorder characterized by disrupted dynamics, impaired biogenesis, and defective quality control. Excessive DRP1-mediated fission, suppression of the AMPK-SIRT-PGC-1α axis, and failure of the PINK1-Parkin mitophagy system converge to drive tubular dysfunction and ferroptosis. Here, we integrate recent insights into a "mitochondrial reprogramming" framework encompassing three axes-dynamic remodeling, metabolic renewal, and proteostatic reinforcement. Therapeutic strategies targeting these axes, such as DRP1 inhibition, AMPK-SIRT-PGC-1α activation, and reinforcement of mitophagy and MAM integrity by agents like melatonin, puerarin, or Schisandrin B, have shown promise in restoring mitochondrial resilience. Furthermore, mitochondrial biomarkers and imaging tools (mtDNA, mitochondrial peptides, [18F]BCPP-EF PET) may enable phenotype-guided interventions. This review outlines the "RIRI-Mitochondria-AKI-CKD continuum," emphasizing that mitochondrial maladaptation bridges acute injury and chronic fibrosis, highlighting mitochondria as precision therapeutic targets in AKI.
    Keywords:  Biomarkers; Ferroptosis; Mitochondria; Mitophagy; Renal ischemia–reperfusion
    DOI:  https://doi.org/10.1016/j.cellsig.2025.112294
  4. Nat Metab. 2025 Dec 10.
    Neuronal fatty acid oxidation fuels memory after intensive learning in Drosophila.
    Alice Pavlowsky, Bryon Silva, Ruchira Basu, Amandine Correia Delecourt, David Geny, Lydia Danglot, Pierre-Yves Plaçais, Thomas Preat.
      Metabolic flexibility allows cells to adapt to different fuel sources, which is particularly important for cells with high metabolic demands1-3. In contrast, neurons, which are major energy consumers, are considered to rely essentially on glucose and its derivatives to support their metabolism. Here, using Drosophila melanogaster, we show that memory formed after intensive massed training is dependent on mitochondrial fatty acid (FA) β-oxidation to produce ATP in neurons of the mushroom body (MB), a major integrative centre in insect brains. We identify cortex glia as the provider of lipids to sustain the usage of FAs for this type of memory. Furthermore, we demonstrate that massed training is associated with mitochondria network remodelling in the soma of MB neurons, resulting in increased mitochondrial size. Artificially increasing mitochondria size in adult MB neurons increases ATP production in their soma and, at the behavioural level, strikingly results in improved memory performance after massed training. These findings challenge the prevailing view that neurons are unable to use FAs for energy production, revealing, on the contrary, that in vivo neuronal FA oxidation has an essential role in cognitive function, including memory formation.
    DOI:  https://doi.org/10.1038/s42255-025-01416-5
  5. J Biochem. 2025 Dec 10. pii: mvaf079. [Epub ahead of print]
    Ubiquitin signaling in PINK1/Parkin-dependent mitophagy.
    Kei Okatsu, Shuya Fukai.
      Mitochondrial quality control plays a critical role in maintaining cellular homeostasis by eliminating dysfunctional mitochondria. The PINK1/Parkin-dependent mitophagy mediates the selective clearance of damaged mitochondria. Dysfunction of PINK1 and Parkin is closely linked to Parkinson's disease. Upon mitochondrial depolarization, PINK1 accumulates on the outer membrane and phosphorylates both ubiquitin and the UBL domain of Parkin to initiate a positive feedback loop of ubiquitination. Parkin catalyzes the assembly of heterogeneous ubiquitin chains on outer mitochondrial membrane proteins, which serve as signals for autophagy adaptors. These adaptors are regulated by kinases such as TANK-binding kinase (TBK1). Deubiquitinating enzymes such as USP30 act as negative regulators. Recent structural and biochemical studies have advanced our understanding of the PINK1/Parkin-dependent mitophagy. Nonetheless, important questions remain regarding the regulatory mechanisms of PINK1, the catalytic mechanism of ubiquitin chain formation by Parkin, and the recognition of ubiquitin chains by autophagy adaptors. Here, we review the current understanding and outstanding questions on the molecular mechanisms underlying the PINK1/Parkin-dependent mitophagy with a focus on ubiquitin signaling.
    Keywords:  autophagy; kinase; mitophagy; ubiquitin
    DOI:  https://doi.org/10.1093/jb/mvaf079
  6. Life Sci Alliance. 2026 Feb;pii: e202503529. [Epub ahead of print]9(2):
    A step-by-step guide to performing cancer metabolism research using custom-made media.
    Sophie Seifert, Francisco Yanqui-Rivera, Tim Kühn, Lena Elise Høyland, Toman Borteçen, Bella Agranovich, Lara Elea Eckhardt, Martin Herdt, Alessa Henneberg, Verena Panitz, Faisal Hayat, Marie Migaud, Gernot Poschet, Ifat Abramovich, Eyal Gottlieb, Jeroen Krijgsveld, Mathias Ziegler, Mirja Tamara Prentzell, Christiane A Opitz.
      The preparation of custom-made media offers precise control over nutrient composition, enabling detailed studies of cellular metabolism. We demonstrate how self-made media formulations enable diverse assay designs and readouts to assess cancer metabolism. Self-made media can be used in Seahorse assays to measure mitochondrial respiration under defined conditions. In nutrient deprivation experiments, amino acid or vitamin removal can uncover how cancer cells adapt to metabolic stress. Using labeled amino acids enables analysis of nascent protein synthesis and translational regulation, while stable-isotope tracing reveals metabolic fluxes through key pathways. This guide presents a suite of metabolic assays using custom-made media, covering experimental design, the selection of controls, sample preparation, data acquisition, and interpretation. The accompanying online media calculator "Media Minds" streamlines the creation of custom media formulations, ensuring accuracy and reproducibility.
    DOI:  https://doi.org/10.26508/lsa.202503529
  7. FEBS Open Bio. 2025 Dec 12.
    The role of lipid metabolism in neuronal senescence.
    Dikaia Tsagkari, Eleftheria Panagiotidou, Nektarios Tavernarakis.
      Senescence is a complex cellular state characterised by irreversible growth arrest and metabolic reprogramming. In neurons, senescence has been mainly observed in the context of ageing and age-related neurodegeneration. Lipid metabolism plays a critical role in cellular homeostasis, with emerging evidence suggesting that alterations in lipid species, including fatty acids, cholesterol, sphingolipids and phospholipids, fundamentally drive or contribute to the senescent phenotype in both neuronal and non-neuronal cells in the brain. Namely, changes in lipid species levels result in the accumulation of lipid droplets (LDs), leading to dysregulation of membrane dynamics, and in turn to the production of bioactive lipid mediators, which collectively shape the senescence-associated secretory phenotype (SASP) in the brain. In this review, we describe the cell type-specific patterns of lipid dysregulation in neurons, astrocytes, microglia and other glial cells during senescence, highlighting the role of key lipid species and their association with senescence markers and phenotypes. Furthermore, we discuss the bidirectional relationship between lipid metabolism and mitochondrial dysfunction in cellular senescence. We also examine the molecular mechanisms through which lipid metabolic pathways can orchestrate neural senescence and their contribution to ageing and age-related neurodegenerative disorders, such as Alzheimer's disease and Parkinson's disease. Finally, we review emerging therapeutic strategies targeting lipid metabolic pathways to modulate neural senescence and potentially ameliorate age-associated brain pathology.
    Keywords:  ageing; autophagy; lipid metabolism; mitochondria; neurodegeneration; neuronal cells; senescence
    DOI:  https://doi.org/10.1002/2211-5463.70181
  8. Biol Chem. 2025 Dec 10.
    Emerging dimensions of mitochondrial specialization.
    Tslil Ast.
      The diverse, and sometimes opposing, roles of mitochondria require sophisticated organizational and regulatory strategies. This review examines emerging evidence that mitochondria can solve this challenge through functional specialization - adopting distinct bioenergetic and metabolic programs based on location, contacts, and cellular conditions. We discuss both established principles and recent technological breakthroughs that reveal this hidden complexity. Ongoing advances promise to move the field from describing mitochondrial diversity to uncovering its regulatory mechanisms and therapeutic potential.
    Keywords:  heterogeneity; metabolic specialization; mitochondria
    DOI:  https://doi.org/10.1515/hsz-2025-0210
  9. Cells. 2025 Nov 28. pii: 1889. [Epub ahead of print]14(23):
    Dihydroorotate Dehydrogenase in Mitochondrial Ferroptosis and Cancer Therapy.
    Jaewang Lee, Jong-Lyel Roh.
      Ferroptosis is an iron-dependent form of regulated cell death driven by lipid peroxidation. Since the identification of dihydroorotate dehydrogenase (DHODH) as a mitochondrial suppressor of ferroptosis in 2021, increasing evidence has highlighted its role in linking nucleotide metabolism, redox regulation, and tumor progression. We conducted a comprehensive review of publications on DHODH, ferroptosis, and cancer. Relevant studies were analyzed to synthesize mechanistic insights, translational implications, and therapeutic perspectives. DHODH, a flavin-dependent mitochondrial enzyme catalyzing the oxidation of dihydroorotate to orotate, integrates pyrimidine biosynthesis with electron transport chain activity. Beyond its canonical metabolic role, DHODH regenerates ubiquinol (CoQ10H2) to suppress mitochondrial lipid peroxidation and ferroptosis. Elevated DHODH expression in colorectal, hepatocellular, breast, renal, and brain cancers correlates with poor prognosis, therapy resistance, and immune evasion. Pharmacological inhibition of DHODH disrupts pyrimidine synthesis and redox defense, sensitizing GPX4-low tumors to ferroptosis. Preclinical studies demonstrate synergy between DHODH inhibitors and chemotherapy, radiotherapy, or immune checkpoint blockade. Nanoparticle-based delivery systems enhance therapeutic efficacy by simultaneously targeting multiple ferroptosis defense arms while reducing toxicity. DHODH serves as both a metabolic and redox checkpoint in cancer, linking ferroptosis suppression to proliferation and immune escape. Targeting DHODH offers a promising strategy to dismantle cancer resilience, particularly in combination with ferroptosis inducers and immunotherapies. Future research should focus on biomarker-guided stratification, nanomedicine platforms, and clinical translation of DHODH inhibitors.
    Keywords:  cancer therapy; dihydroorotate dehydrogenase; ferroptosis; immunotherapy; pyrimidine metabolism
    DOI:  https://doi.org/10.3390/cells14231889
  10. Nat Commun. 2025 Dec 12. 16(1): 11104
    Mitochondria are absent from microglial processes performing surveillance, chemotaxis, and phagocytic engulfment.
    Alicia N Pietramale, Xhoela Bame, Megan E Doty, Kiera E Schwarz, Robert A Hill.
      Microglia continually surveil the brain allowing for rapid detection of tissue damage or infection. Microglial metabolism is linked to tissue homeostasis, yet how mitochondria are subcellularly partitioned in microglia and dynamically reorganize during surveillance, injury responses, and phagocytic engulfment in the intact brain are not known. Here, we performed intravital imaging and ultrastructural analyses of microglia mitochondria in mice and human tissue, revealing that microglial processes diverge in their mitochondrial content, with some containing multiple mitochondria while others are completely void. Microtubules and hexokinase 2 mirror this uneven mitochondrial distribution indicating that these cytoskeletal and metabolic components are linked to mitochondrial organization in microglia. Microglial processes that engage in minute-to-minute surveillance typically do not have mitochondria. Moreover, unlike process surveillance, mitochondrial motility does not change with animal anesthesia. Likewise, the processes that acutely chemoattract to a lesion site or initially engage with a neuron undergoing programmed cell death do not contain mitochondria. Rather, microglia mitochondria have a delayed arrival into the responding cell processes. Thus, there is subcellular heterogeneity of mitochondrial partitioning. Moreover, microglial processes that surveil and acutely respond to damage do not contain mitochondria.
    DOI:  https://doi.org/10.1038/s41467-025-66708-6
  11. Proc Natl Acad Sci U S A. 2025 Dec 16. 122(50): e2518622122
    Multiple weak brakes act in concert to control STIM1 and store-operated calcium entry.
    Ruoyi Qiu, Richard S Lewis.
      Store-operated Ca2+ entry is a key signaling pathway controlled by the interaction of the ER Ca2+ sensor STIM1 with the Orai1 Ca2+ channel following ER Ca2+ depletion. To avoid generating pathological effects, STIM1 must remain mostly inactive under resting, ER-replete conditions yet respond rapidly and reversibly to changes in ER Ca2+ content. It is not well understood how these conflicting requirements are met. Here we combine single-molecule FRET measurements of full-length dimeric STIM1 in lipid membranes with an AlphaFold2 structural model to describe the structure and regulation of the resting state. We show that STIM1 activity is controlled by the combined operation of four relatively weak restraints, or brakes. The Ca2+-bound EF-SAM luminal domain acts as a steric restraint to inhibit spontaneous activity. In the cytosolic region, the domain-swapped hydrophobic interaction and alignment of CC1α1 with CC3 of the CRAC activation domain (CAD) positions the apex of CAD next to the ER membrane, where electrostatic lipid-protein interactions further stabilize the inactive conformation. A fourth brake is created by hydrophobic and electrostatic interactions of the two CC1α2/3 domains attached to the base of CAD. Disruption of any one of these brakes triggers spontaneous STIM1 activation, showing that the concerted action of these relatively weak restraints serves to minimize spontaneous activity in resting cells with full ER Ca2+ stores, while allowing rapid activation in response to changes in store content.
    Keywords:  STIM1; calcium signaling; single-molecule FRET; store-operated calcium entry
    DOI:  https://doi.org/10.1073/pnas.2518622122
  12. Commun Biol. 2025 Dec 11. 8(1): 1759
    Metabolic costs and trade-offs of hypermetabolism in human motor neurons with ATP synthase deficiency.
    Rubén Torregrosa-Muñumer, Jeremi Turkia, Rumeysa Ermiş, Jouni Kvist, Sandra Harjuhaahto, Jana Pennonen, Ville Hietakangas, Emil Ylikallio, Henna Tyynismaa.
      Hypermetabolism, a futile cycle of energy production and consumption, has been proposed as an adaptative response to deficiencies in mitochondrial oxidative phosphorylation. However, the cellular costs of hypermetabolism remain largely unknown. Here we studied the consequences of hypermetabolism in human motor neurons harboring a heteroplasmic mutation in MT-ATP6, which impairs ATP synthase assembly. Respirometry, metabolomics, and proteomics analyses of the motor neurons showed that elevated ATP production rates were accompanied with increased demand for acetyl-Coenzyme A (acetyl-CoA) and depleted pantothenate (vitamin B5), and the proteome was remodeled to support the metabolic adaptation. Mitochondrial membrane potential and coupling efficiency remained stable, and the therapeutic agent avanafil did not affect metabolite levels. However, a redistribution of acetyl-CoA usage resulted in metabolic trade-offs, including reduced histone acetylation and altered maintenance of the neurotransmitter acetylcholine, revealing potential vulnerabilities in motor neurons. These findings advance the understanding of cellular metabolic consequences imposed by hypermetabolic conditions.
    DOI:  https://doi.org/10.1038/s42003-025-09149-7
  13. Nat Cardiovasc Res. 2025 Dec 11.
    Rapid mitochondrial repolarization upon reperfusion after cardiac ischemia.
    Abigail V Giles, Raul Covian, Hiran A Prag, Nils Burger, Bertrand Lucotte, Chak Shun Yu, Junhui Sun, Elizabeth Murphy, Thomas Krieg, Michael P Murphy, Robert S Balaban.
      The mitochondrial membrane potential (ΔΨm) drives oxidative phosphorylation and alterations contribute to cardiac pathologies, but real-time assessment of ΔΨm has not been possible. Here we describe noninvasive measurements using mitochondrial heme bL and bH absorbances, which rapidly respond to ΔΨm. Multi-wavelength absorbance spectroscopy enabled their continuous monitoring in isolated mitochondria and the perfused heart. Calibration of heme b absorbance in isolated mitochondria revealed that reduced heme bL relative to total reduced heme b (fbL = bL/(bL + bH)) exhibits a sigmoidal relationship with ΔΨm. Extrapolating this relationship to the heart enabled estimation of ΔΨm as 166 ± 18 mV (n = 25, mean ± s.d.). We used this approach to assess how ΔΨm changes during ischemia-reperfusion injury, an unknown limiting the understanding of ischemia-reperfusion injury. In perfused hearts, ΔΨm declined during ischemia and rapidly reestablished upon reperfusion, supported by oxidation of the succinate accumulated during ischemia. These findings expand our understanding of ischemia-reperfusion injury.
    DOI:  https://doi.org/10.1038/s44161-025-00752-9
  14. Nat Commun. 2025 Dec 10. 16(1): 11010
    GLP-1R associates with VAPB and SPHKAP at ERMCSs to regulate β-cell mitochondrial remodelling and function.
    Gregory Austin, Affiong I Oqua, Liliane El Eid, Mingli Zhu, Yusman Manchanda, Priyanka Peres, Helena Coyle, Yelyzaveta Poliakova, Zhanna Balkhiyarova, Karim Bouzakri, Alex Montoya, Dominic J Withers, Michele Solimena, Ben Jones, Steven J Millership, Steffen Burgold, David C A Gaboriau, Endre Majorovits, Evelyn Garlick, Maria Augusta do R B F Lima, Inga Prokopenko, Jonathon Nixon-Abell, Andreas Müller, Alejandra Tomas.
      Glucagon-like peptide-1 receptor (GLP-1R) agonists (GLP-1RAs) ameliorate mitochondrial health by increasing mitochondrial turnover in metabolically relevant tissues. Mitochondrial adaptation to metabolic stress is crucial to maintain pancreatic β-cell function and prevent type 2 diabetes (T2D) progression. While the GLP-1R is well-known to stimulate cAMP production leading to Protein Kinase A (PKA) and Exchange Protein Activated by cyclic AMP 2 (Epac2) activation, there is a lack of understanding of the molecular mechanisms linking GLP-1R signalling with mitochondrial and β-cell functional adaptation. Here, we present a comprehensive study in β-cell lines and primary islets that demonstrates that, following GLP-1RA stimulation, GLP-1R-positive endosomes associate with the endoplasmic reticulum (ER) membrane contact site (MCS) tether VAPB at ER-mitochondria MCSs (ERMCSs), where active GLP-1R engages with SPHKAP, an A-kinase anchoring protein (AKAP) previously linked to T2D and adiposity risk in genome-wide association studies (GWAS). The inter-organelle complex formed by endosomal GLP-1R, ER VAPB and SPHKAP triggers a pool of ERMCS-localised cAMP/PKA signalling via the formation of a PKA-RIα biomolecular condensate which leads to changes in mitochondrial contact site and cristae organising system (MICOS) complex phosphorylation, mitochondrial remodelling, and β-cell functional adaptation, with important consequences for the regulation of β-cell insulin secretion and survival to stress.
    DOI:  https://doi.org/10.1038/s41467-025-66115-x
  15. Int J Biol Macromol. 2025 Dec 06. pii: S0141-8130(25)10046-9. [Epub ahead of print] 149489
    Protein succinylation in tumors-from biology to clinical therapy.
    Huiling Li, Huijuan Zhang, Jing Zhu, Yu Tang, Jing An.
      Lysine succinylation is a recently identified post-translational modification (PTM) characterized by the transfer of a succinyl group (-CO-CH2-CH2-CO2H) to lysine residues, primarily mediated by succinyl-CoA. This modification plays a critical role in maintaining protein stability and function, and is involved in diverse biological processes, including energy metabolism, substrate transport, and signal transduction. Accumulating evidence indicates that lysine succinylation contributes to tumorigenesis and cancer progression, with both enzymatic and non-enzymatic mechanisms playing regulatory roles. This review summarizes recent advances in succinylation research within the context of tumor metabolism, the tumor immune microenvironment, and its interplay with other epigenetic modifications. Furthermore, we highlight current developments in anti-tumor therapeutics and succinylation inhibitors, aiming to provide novel insights into protein post-translational modifications and to support the identification of potential drug targets for clinical applications.
    Keywords:  Cell metabolism; Epigenetic regulation; Immune microenvironment; Post-translational modification; Succinylation; Therapy
    DOI:  https://doi.org/10.1016/j.ijbiomac.2025.149489
  16. J Biol Chem. 2025 Dec 05. pii: S0021-9258(25)02861-3. [Epub ahead of print] 111009
    Three mammalian VDAC isoforms distinctly regulate mitochondrial function and proteome to maintain cell metabolism.
    Megha Rajendran, William M Rosencrans, Nina A Bautista, Wendy Fitzgerald, Diana Huynh, Bethel G Beyene, Baiyi Quan, Jennifer D Petersen, Julie Hwang, Tsui-Fen Chou, Sergey M Bezrukov, Tatiana K Rostovtseva.
      The Voltage Dependent Anion Channel (VDAC) is the most ubiquitous protein in the mitochondrial outer membrane. This channel facilitates the flux of water-soluble metabolites and ions like calcium across the mitochondrial outer membrane. Beyond this canonical role, VDAC has been implicated, through interactions with protein partners, in several cellular processes such as apoptosis, calcium signaling, and lipid metabolism. There are three VDAC isoforms in mammalian cells, VDAC1, VDAC2, and VDAC3, with varying tissue-specific expression profiles. From a biophysical standpoint, all three isoforms conduct metabolites and ions with similar efficiency. However, isoform knockouts (KOs) in mice lead to distinct phenotypes, which may be due to differences in VDAC isoform interactions with partner proteins. To understand the functional role of each VDAC isoform within a single cell type, we created functional KOs of each isoform in HeLa cells and performed a comparative study of their metabolic activity and proteomics. We found that each isoform KO alters the proteome differently, with VDAC3 KO dramatically downregulating key members of the electron transport chain (ETC) while shifting the mitochondria into a glutamine-dependent state. Importantly, this unexpected dependence of mitochondrial function on the VDAC3 isoform is not compensated for by the more ubiquitously expressed VDAC1 and VDAC2 isoforms. In contrast, VDAC2 KO did not affect respiration but upregulated ETC components and decreased key enzymes in the glutamine metabolic pathway. VDAC1 KO specifically reduced glycolytic activity linked to decreased hexokinase localization to mitochondria. These results reveal non-redundant roles of VDAC isoforms in cancer cell metabolic adaptability.
    Keywords:  CRISPR/Cas9 gene knockout; metabolic regulation; mitochondrial respiratory chain complex; proteomics; voltage-dependent anion channel
    DOI:  https://doi.org/10.1016/j.jbc.2025.111009
  17. Cells. 2025 Dec 04. pii: 1929. [Epub ahead of print]14(23):
    PeriTox-M, a Cell-Based Assay for Peripheral Neurotoxicity with Improved Sensitivity to Mitochondrial Inhibitors.
    Anna-Katharina Holzer, Mira Dürr, Selina Multrus, Laura Dangel, Viktoria Magel, Marcel Leist.
      Human cell-based assays for neurotoxicity (NT) and developmental neurotoxicity (DNT) have reached a high level of readiness, but some tests require improvements in the specificity and sensitivity at which mitochondrial toxicants are detected. This study aimed to optimize the PeriTox assay, which uses peripheral neurons (PNs) and predicts the potential of chemicals to trigger peripheral neuropathies. By introducing a glucose-to-galactose switch in the medium composition, cells were forced to rely on mitochondrial respiration. Using pre-differentiated PNs cultured in either glucose (Glc) or galactose (Gal), we observed no major differences in baseline phenotype, gene expression, neurite outgrowth, or total ATP content. However, a marked metabolic shift was confirmed by the increased oxygen consumption in Gal conditions. Based on measurements of neurite growth and ATP levels, Gal-adapted neurons showed a heightened sensitivity, up to 7500-fold, to a range of mitochondrial respiratory chain (MRC) inhibitors. The sensitivity shift was high for inhibitors of MRC complexes I and III and modest or absent for unrelated compounds such as proteasome inhibitors or cytoskeletal poisons. For complex I-III inhibitors, the enhanced detection of mitochondrial neurotoxicants was coupled with a more accurate distinction between cytotoxic and neurite-specific effects, i.e., an improved assay specificity. In conclusion, our study on 39 compounds suggests that running the PeriTox assay in galactose increases its sensitivity and specificity for several mitochondrial toxicants, while no general disadvantages or shortcomings were observed. The modified version (PeriTox-M) may increase the performance of in vitro test batteries for scientific and regulatory applications.
    Keywords:  high-throughput toxicity screening; metabolic switch; mitochondrial toxicity; peripheral neurotoxicity
    DOI:  https://doi.org/10.3390/cells14231929
  18. Biochim Biophys Acta Rev Cancer. 2025 Dec 06. pii: S0304-419X(25)00252-5. [Epub ahead of print]1881(1): 189510
    Dysregulated mitochondrial dynamics in cancer: Unlocking new strategies to combat drug resistance.
    Teresa Rossi, Roberta Torcasio, Ludovica Ganino, Ilenia Valentino, Christian Boni, Massimo Gentile, Antonino Neri, Nicola Amodio, Mariaelena Pistoni.
      Mitochondria continuously alternate between fragmented and fused states, a process known as mitochondrial dynamics, which plays a pivotal role in essential cellular functions, including metabolism, apoptosis, reactive oxygen species production, and signal transduction. Disruptions in this dynamic equilibrium, frequently observed in aggressive cancers, can promote malignant transformation and tumor progression. A growing body of evidence indicates that dysregulated mitochondrial dynamics contribute to resistance against both conventional and targeted anticancer therapies. In this review, we explore the regulatory mechanisms governing mitochondrial dynamics, with a focus on the genetic and epigenetic modulation of key drivers such as DRP1, MFN1/2 and OPA1. We also discuss how altered mitochondrial dynamics converge into diverse mechanisms of drug resistance in cancer. Overall, these insights underscore aberrant mitochondrial dynamics as a potential biomarker of therapeutic resistance, and position mitochondrial dynamics-related GTPases, particularly DRP1 and Mitofusins, as exploitable targets for novel treatments in advanced solid and hematologic malignancies.
    Keywords:  Cancer therapy; DRP1; Drug resistance; MFF; MFN2; Mitochondrial dynamics
    DOI:  https://doi.org/10.1016/j.bbcan.2025.189510
  19. Proc Natl Acad Sci U S A. 2025 Dec 16. 122(50): e2522444122
    A metabolic cell death program downstream of SARM1 couples NAD+ depletion to BAX activation and APAF1 degradation.
    Weilong Pan, Dejia Guo, Daiyuan Liu, Xiaodong Wang.
      SARM1 is a neuronal Nicotinamide adenine dinucleotide (NAD+) hydrolase that drives axonal degeneration and neuronal death by depleting NAD+, yet how NAD+ loss triggers axon loss and cell death has remained unclear. Here, we define a nonapoptotic death program downstream of endogenous SARM1 activation and NAD+ loss using a genetically tractable nonneuronal eHAP cell model. Upon NAD+ depletion, BAX is activated but caspase activation is suppressed due to APAF1 degradation via the E3 ligase HERC4, effectively uncoupling mitochondrial outer membrane permeabilization from apoptosome formation. Mechanistically, NAD+ depletion inhibits mTOR/AKT signaling, destabilizing MCL1 and relieving BAX from repression. We further identified Neurofibromatosis type II, NF2, as a regulator that promotes SARM1 transcription through the Hippo-YAP/TAZ pathway. The SARM1-dependent BAX activation and the role of NF2 in axon degradation were validated in neuronal models of axon degeneration. Together, these findings reveal how SARM1-driven metabolic collapse rewires cell death execution, positioning BAX, MCL1, APAF1, NF2, and HERC4 as core effectors in a nonapoptotic degenerative pathway linking metabolic stress to neurodegeneration.
    Keywords:  APAF1; Apoptosis; BAX; NAD+; SARM1
    DOI:  https://doi.org/10.1073/pnas.2522444122
  20. Proc Natl Acad Sci U S A. 2025 Dec 16. 122(50): e2504528122
    Molecular mechanisms underlying p62-dependent secretion of the Alzheimer-associated ubiquitin variant UBB+1.
    Ajay R Wagh, Michael H Glickman.
      UBB+1, a ubiquitin variant protein resulting from a frameshift in the ubiquitin-B gene, is a pathological hallmark of Alzheimer disease (AD). At the cellular level, UBB+1 disrupts the ubiquitin-proteasome system while inducing autophagy. Notably, UBB+1 itself is secreted via autophagosome-like vesicles. Here, we demonstrate that UBB+1 can be removed from the cell by degradative and secretory autophagy. Sequestosome 1 (SQSTM1)/p62 functions as a pivotal ubiquitin receptor for UBB+1, recognizing its ubiquitin domain and facilitating loading into autophagosomes. Oligomerization of SQSTM1/p62 was critical to isolate UBB+1 in bodies preventing its aggregation. Intriguingly, both gain- and loss-of-function SQSTM1/p62 suppressed UBB+1 secretion, causing intracellular retention: SQSTM1/p62 knockout led to UBB+1 accumulation in insoluble aggregates, while its overexpression promoted the formation of p62-UBB+1 bodies. We further identified distinct roles for SNARE-mediated membrane fusion in secretory autophagy of UBB+1. Specifically, the R-SNARE SEC22B and the Q-SNAREs Syntaxin-4 and SNAP23 participated in UBB+1 exocytosis. Disruption of SEC22B impaired the fusion of UBB+1-containing autophagosomes with the plasma membrane, reducing UBB+1 secretion without affecting its intracellular turnover. Inhibition of lysosomes partially stabilized UBB+1 indicating that degradation and secretion are complementary processes that determine the fate of UBB+1. This study elucidates the dual roles of autophagy in managing neurotoxic proteins, highlighting SQSTM1/p62 as a key mediator of UBB+1 trafficking and secretion. Although ubiquitin typically acts as a degradation signal, our findings reveal a rare instance of a ubiquitin-related protein driving secretory autophagy. These findings advance our understanding of cellular mechanisms underlying the clearance of misfolded proteins in neurodegenerative diseases.
    Keywords:  Alzheimer’s disease; autophagy; p62; trafficking; ubiquitin
    DOI:  https://doi.org/10.1073/pnas.2504528122
  21. J Vis Exp. 2025 Nov 21.
    Modeling Hypoxia/Reoxygenation Injury in Proximal Tubular Epithelial Cells.
    Mariano Marin-Blazquez, Alessandra Tammaro, Ruben Rabadan-Ros, Ruben Zapata-Perez.
      Kidney transplantation accounts for approximately 60%-65% of all transplanted solid organs. Most donor kidneys are obtained from deceased individuals, requiring extended cold preservation, which is a known contributor to poor transplant outcomes. Despite current preservation strategies, ischemia-reperfusion injury (IRI) remains an unavoidable consequence of transient blood flow interruption, leading to oxygen and nutrient deprivation. Within the nephron, proximal tubular epithelial cells (PTECs) of the S3 segment are particularly susceptible to IRI due to their high metabolic demand and dependence on mitochondrial oxidative phosphorylation. At the molecular level, IRI disrupts mitochondrial metabolism and reduces ATP production, compromising the energy requirements of proximal tubular epithelial cells (PTECs) and promoting apoptosis and necrosis. To investigate these mechanisms and evaluate potential therapeutic strategies, robust and reproducible in vitro models of renal IRI that accurately recapitulate the metabolic vulnerability of PTECs are essential. Here, we describe a protocol for the induction and assessment of hypoxia/reoxygenation (H/R) injury in murine immortalized PTECs (IM-PTECs). The protocol includes detailed information on the medium composition and culture conditions required to maintain these cells, followed by the induction of H/R injury through controlled hypoxia and reoxygenation phases that closely mimic the ischemia and reperfusion events in transplanted kidneys. This model provides a valuable platform for evaluating the effects of different interventions on renal epithelial cells exposed to H/R injury. The impact of these treatments can be assessed through the analysis of the expression of markers associated with PT damage, as well as through the assessment of the mitochondrial respiratory function. Together, these readouts offer mechanistic insights into compound efficacy and cellular recovery processes, supporting the development of targeted therapies for renal IRI.
    DOI:  https://doi.org/10.3791/69077
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