bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2025–01–26
sixty papers selected by
Christian Frezza, Universität zu Köln
  1. Selective deficiency of mitochondrial respiratory complex I subunits Ndufs4/6 causes tumor immunogenicity.
  2. Fine-tuning tumor immunogenicity with mitochondrial complex I.
  3. Targeting aldolase A in hepatocellular carcinoma leads to imbalanced glycolysis and energy stress due to uncontrolled FBP accumulation.
  4. Mitochondrial swap from cancer to immune cells thwarts anti-tumour defences.
  5. Mechanosensitive neurons innervating the gut and heart control metabolic and emotional state.
  6. Mitochondrial protein import stress.
  7. Circadian metabolic adaptations to infections.
  8. Cancer cells 'poison' the immune system with tainted mitochondria.
  9. SLC13A2 promotes hepatocyte metabolic remodeling and liver regeneration by enhancing de novo cholesterol biosynthesis.
  10. Splice age: mTORC1-mediated RNA splicing in metabolism and ageing.
  11. Impaired oxidative phosphorylation drives primary tumor escape and metastasis.
  12. The adult table: Chronic intermittent fasting improves β cell health only in adults.
  13. Mitochondrial fatty acid oxidation regulates monocytic type I interferon signaling via histone acetylation.
  14. Hypoxia as a medicine.
  15. Mannose: A game-changer for T cell immunotherapy.
  16. FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis.
  17. The oxygen level in air directs airway epithelial cell differentiation by controlling mitochondrial citrate export.
  18. RNA molecule rejuvenates ageing mice by restoring old cells.
  19. Fuel for thought: targeting metabolism in lung cancer.
  20. Mitochondrial respiratory complex III sustains IL-10 production in activated macrophages and promotes tumor-mediated immune evasion.
  21. Circadian gating: concepts, processes, and opportunities.
  22. SMAD4 and KRAS Status Shape Cancer Cell-Stromal Crosstalk and Therapeutic Response in Pancreatic Cancer.
  23. Immune evasion through mitochondrial transfer in the tumour microenvironment.
  24. KAT6A acetylation drives metabolic adaptation to mediate cellular growth and mitochondrial metabolism through AMPK interaction.
  25. Ergothioneine improves healthspan of aged animals by enhancing cGPDH activity through CSE-dependent persulfidation.
  26. Palmitoylation-dependent regulation of GPX4 suppresses ferroptosis.
  27. mTOR Ser1261 is an AMPK-dependent phosphosite in mouse and human skeletal muscle not required for mTORC2 activity.
  28. The mitochondrial choline transporter, SLC25A48, regulates urine and blood choline levels in humans.
  29. Tissue-specific modulation of NADH consumption as an anti-aging intervention in Drosophila.
  30. CD44-Mediated Metabolic Rewiring is A Targetable Dependency of IDH-Mutant Leukemia.
  31. Single-cell DNA sequencing reveals pervasive positive selection throughout preleukemic evolution.
  32. A novel allosteric driver mutation of β-glucuronidase promotes head and neck squamous cell carcinoma progression through STT3B-mediated PD-L1 N-glycosylation.
  33. Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted.
  34. Evidence of DNA methylation heterogeneity and epipolymorphism in kidney cancer tissue samples.
  35. Metabolism-driven chromatin dynamics: Molecular principles and technological advances.
  36. Mitochondria mechanosensing: The powerhouse fueling cellular force signaling.
  37. Circadian rhythms: pervasive, and often times evasive.
  38. Complement C3 of tumor-derived extracellular vesicles promotes metastasis of RCC via recruitment of immunosuppressive myeloid cells.
  39. Cryo-EM structure and regulation of human NAD kinase.
  40. Metabolic interplays between the tumour and the host shape the tumour macroenvironment.
  41. Mechanisms of Lipid-Associated Macrophage Accrual in Metabolically Stressed Adipose Tissue.
  42. Aldolase A: the broker of glycolysis.
  43. Chronic CRYPTOCHROME deficiency enhances cell-intrinsic antiviral defences.
  44. Long somatic DNA-repeat expansion drives neurodegeneration in Huntington's disease.
  45. Effects of vitamin B12 supply on cellular processes of the facultative vitamin B12 consumer Vibrio campbellii.
  46. Current and future perspectives of lysine lactylation in cancer.
  47. Succinate receptor 1 signaling mutually depends on subcellular localization and cellular metabolism.
  48. CD45-PET is a robust, non-invasive tool for imaging inflammation.
  49. Aging and Cancer-Inextricably Linked Across the Lifespan.
  50. Rethinking cancer evolution: from genetic mutations to complex information systems in tumor reversion.
  51. Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.
  52. Aberrant fumarate metabolism links interferon release in diffuse systemic sclerosis.
  53. PERspectives on circadian cell biology.
  54. Lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension.
  55. Identification of three distinct cell populations for urate excretion in human kidneys.
  56. Redox proteomics reveal a role for peroxiredoxinylation in stress protection.
  57. A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer.
  58. Bypassing senescence.
  59. Mammalian nucleophagy: process and function.
  60. Plasticity in metastatic colorectal cancer.
  1. Nat Cancer. 2025 Jan 17.
    Selective deficiency of mitochondrial respiratory complex I subunits Ndufs4/6 causes tumor immunogenicity.
    Jiaxin Liang, Tevis Vitale, Xixi Zhang, Thomas D Jackson, Deyang Yu, Mark Jedrychowski, Steve P Gygi, Hans R Widlund, Kai W Wucherpfennig, Pere Puigserver.
      Cancer cells frequently rewire their metabolism to support proliferation and evade immune surveillance, but little is known about metabolic targets that could increase immune surveillance. Here we show a specific means of mitochondrial respiratory complex I (CI) inhibition that improves tumor immunogenicity and sensitivity to immune checkpoint blockade (ICB). Targeted genetic deletion of either Ndufs4 or Ndufs6, but not other CI subunits, induces an immune-dependent growth attenuation in melanoma and breast cancer models. We show that deletion of Ndufs4 induces expression of the major histocompatibility complex (MHC) class I co-activator Nlrc5 and antigen presentation machinery components, most notably H2-K1. This induction of MHC-related genes is driven by a pyruvate dehydrogenase-dependent accumulation of mitochondrial acetyl-CoA, which leads to an increase in histone H3K27 acetylation within the Nlrc5 and H2-K1 promoters. Taken together, this work shows that selective CI inhibition restricts tumor growth and that specific targeting of Ndufs4 or Ndufs6 increases T cell surveillance and ICB responsiveness.
    DOI:  https://doi.org/10.1038/s43018-024-00895-x
  2. Nat Cancer. 2025 Jan 17.
    Fine-tuning tumor immunogenicity with mitochondrial complex I.
    Désirée Schatton, Christian Frezza.
      
    DOI:  https://doi.org/10.1038/s43018-024-00874-2
  3. Nat Metab. 2025 Jan 20.
    Targeting aldolase A in hepatocellular carcinoma leads to imbalanced glycolysis and energy stress due to uncontrolled FBP accumulation.
    Marteinn T Snaebjornsson, Philipp Poeller, Daria Komkova, Florian Röhrig, Lisa Schlicker, Alina M Winkelkotte, Adriano B Chaves-Filho, Kamal M Al-Shami, Carolina Dehesa Caballero, Ioanna Koltsaki, Felix C E Vogel, Roberto Carlos Frias-Soler, Ramona Rudalska, Jessica D Schwarz, Elmar Wolf, Daniel Dauch, Ralf Steuer, Almut Schulze.
      Increased glycolytic flux is a hallmark of cancer; however, an increasing body of evidence indicates that glycolytic ATP production may be dispensable in cancer, as metabolic plasticity allows cancer cells to readily adapt to disruption of glycolysis by increasing ATP production via oxidative phosphorylation. Using functional genomic screening, we show here that liver cancer cells show a unique sensitivity toward aldolase A (ALDOA) depletion. Targeting glycolysis by disrupting the catalytic activity of ALDOA led to severe energy stress and cell cycle arrest in murine and human hepatocellular carcinoma cell lines. With a combination of metabolic flux analysis, metabolomics, stable-isotope tracing and mathematical modelling, we demonstrate that inhibiting ALDOA induced a state of imbalanced glycolysis in which the investment phase outpaced the payoff phase. Targeting ALDOA effectively converted glycolysis from an energy producing into an energy-consuming process. Moreover, we found that depletion of ALDOA extended survival and reduced cancer cell proliferation in an animal model of hepatocellular carcinoma. Thus, our findings indicate that induction of imbalanced glycolysis by targeting ALDOA presents a unique opportunity to overcome the inherent metabolic plasticity of cancer cells.
    DOI:  https://doi.org/10.1038/s42255-024-01201-w
  4. Nature. 2025 Jan 22.
    Mitochondrial swap from cancer to immune cells thwarts anti-tumour defences.
    Jonathan R Brestoff.
      
    Keywords:  Cancer; Immunology; Medical research
    DOI:  https://doi.org/10.1038/d41586-025-00077-4
  5. Nat Metab. 2025 Jan 17.
    Mechanosensitive neurons innervating the gut and heart control metabolic and emotional state.
      
    DOI:  https://doi.org/10.1038/s42255-024-01208-3
  6. Nat Cell Biol. 2025 Jan 22.
    Mitochondrial protein import stress.
    Nikolaus Pfanner, Fabian den Brave, Thomas Becker.
      Mitochondria have to import a large number of precursor proteins from the cytosol. Chaperones keep these proteins in a largely unfolded state and guide them to the mitochondrial import sites. Premature folding, mitochondrial stress and import defects can cause clogging of import sites and accumulation of non-imported precursors, representing a critical burden for cellular proteostasis. Here we discuss how cells respond to mitochondrial protein import stress by regenerating clogged import sites and inducing stress responses. The mitochondrial protein import machinery has a dual role by serving as sensor for detecting mitochondrial dysfunction and inducing stress-response pathways. The production of chaperones that fold or sequester precursor proteins in deposits is induced and the proteasomal activity is increased to remove the excess precursor proteins. Together, these pathways reveal how mitochondria are tightly integrated into a cellular proteostasis and stress response network to maintain cell viability.
    DOI:  https://doi.org/10.1038/s41556-024-01590-w
  7. Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230473
    Circadian metabolic adaptations to infections.
    Claudio Costantini, Stefano Brancorsini, Francesco Grignani, Luigina Romani, Marina Maria Bellet.
      Circadian clocks are biological oscillators that evolved to coordinate rhythms in behaviour and physiology around the 24-hour day. In mammalian tissues, circadian rhythms and metabolism are highly intertwined. The clock machinery controls rhythmic levels of circulating hormones and metabolites, as well as rate-limiting enzymes catalysing biosynthesis or degradation of macromolecules in metabolic tissues, such control being exerted both at the transcriptional and post-transcriptional level. During infections, major metabolic adaptation occurs in mammalian hosts, at the level of both the single immune cell and the whole organism. Under these circumstances, the rhythmic metabolic needs of the host intersect with those of two other players: the pathogen and the microbiota. These three components cooperate or compete to meet their own metabolic demands across the 24 hours. Here, we review findings describing the circadian regulation of the host response to infection, the circadian metabolic adaptations occurring during host-microbiota-pathogen interactions and how such regulation can influence the immune response of the host and, ultimately, its own survival.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.
    Keywords:  circadian clock; immune response; metabolism; microbiota; pathogen
    DOI:  https://doi.org/10.1098/rstb.2023.0473
  8. Nature. 2025 Jan 22.
    Cancer cells 'poison' the immune system with tainted mitochondria.
    Asher Mullard.
      
    Keywords:  Cancer; Cell biology; Immunology
    DOI:  https://doi.org/10.1038/d41586-025-00176-2
  9. EMBO J. 2025 Jan 17.
    SLC13A2 promotes hepatocyte metabolic remodeling and liver regeneration by enhancing de novo cholesterol biosynthesis.
    Li Shi, Hao Chen, Yuxin Zhang, Donghao An, Mengyao Qin, Wanting Yu, Bin Wen, Dandan He, Haiping Hao, Jing Xiong.
      Metabolic requirements of dividing hepatocytes are prerequisite for liver regeneration after injury. In contrast to transcriptional dynamics during liver repair, its metabolic dependencies remain poorly defined. Here, we screened metabolic genes differentially regulated during liver regeneration, and report that SLC13A2, a transporter for TCA cycle intermediates, is decreased in rapid response to partial hepatectomy in mice and recovered along restoration of liver mass and function. Liver-specific overexpression or depletion of SLC13A2 promoted or attenuated liver regeneration, respectively. SLC13A2 increased cleavage of SREBP2, and expression of cholesterol metabolism genes, including LDLR and HMGCR. Mechanistically, SLC13A2 promotes import of citrate into hepatocytes, serving as building block for ACLY-dependent acetyl-CoA formation and de novo synthesis of cholesterol. In line, the pre-administration of the HMGCR inhibitor lovastatin abolished SLC13A2-mediated liver regeneration. Similarly, ACLY inhibition suppressed SLC13A2-promoted cholesterol synthesis for hepatocellular proliferation and liver regeneration in vivo. In sum, this study demonstrates that citrate transported by SLC13A2 acts as an intermediate metabolite to restore the metabolic homeostasis during liver regeneration, suggesting SLC13A2 as a potential drug target after liver damage.
    Keywords:  ATP-citate Lyase; Cell Division; De Novo Cholesterol Synthesis; Metabolic Remodeling; Partial Hepatectomy; TCA Cycle
    DOI:  https://doi.org/10.1038/s44318-025-00362-y
  10. Trends Cell Biol. 2025 Jan 21. pii: S0962-8924(25)00001-7. [Epub ahead of print]
    Splice age: mTORC1-mediated RNA splicing in metabolism and ageing.
    Pablo Lanuza-Gracia, Jonas Juan-Mateu, Juan Valcárcel.
      The target of rapamycin complex mTORC1 has key roles in cell growth and metabolism and its inhibition delays ageing. Recent work by Ogawa et al. in Caenorhabditis elegans argues that modulation of pre-mRNA splicing factors and alternative splicing are key mediators of mTORC1 signalling and can enhance longevity.
    DOI:  https://doi.org/10.1016/j.tcb.2025.01.001
  11. bioRxiv. 2025 Jan 09. pii: 2025.01.08.631936. [Epub ahead of print]
    Impaired oxidative phosphorylation drives primary tumor escape and metastasis.
    Emily N Arner, Erin Q Jennings, Daniel R Crooks, Christopher J Ricketts, Melissa M Wolf, Matthew A Cottam, Emilie L Fisher-Gupta, Martin Lang, Nunziata Maio, Yuki Shibata, Evan S Krystofiak, Logan M Vlach, Zaid Hatem, Alexander M Blatt, Darren R Heintzman, Allison E Sewell, Emma S Hathaway, KayLee K Steiner, Xiang Ye, Samuel Schaefer, Zachary A Bacigalupa, W Marston Linehan, Kathryn E Beckermann, Frank M Mason, Kamran Idrees, W Kimryn Rathmell, Jeffrey C Rathmell.
      Metastasis causes most cancer deaths and reflects transitions from primary tumor escape to seeding and growth at metastatic sites. Epithelial-to-mesenchymal transition (EMT) is important early in metastasis to enable cancer cells to detach from neighboring cells, become migratory, and escape the primary tumor. While different phases of metastasis expose cells to variable nutrient environments and demands, the metabolic requirements and plasticity of each step are uncertain. Here we show that EMT and primary tumor escape are stimulated by disrupted oxidative metabolism. Using Renal Cell Carcinoma (RCC) patient samples, we identified the mitochondrial electron transport inhibitor NDUFA4L2 as upregulated in cells undergoing EMT. Deletion of NDUFA4L2 enhanced oxidative metabolism and prevented EMT and metastasis while NDUFA4L2 overexpression enhanced these processes. Mechanistically, NDUFA4L2 suppressed oxidative phosphorylation and caused citric acid cycle intermediates to accumulate, which modified chromatin accessibility of EMT-related loci to drive primary tumor escape. The effect of impaired mitochondrial metabolism to drive EMT appeared general, as renal cell carcinoma patient tumors driven by fumarate hydratase mutations with disrupted oxidative phosphorylation were highly metastatic and also had robust EMT. These findings highlight the importance of dynamic shifts in metabolism for cell migration and metastasis, with mitochondrial impairment driving early phases of this process. Understanding mitochondrial dynamics may have important implications in both basic and translational efforts to prevent cancer deaths.
    DOI:  https://doi.org/10.1101/2025.01.08.631936
  12. Cell Rep. 2025 Jan 18. pii: S2211-1247(25)00015-4. [Epub ahead of print]44(2): 115244
    The adult table: Chronic intermittent fasting improves β cell health only in adults.
    Kathrin Maedler, Heena Pahwa.
      Intermittent fasting (IF) improves metabolic health in some individuals but increases health risks in others. Matta et al. now show that IF oppositely affects β cells depending on age: beneficial at old but deleterious at young age.
    Keywords:  CP: Metabolism
    DOI:  https://doi.org/10.1016/j.celrep.2025.115244
  13. Sci Adv. 2025 Jan 24. 11(4): eadq9301
    Mitochondrial fatty acid oxidation regulates monocytic type I interferon signaling via histone acetylation.
    Jing Wu, Komudi Singh, Vivian Shing, Anand Gupta, Brett C Arenberg, Rebecca D Huffstutler, Duck-Yeon Lee, Michael N Sack.
      Although lipid-derived acetyl-coenzyme A (CoA) is a major carbon source for histone acetylation, the contribution of fatty acid β-oxidation (FAO) to this process remains poorly characterized. To investigate this, we generated mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1, distal FAO enzyme) knockout macrophages. 13C-carbon tracing confirmed reduced FA-derived carbon incorporation into histone H3, and RNA sequencing identified diminished interferon-stimulated gene expression in the absence of ACAT1. Chromatin accessibility at the Stat1 locus was diminished in ACAT1-/- cells. Chromatin immunoprecipitation analysis demonstrated reduced acetyl-H3 binding to Stat1 promoter/enhancer regions, and increasing histone acetylation rescued Stat1 expression. Interferon-β release was blunted in ACAT1-/- and recovered by ACAT1 reconstitution. Furthermore, ACAT1-dependent histone acetylation required an intact acetylcarnitine shuttle. Last, obese subjects' monocytes exhibited increased ACAT1 and histone acetylation levels. Thus, our study identifies an intriguing link between FAO-mediated epigenetic control of type I interferon signaling and uncovers a potential mechanistic nexus between obesity and type I interferon signaling.
    DOI:  https://doi.org/10.1126/sciadv.adq9301
  14. Sci Transl Med. 2025 Jan 22. 17(782): eadr4049
    Hypoxia as a medicine.
    Robert S Rogers, Vamsi K Mootha.
      Oxygen is essential for human life, yet a growing body of preclinical research is demonstrating that chronic continuous hypoxia can be beneficial in models of mitochondrial disease, autoimmunity, ischemia, and aging. This research is revealing exciting new and unexpected facets of oxygen biology, but translating these findings to patients poses major challenges, because hypoxia can be dangerous. Overcoming these barriers will require integrating insights from basic science, high-altitude physiology, clinical medicine, and sports technology. Here, we explore the foundations of this nascent field and outline a path to determine how chronic continuous hypoxia can be safely, effectively, and practically delivered to patients.
    DOI:  https://doi.org/10.1126/scitranslmed.adr4049
  15. Cell Metab. 2025 Jan 15. pii: S1550-4131(24)00496-0. [Epub ahead of print]
    Mannose: A game-changer for T cell immunotherapy.
    Jingwei Ma, Shuai Tong, Jingxuan Xiao, Bo Huang.
      Metabolism influences the behavior of various immune cell types. In a recent Cancer Cell study, Qiu et al. revealed mannose metabolism as a prominent metabolic feature of tumor precursor exhausted T cells (Tpex) that is crucial for maintaining T cell stemness. Their work uncovers a novel metabolic mechanism that decouples T cell proliferation from differentiation, providing valuable insights into how metabolic modulation can be used to generate "better" T cells during the manufacturing process.
    DOI:  https://doi.org/10.1016/j.cmet.2024.12.014
  16. bioRxiv. 2025 Jan 06. pii: 2025.01.06.631537. [Epub ahead of print]
    FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis.
    Mike Lange, Michele Wölk, Cody E Doubravsky, Joseph M Hendricks, Shunji Kato, Yurika Otoki, Benjamin Styler, Kiyotaka Nakagawa, Maria Fedorova, James A Olzmann.
      Lipid droplets (LDs) are organelles that store and supply lipids based on cellular needs. While mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here, we identify LD-localized Ferroptosis Suppressor Protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidation in vitro. Notably, polyunsaturated fatty acid (PUFA)-rich triacylglycerols enhance cancer cell sensitivity to FSP1 loss and inducing PUFA-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the buildup of oxidized lipids and induction of ferroptosis.
    DOI:  https://doi.org/10.1101/2025.01.06.631537
  17. Sci Adv. 2025 Jan 24. 11(4): eadr2282
    The oxygen level in air directs airway epithelial cell differentiation by controlling mitochondrial citrate export.
    Bo Ram Kim, Adam J Rauckhorst, Michael S Chimenti, Tayyab Rehman, Henry L Keen, Philip H Karp, Eric B Taylor, Michael J Welsh.
      Oxygen controls most metazoan metabolism, yet in mammals, tissue O2 levels vary widely. While extensive research has explored cellular responses to hypoxia, understanding how cells respond to physiologically high O2 levels remains uncertain. To address this problem, we investigated respiratory epithelia as their contact with air exposes them to some of the highest O2 levels in the body. We asked how the O2 level in air controls differentiation of airway basal stem cells into the ciliated epithelial cells essential for clearing airborne pathogens from the lung. Through a metabolomics screen and 13C tracing on primary cultures of human airway basal cells, we found that the O2 level in air directs ciliated cell differentiation by increasing mitochondrial citrate export. Unexpectedly, disrupting mitochondrial citrate export elicited hypoxia transcriptional responses independently of HIF1α stabilization and at O2 levels that would be hyperoxic for most tissues. These findings identify mitochondrial citrate export as a cellular mechanism for responding to physiologically high O2 levels.
    DOI:  https://doi.org/10.1126/sciadv.adr2282
  18. Nature. 2025 Jan 17.
    RNA molecule rejuvenates ageing mice by restoring old cells.
    Chris Simms.
      
    Keywords:  Ageing
    DOI:  https://doi.org/10.1038/d41586-025-00032-3
  19. Transl Lung Cancer Res. 2024 Dec 31. 13(12): 3692-3717
    Fuel for thought: targeting metabolism in lung cancer.
    Jaime L Schneider, SeongJun Han, Christopher S Nabel.
      For over a century, we have appreciated that the biochemical processes through which micro- and macronutrients are anabolized and catabolized-collectively referred to as "cellular metabolism"-are reprogrammed in malignancies. Cancer cells in lung tumors rewire pathways of nutrient acquisition and metabolism to meet the bioenergetic demands for unchecked proliferation. Advances in precision medicine have ushered in routine genotyping of patient lung tumors, enabling a deeper understanding of the contribution of altered metabolism to tumor biology and patient outcomes. This paradigm shift in thoracic oncology has spawned a new enthusiasm for dissecting oncogenotype-specific metabolic phenotypes and creates opportunity for selective targeting of essential tumor metabolic pathways. In this review, we discuss metabolic states across histologic and molecular subtypes of lung cancers and the additional changes in tumor metabolic pathways that occur during acquired therapeutic resistance. We summarize the clinical investigation of metabolism-specific therapies, addressing successes and limitations to guide the evaluation of these novel strategies in the clinic. Beyond changes in tumor metabolism, we also highlight how non-cellular autonomous processes merit particular consideration when manipulating metabolic processes systemically, such as efforts to disentangle how lung tumor cells influence immunometabolism. As the future of metabolic therapeutics hinges on use of models that faithfully recapitulate metabolic rewiring in lung cancer, we also discuss best practices for harmonizing workflows to capture patient specimens for translational metabolic analyses.
    Keywords:  Lung cancer; immunometabolism; metabolism; resistance
    DOI:  https://doi.org/10.21037/tlcr-24-662
  20. Sci Adv. 2025 Jan 24. 11(4): eadq7307
    Mitochondrial respiratory complex III sustains IL-10 production in activated macrophages and promotes tumor-mediated immune evasion.
    Alessia Zotta, Juliana Toller-Kawahisa, Eva M Palsson-McDermott, Shane M O'Carroll, Órlaith C Henry, Emily A Day, Anne F McGettrick, Ross W Ward, Dylan G Ryan, Mark A Watson, Martin D Brand, Marah C Runtsch, Kathrin Maitz, Anna Lueger, Julia Kargl, Jan L Miljkovic, Ed C Lavelle, Luke A J O'Neill.
      The cytokine interleukin-10 (IL-10) limits the immune response and promotes resolution of acute inflammation. Because of its immunosuppressive effects, IL-10 up-regulation is a common feature of tumor progression and metastasis. Recently, IL-10 regulation has been shown to depend on mitochondria and redox-sensitive signals. We have found that Suppressor of site IIIQo Electron Leak 1.2 (S3QEL 1.2), a specific inhibitor of reactive oxygen species (ROS) production from mitochondrial complex III, and myxothiazol, a complex III inhibitor, decrease IL-10 in lipopolysaccharide (LPS)-activated macrophages. IL-10 down-regulation is likely to be mediated by suppression of c-Fos, which is a subunit of activator protein 1 (AP1), a transcription factor required for IL-10 gene expression. S3QEL 1.2 impairs IL-10 production in vivo after LPS challenge and promotes the survival of mice bearing B16F10 melanoma by lowering tumor growth. Our data identify a link between complex III-dependent ROS generation and IL-10 production in macrophages, the targeting of which could have potential in boosting antitumor immunity.
    DOI:  https://doi.org/10.1126/sciadv.adq7307
  21. Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230346
    Circadian gating: concepts, processes, and opportunities.
    Pirita Paajanen, Jacqueline M Kimmey, Antony N Dodd.
      Circadian clocks provide a biological measure of time that coordinates metabolism, physiology and behaviour with 24 h cycles in the environment. Circadian systems have a variety of characteristic properties, such as entrainment to environmental cues, a self-sustaining rhythm of about 24 h and temperature compensation of the circadian rhythm. In this perspective, we discuss the process of circadian gating, which refers to the restriction of a biological event to particular times of day by the circadian clock. We introduce principles and processes associated with circadian gating in a variety of organisms, including some associated mechanisms. We highlight socioeconomic opportunities presented by the investigation of circadian gating, using selected examples from circadian medicine and agricultural crop production to illustrate its importance.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.
    Keywords:  agriculture; chronobiology; chronotherapy; circadian gating; circadian rhythms
    DOI:  https://doi.org/10.1098/rstb.2023.0346
  22. Cancer Res. 2025 Jan 22.
    SMAD4 and KRAS Status Shape Cancer Cell-Stromal Crosstalk and Therapeutic Response in Pancreatic Cancer.
    Eloise G Lloyd, Muntadher Jihad, Judhell S Manansala, Wenlong Li, Priscilla S W Cheng, Gianluca Mucciolo, Marta Zaccaria, Sara Pinto Teles, Joaquín Araos Henríquez, Sneha Harish, Rebecca Brais, Sally Ashworth, Weike Luo, Paul M Johnson, Lisa Veghini, Mireia Vallespinos, Vincenzo Corbo, Giulia Biffi.
      Pancreatic ductal adenocarcinoma (PDAC) contains an extensive stroma that modulates response to therapy, contributing to the dismal prognosis associated with this cancer. Evidence suggests that PDAC stromal composition is shaped by mutations within malignant cells, but most previous work has focused on pre-clinical models driven by KrasG12D and mutant Trp53. Elucidation of the contribution of additional known oncogenic drivers, including KrasG12V mutation and Smad4 loss, is needed to increase understanding of malignant cell-stroma crosstalk in PDAC. Here, we used single-cell RNA-sequencing to analyze the cellular landscape of Trp53-mutant mouse models driven by KrasG12D or KrasG12V in which Smad4 was wild-type or deleted. KrasG12D Smad4-deleted PDAC developed a fibro-inflammatory rich stroma with increased malignant JAK/STAT cell signaling and enhanced therapeutic response to JAK/STAT inhibition. SMAD4 loss in KrasG12V PDAC differently altered the tumor microenvironment compared to KrasG12D PDAC, and the malignant compartment lacked JAK/STAT signaling dependency. Thus, malignant cell genotype impacts cancer cell and stromal cell phenotypes in PDAC, directly affecting therapeutic efficacy.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-2330
  23. Nature. 2025 Jan 22.
    Immune evasion through mitochondrial transfer in the tumour microenvironment.
    Hideki Ikeda, Katsushige Kawase, Tatsuya Nishi, Tomofumi Watanabe, Keizo Takenaga, Takashi Inozume, Takamasa Ishino, Sho Aki, Jason Lin, Shusuke Kawashima, Joji Nagasaki, Youki Ueda, Shinichiro Suzuki, Hideki Makinoshima, Makiko Itami, Yuki Nakamura, Yasutoshi Tatsumi, Yusuke Suenaga, Takao Morinaga, Akiko Honobe-Tabuchi, Takehiro Ohnuma, Tatsuyoshi Kawamura, Yoshiyasu Umeda, Yasuhiro Nakamura, Yukiko Kiniwa, Eiki Ichihara, Hidetoshi Hayashi, Jun-Ichiro Ikeda, Toyoyuki Hanazawa, Shinichi Toyooka, Hiroyuki Mano, Takuji Suzuki, Tsuyoshi Osawa, Masahito Kawazu, Yosuke Togashi.
      Cancer cells in the tumour microenvironment use various mechanisms to evade the immune system, particularly T cell attack1. For example, metabolic reprogramming in the tumour microenvironment and mitochondrial dysfunction in tumour-infiltrating lymphocytes (TILs) impair antitumour immune responses2-4. However, detailed mechanisms of such processes remain unclear. Here we analyse clinical specimens and identify mitochondrial DNA (mtDNA) mutations in TILs that are shared with cancer cells. Moreover, mitochondria with mtDNA mutations from cancer cells are able to transfer to TILs. Typically, mitochondria in TILs readily undergo mitophagy through reactive oxygen species. However, mitochondria transferred from cancer cells do not undergo mitophagy, which we find is due to mitophagy-inhibitory molecules. These molecules attach to mitochondria and together are transferred to TILs, which results in homoplasmic replacement. T cells that acquire mtDNA mutations from cancer cells exhibit metabolic abnormalities and senescence, with defects in effector functions and memory formation. This in turn leads to impaired antitumour immunity both in vitro and in vivo. Accordingly, the presence of an mtDNA mutation in tumour tissue is a poor prognostic factor for immune checkpoint inhibitors in patients with melanoma or non-small-cell lung cancer. These findings reveal a previously unknown mechanism of cancer immune evasion through mitochondrial transfer and can contribute to the development of future cancer immunotherapies.
    DOI:  https://doi.org/10.1038/s41586-024-08439-0
  24. bioRxiv. 2025 Jan 14. pii: 2025.01.14.633047. [Epub ahead of print]
    KAT6A acetylation drives metabolic adaptation to mediate cellular growth and mitochondrial metabolism through AMPK interaction.
    Mariko Aoyagi Keller, Andreas Ivessa, Tong Liu, Hong Li, Peter J Romanienko, Michinari Nakamura.
      Diets influence metabolism and disease susceptibility, with lysine acetyltransferases (KATs) serving as key regulators through acetyl-CoA. We have previously demonstrated that a ketogenic diet alleviates cardiac pathology, though the underlying mechanisms remain largely unknown. Here we show that KAT6A acetylation is crucial for mitochondrial function and cell growth. Proteomic analysis revealed that KAT6A is acetylated at lysine (K)816 in the hearts of mice fed a ketogenic diet under hypertension, which enhances its interaction with AMPK regulatory subunits. RNA-sequencing analysis demonstrated that the KAT6A acetylation-mimetic mutant stimulates AMPK signaling in cardiomyocytes. Moreover, the acetylation-mimetic mutant mitigated phenylephrine-induced mitochondrial dysfunction and cardiomyocyte hypertrophy via AMPK activation. However, KAT6A-K816R acetylation-resistant knock-in mice unexpectedly exhibited smaller hearts with enhanced AMPK activity, conferring protection against neurohumoral stress-induced cardiac hypertrophy and remodeling. These findings indicate that KAT6A regulates metabolism and cellular growth by interacting with and modulating AMPK activity through K816-acetylation in a cell type-specific manner.
    DOI:  https://doi.org/10.1101/2025.01.14.633047
  25. Cell Metab. 2025 Jan 15. pii: S1550-4131(24)00490-X. [Epub ahead of print]
    Ergothioneine improves healthspan of aged animals by enhancing cGPDH activity through CSE-dependent persulfidation.
    Dunja Petrovic, Luke Slade, Yiorgos Paikopoulos, Davide D'Andrea, Nevena Savic, Ana Stancic, Jan Lj Miljkovic, Thibaut Vignane, Maria Kyriaki Drekolia, Dusan Mladenovic, Nikola Sutulovic, Alice Refeyton, Milica Kolakovic, Vladimir M Jovanovic, Jasmina Zivanovic, Marko Miler, Valentina Vellecco, Vincenzo Brancaleone, Mariarosaria Bucci, Alva M Casey, ChakShun Yu, Siva Swapna Kasarla, Karl William Smith, Ayten Kalfe-Yildiz, Martin Stenzel, Antonio Miranda-Vizuete, Roland Hergenröder, Prasad Phapale, Olivera Stanojlovic, Ivana Ivanovic-Burmazovic, Marija Vlaski-Lafarge, Sofia-Iris Bibli, Michael P Murphy, Vesna Otasevic, Milos R Filipovic.
      Ergothioneine (ET), a dietary thione/thiol, is receiving growing attention for its possible benefits in healthy aging and metabolic resilience. Our study investigates ET's effects on healthspan in aged animals, revealing lifespan extension and enhanced mobility in Caenorhabditis elegans, accompanied by improved stress resistance and reduced age-associated biomarkers. In aged rats, ET administration enhances exercise endurance, muscle mass, and vascularization, concomitant with higher NAD+ levels in muscle. Mechanistically, ET acts as an alternative substrate for cystathionine gamma-lyase (CSE), stimulating H2S production, which increases protein persulfidation of more than 300 protein targets. Among these, protein-persulfidation-driven activation of cytosolic glycerol-3-phosphate dehydrogenase (cGPDH) primarily contributes to the ET-induced NAD+ increase. ET's effects are abolished in models lacking CSE or cGPDH, highlighting the essential role of H2S signaling and protein persulfidation. These findings elucidate ET's multifaceted actions and provide insights into its therapeutic potential for combating age-related muscle decline and metabolic perturbations.
    Keywords:  NAD; ergothioneine; healthspan; hydrogen sulfide; persulfidation
    DOI:  https://doi.org/10.1016/j.cmet.2024.12.008
  26. Nat Commun. 2025 Jan 20. 16(1): 867
    Palmitoylation-dependent regulation of GPX4 suppresses ferroptosis.
    Bin Huang, Hui Wang, Shuo Liu, Meng Hao, Dan Luo, Yi Zhou, Ying Huang, Yong Nian, Lei Zhang, Bo Chu, Chengqian Yin.
      S-palmitoylation is a reversible and widespread post-translational modification, but its role in the regulation of ferroptosis has been poorly understood. Here, we elucidate that GPX4, an essential regulator of ferroptosis, is reversibly palmitoylated on cysteine 66. The acyltransferase ZDHHC20 palmitoylates GPX4 and increases its protein stability. ZDHHC20 depletion or inhibition of protein palmitoylation by 2-BP sensitizes cancer cells to ferroptosis. Moreover, we identify APT2 as the depalmitoylase of GPX4. Genetic silencing or pharmacological inhibition of APT2 with ML349 increases GPX4 palmitoylation, thereby stabilizing the protein and conferring resistance to ferroptosis. Notably, disrupting GPX4 palmitoylation markedly potentiates ferroptosis in xenografted and orthotopically implanted tumor models, and inhibits tumor metastasis through blood vessels. In the chemically induced colorectal cancer model, knockout of APT2 significantly aggravates cancer progression. Furthermore, pharmacologically modulating GPX4 palmitoylation impacts liver ischemia-reperfusion injury. Overall, our findings uncover the intricate network regulating GPX4 palmitoylation, highlighting its pivotal role in modulating ferroptosis sensitivity.
    DOI:  https://doi.org/10.1038/s41467-025-56344-5
  27. FASEB J. 2025 Jan 31. 39(2): e70277
    mTOR Ser1261 is an AMPK-dependent phosphosite in mouse and human skeletal muscle not required for mTORC2 activity.
    Jingwen Li, Agnete B Madsen, Jonas R Knudsen, Carlos Henriquez-Olguin, Kaspar W Persson, Zhencheng Li, Steffen H Raun, Tianjiao Li, Bente Kiens, Jørgen F P Wojtaszewski, Erik A Richter, Leonardo Nogara, Bert Blaauw, Riki Ogasawara, Thomas E Jensen.
      The kinases AMPK, and mTOR as part of either mTORC1 or mTORC2, are major orchestrators of cellular growth and metabolism. Phosphorylation of mTOR Ser1261 is reportedly stimulated by both insulin and AMPK activation and a regulator of both mTORC1 and mTORC2 activity. Intrigued by the possibilities that Ser1261 might be a convergence point between insulin and AMPK signaling in skeletal muscle, we investigated the regulation and function of this site using a combination of human exercise, transgenic mouse, and cell culture models. Ser1261 phosphorylation on mTOR did not respond to insulin in any of our tested models, but instead responded acutely to contractile activity in human and mouse muscle in an AMPK activity-dependent manner. Contraction-stimulated mTOR Ser1261 phosphorylation in mice was decreased by Raptor muscle knockout (mKO) and increased by Raptor muscle overexpression, yet was not affected by Rictor mKO, suggesting most of Ser1261 phosphorylation occurs within mTORC1 in skeletal muscle. In accordance, HEK293 cells mTOR Ser1261Ala mutation strongly impaired phosphorylation of mTORC1 substrates but not mTORC2 substrates. However, neither mTORC1 nor mTORC2-dependent phosphorylations were affected in muscle-specific kinase-dead AMPK mice with no detectable mTOR Ser1261 phosphorylation in skeletal muscle. Thus, mTOR Ser1261 is an exercise but not insulin-responsive AMPK-dependent phosphosite in human and murine skeletal muscle, playing an unclear role in mTORC1 regulation but clearly not required for mTORC2 activity.
    Keywords:  AMPK; exercise; mTORC1; mTORC2; skeletal muscle
    DOI:  https://doi.org/10.1096/fj.202402064R
  28. Kidney Int. 2025 Feb;pii: S0085-2538(24)00811-1. [Epub ahead of print]107(2): 225-227
    The mitochondrial choline transporter, SLC25A48, regulates urine and blood choline levels in humans.
    Soumya Maity, Kumar Sharma.
      Choline is an essential nutrient for the biosynthesis of phospholipids and neurotransmitters and controls several physiological functions in mammals. It is metabolized in the organelles within cells, including mitochondria. However, its subcellular distribution and mode of mitochondrial transport remain poorly understood. Patil et al. identified SLC25A48 as a mitochondrial choline transporter, and its loss-of-function mutations were associated with elevated urine and plasma choline levels in humans.
    DOI:  https://doi.org/10.1016/j.kint.2024.11.014
  29. bioRxiv. 2025 Jan 06. pii: 2025.01.06.631511. [Epub ahead of print]
    Tissue-specific modulation of NADH consumption as an anti-aging intervention in Drosophila.
    Shweta Yadav, Xingxiu Pan, Shengxi Li, Paige LaRae Martin, Ngoc Hoang, Kejin Chen, Aditi Karhadkar, Jatin Malhotra, Austin L Zuckerman, Subrata Munan, Markus K Klose, Lin Wang, Valentin Cracan, Andrey A Parkhitko.
      Aging is characterized by extensive metabolic dysregulation. Redox coenzyme nicotinamide adenine dinucleotide (NAD) can exist in oxidized (NAD+) or reduced (NADH) states, which together form a key NADH/NAD+ redox pair. Total levels of NAD decline with age in a tissue-specific manner, thereby playing a significant role in the aging process. Supplementation with NAD precursors boosts total cellular NAD levels and provides some therapeutic benefits in human clinical trials. However, supplementation studies cannot determine tissue-specific effects of an altered NADH/NAD+ ratio. Here, we created transgenic Drosophila expressing a genetically encoded xenotopic tool LbNOX to directly manipulate the cellular NADH/NAD+ ratio. We found that LbNOX expression in Drosophila impacts both NAD(H) and NADP(H) metabolites in a sex-specific manner. LbNOX rescues neuronal cell death induced by the expression of mutated alpha-B crystallin in the Drosophila eye, a widely used system to study reductive stress. Utilizing LbNOX, we demonstrate that targeting redox NAD metabolism in different tissues may have drastically different outcomes, as the expression of LbNOX solely in the muscle is much more effective for rescuing paraquat-induced oxidative stress compared to whole-body expression. Excitingly, we demonstrate that perturbing NAD(P) metabolism in non-neuronal tissues is sufficient to rejuvenate sleep profiles in aged flies to a youthful state. In summary, we used xenotopic tool LbNOX to identify tissues and metabolic processes which benefited the most from the modulation of the NAD metabolism thereby highlighting important aspects of rebalancing the NAD and NADP pools, all of which can be translated into novel designs of NAD-related human clinical trials.
    Keywords:  B-mediated reductive stress; Drosophila; LbNOX; NAD+; NADH; NADP+; NADPH; aging; mitochondria; mutated α-crystallin; xenotopic tool
    DOI:  https://doi.org/10.1101/2025.01.06.631511
  30. Blood. 2025 Jan 22. pii: blood.2024027207. [Epub ahead of print]
    CD44-Mediated Metabolic Rewiring is A Targetable Dependency of IDH-Mutant Leukemia.
    Junhua Lyu, Yuxuan Liu, Ningning Liu, Hieu Vu, Feng Cai, Hui Cao, Pranita Kaphle, Zheng Wu, Giovanni A Botten, Yuannyu Zhang, Jin Wang, Sarada Achyutuni, Xiaofei Gao, Ilaria Iacobucci, Charles G Mullighan, Stephen S Chung, Min Ni, Ralph J DeBerardinis, Jian Xu.
      Recurrent IDH mutations catalyze NADPH-dependent production of oncometabolite R-2HG for tumorigenesis. IDH inhibition provides clinical response in a subset of acute myeloid leukemia (AML) cases; however, most patients develop resistance, highlighting the need for more effective IDH-targeting therapies. By comparing transcriptomic alterations in isogenic leukemia cells harboring CRISPR base-edited IDH mutations, we identify the activation of adhesion molecules including CD44, a transmembrane glycoprotein, as a shared feature of IDH-mutant leukemia, consistent with elevated CD44 expression in IDH-mutant AML patients. CD44 is indispensable for IDH-mutant leukemia cells through activating pentose phosphate pathway and inhibiting glycolysis by phosphorylating G6PD and PKM2, respectively. This metabolic rewiring ensures efficient NADPH generation for mutant IDH-catalyzed R-2HG production. Combining IDH inhibition with CD44 blockade enhances the elimination of IDH-mutant leukemia cells. Hence, we describe an oncogenic feedforward pathway involving CD44-mediated metabolic rewiring for oncometabolite production, representing a targetable dependency of IDH-mutant malignancies.
    DOI:  https://doi.org/10.1182/blood.2024027207
  31. Cell Genom. 2025 Jan 16. pii: S2666-979X(24)00373-2. [Epub ahead of print] 100744
    Single-cell DNA sequencing reveals pervasive positive selection throughout preleukemic evolution.
    Gladys Poon, Aditi Vedi, Mathijs Sanders, Elisa Laurenti, Peter Valk, Jamie R Blundell.
      The representation of driver mutations in preleukemic hematopoietic stem cells (pHSCs) provides a window into the somatic evolution that precedes acute myeloid leukemia (AML). Here, we isolate pHSCs from the bone marrow of 16 patients diagnosed with AML and perform single-cell DNA sequencing on thousands of cells to reconstruct phylogenetic trees of the major driver clones in each patient. We develop a computational framework that can infer levels of positive selection operating during preleukemic evolution from the statistical properties of these phylogenetic trees. Combining these data with 67 previously published phylogenetic trees, we find that the highly variable structures of preleukemic trees emerge naturally from a simple model of somatic evolution with pervasive positive selection typically in the range of 9%-24% per year. At these levels of positive selection, we show that the identification of early multiple-mutant clones could be used to identify individuals at risk of future AML.
    Keywords:  acute myeloid leukemia; cancer evolution; clonal hematopoiesis; early detection; evolutionary dynamics; pre-cancer; somatic mutation
    DOI:  https://doi.org/10.1016/j.xgen.2024.100744
  32. MedComm (2020). 2025 Feb;6(2): e70062
    A novel allosteric driver mutation of β-glucuronidase promotes head and neck squamous cell carcinoma progression through STT3B-mediated PD-L1 N-glycosylation.
    Zhonglong Liu, Xiaoyan Meng, Xiao Tang, Jian Zhang, Zhiyuan Zhang, Yue He.
      Head and neck squamous cell carcinoma (HNSCC) develops and advances because of the accumulation of somatic mutations located in orthosteric and allosteric areas. However, the biological effects of allosteric driver mutations during tumorigenesis are mostly unknown. Here, we mapped somatic mutations generated from 10 tumor-normal matched HNSCC samples into allosteric sites to prioritize the mutated allosteric proteins via whole-exome sequencing and AlloDriver, identifying the specific mutation H351Q in β-glucuronidase (GUSB), a lysosomal enzyme, as a novel allosteric driver mutation, which considerably encouraged HNSCC progression both in vitro and in vivo. Mechanistically, the allosteric mutation of H351Q remarkably attenuated protein trafficking from the endoplasmic reticulum (ER) to lysosomes, leading to ER retention, in which GUSB-H351Q facilitated the aberrant N-glycosylation of PD-L1 through increasing protein stability and mRNA transcripts of the STT3 oligosaccharyltransferase complex catalytic subunit B, an oligosaccharyltransferase complex. Moreover, GUSB-H351Q reshaped a more immunosuppressive microenvironment featuring increased infiltration of exhausted CD8+ T cells and remodeled tumor metabolism, characterized by increased activity of the purine metabolism pathways and pyruvic acid accumulation. This study provides a mechanism-driven approach to overcoming HNSCC progression and immune evasion and identifies novel druggable targets based on the presence of GUSB allosteric driver mutation.
    Keywords:  PD‐L1; STT3B; allosteric driver mutation; glycosylation; head and neck squamous cell carcinoma (HNSCC); β‐glucuronidase (GUSB)
    DOI:  https://doi.org/10.1002/mco2.70062
  33. Nature. 2025 Jan 22.
    Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted.
    Miguel Reina-Campos, Alexander Monell, Amir Ferry, Vida Luna, Kitty P Cheung, Giovanni Galletti, Nicole E Scharping, Kennidy K Takehara, Sara Quon, Peter P Challita, Brigid Boland, Yun Hsuan Lin, William H Wong, Cynthia S Indralingam, Hayley Neadeau, Suzie Alarcón, Gene W Yeo, John T Chang, Maximilian Heeg, Ananda W Goldrath.
      Tissue-resident memory CD8 T (TRM) cells provide protection from infection at barrier sites. In the small intestine, TRM cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential1. However, the origins of this diversity remain unknown. Here we proposed that distinct tissue niches drive the phenotypic heterogeneity of TRM cells. To test this, we leveraged spatial transcriptomics of human samples, a mouse model of acute systemic viral infection and a newly established strategy for pooled optically encoded gene perturbations to profile the locations, interactions and transcriptomes of pathogen-specific TRM cell differentiation at single-transcript resolution. We developed computational approaches to capture cellular locations along three anatomical axes of the small intestine and to visualize the spatiotemporal distribution of cell types and gene expression. Our study reveals that the regionalized signalling of the intestinal architecture supports two distinct TRM cell states: differentiated TRM cells and progenitor-like TRM cells, located in the upper villus and lower villus, respectively. This diversity is mediated by distinct ligand-receptor activities, cytokine gradients and specialized cellular contacts. Blocking TGFβ or CXCL9 and CXCL10 sensing by antigen-specific CD8 T cells revealed a model consistent with anatomically delineated, early fate specification. Ultimately, our framework for the study of tissue immune networks reveals that T cell location and functional state are fundamentally intertwined.
    DOI:  https://doi.org/10.1038/s41586-024-08466-x
  34. Oncogene. 2025 Jan 17.
    Evidence of DNA methylation heterogeneity and epipolymorphism in kidney cancer tissue samples.
    Sabrina H Rossi, Victoria Dombrowe, Laura Godfrey, Teodora Bucaciuc Mracica, Sara Pita, Toby Milne-Clark, Justicia Kyeremeh, Gahee Park, Christopher G Smith, Radoslaw P Lach, Anne Babbage, Anne Y Warren, Thomas J Mitchell, Grant D Stewart, Roland Schwarz, Charlie E Massie.
      Clear cell renal cell carcinoma (ccRCC) is characterised by significant genetic heterogeneity, which has diagnostic and prognostic implications. Very limited evidence is available regarding DNA methylation heterogeneity. We therefore generate sequence level DNA methylation data on 136 multi-region tumour and normal kidney tissue from 18 ccRCC patients, along with matched whole exome sequencing (85 samples) and gene expression (47 samples) data on a subset of samples. We perform a comprehensive systematic analysis of heterogeneity between patients, within a patient and within a sample. We demonstrate that bulk methylation data may be deconvoluted into cell-type-specific latent methylation components (LMCs), and that LMC1, which is likely to represent T cells, is associated with prognostic parameters. Differential epipolymorphism was noted between ccRCC and normal tissue in the promoter region of genes which are known to be associated with kidney cancer. This was externally validated in an independent cohort of 71 ccRCC and normal kidney tissues. Differential epipolymorphism in the gene promoter was a predictor of gene expression, after adjusting for average methylation. This represents the first evaluation of epipolymorphism in ccRCC and suggests that gains and losses in methylation disorder may have a functional relevance, gleaning important information on tumourigenesis.
    DOI:  https://doi.org/10.1038/s41388-024-03270-3
  35. Mol Cell. 2025 Jan 16. pii: S1097-2765(24)01007-4. [Epub ahead of print]85(2): 262-275
    Metabolism-driven chromatin dynamics: Molecular principles and technological advances.
    Varun Sahu, Chao Lu.
      Cells integrate metabolic information into core molecular processes such as transcription to adapt to environmental changes. Chromatin, the physiological template of the eukaryotic genome, has emerged as a sensor and rheostat for fluctuating intracellular metabolites. In this review, we highlight the growing list of chromatin-associated metabolites that are derived from diverse sources. We discuss recent advances in our understanding of the mechanisms by which metabolic enzyme activities shape the chromatin structure and modifications, how specificity may emerge from their seemingly broad effects, and technologies that facilitate the study of epigenome-metabolome interplay. The recognition that metabolites are immanent components of the chromatin regulatory network has significant implications for the evolution, function, and therapeutic targeting of the epigenome.
    Keywords:  chromatin; epigenome; histone acylation; histone methylation; metabolism; oncometabolite; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2024.12.012
  36. Curr Biol. 2025 Jan 20. pii: S0960-9822(24)01646-4. [Epub ahead of print]35(2): R76-R79
    Mitochondria mechanosensing: The powerhouse fueling cellular force signaling.
    Jorge Oliver-De La Cruz, Pere Roca-Cusachs.
      Mechanical forces influence mitochondrial dynamics through previously unexplored mechanisms. A new study demonstrates that actomyosin tension inhibits mitochondrial fission by phosphorylating a key component of the fission complex and that this event regulates the nuclear accumulation of critical transcription factors.
    DOI:  https://doi.org/10.1016/j.cub.2024.12.006
  37. Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230477
    Circadian rhythms: pervasive, and often times evasive.
    Luis F Larrondo.
      Most circadian texts begin by stating that clocks are pervasive throughout the tree of life. Indeed, clock mechanisms have been described from cyanobacteria to humans, representing a notable example of convergent evolution: yet, there are several phyla in animals, protists or within fungi and bacteria, in which homologs of some-or all-known clock components seem to be absent, posing inevitable questions about the evolution of circadian systems. Moreover, as we move away from model organisms, there are several taxa in which core clock elements can be identified at the genomic levels. However, the functional description of those putative clocks has been hard to achieve, as rhythmicity is not observed unless defined abiotic or nutritional cues are provided. The mechanisms 'conditioning' the functionality of clocks remain uncertain, emphasizing the need to delve further into non-model circadian systems. As the absence of evidence is not evidence of absence, the lack of known core-clock homologs or of observable rhythms in a given organism, cannot be an a priori criterion to discard the presence of a functional clock, as rhythmicity may be limited to yet untested experimental conditions or phenotypes. This article seeks to reflect on these topics, highlighting some of the pressing questions awaiting to be addressed.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.
    Keywords:  TTFL; circadian rhythms; conditional rhythms; evolution; fungal clocks
    DOI:  https://doi.org/10.1098/rstb.2023.0477
  38. Proc Natl Acad Sci U S A. 2025 Jan 28. 122(4): e2420005122
    Complement C3 of tumor-derived extracellular vesicles promotes metastasis of RCC via recruitment of immunosuppressive myeloid cells.
    Yibi Zhang, Xiaodong Wang, Yinmin Gu, Tongfeng Liu, Xujie Zhao, Shuwen Cheng, Liqiang Duan, Chang Huang, Songzhe Wu, Shan Gao.
      Heterogeneous roles of complement C3 have been implicated in tumor metastasis and are highly context dependent. However, the underlying mechanisms linking C3 to tumor metastasis remain elusive in renal cell carcinoma (RCC). Here, we demonstrate that C3 of RCC cell-derived extracellular vesicles (EVs) contributes to metastasis via polarizing tumor-associated macrophages (TAMs) into the immunosuppressive phenotype and recruiting polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs). Mechanistically, EV C3 induces the secretion of CCL2 and CXCL1 by lung macrophages and subsequently enhances TAM polarization and PMN-MDSC recruitment. Notably, targeting the CCL2/CCR2 or CXCL1/CXCR2 axis with the inhibitors RS504393 or Navarixin, respectively, effectively suppresses lung metastasis induced by RCC-derived C3 in a mouse model. Clinically, RCC patients with high expression of C3 demonstrate poor prognosis. Collectively, our findings reveal that tumor-derived EV C3 induces an immunosuppressive tumor microenvironment via TAMs, and thus promoting RCC metastasis.
    Keywords:  PMN-MDSCs; RCC; TAMs; metastasis; tumor-derived EV C3
    DOI:  https://doi.org/10.1073/pnas.2420005122
  39. Sci Adv. 2025 Jan 24. 11(4): eads2664
    Cryo-EM structure and regulation of human NAD kinase.
    Prakash P Praharaj, Yang Li, Charline Mary, Mona H Soflaee, Kevin Ryu, Dohun Kim, Diem H Tran, Trishna Dey, Harrison J Tom, Halie Rion, Muriel Gelin, Andrew Lemoff, Lauren G Zacharias, João S Patricio, Thomas P Mathews, Zhe Chen, Corinne Lionne, Gerta Hoxhaj, Gilles Labesse.
      Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a crucial reducing cofactor for reductive biosynthesis and protection from oxidative stress. To fulfill their heightened anabolic and reductive power demands, cancer cells must boost their NADPH production. Progrowth and mitogenic protein kinases promote the activity of cytosolic NAD kinase (NADK), which produces NADP+, a limiting NADPH precursor. However, the molecular architecture and mechanistic regulation of human NADK remain undescribed. Here, we report the cryo-electron microscopy structure of human NADK, both in its apo-form and in complex with its substrate NAD+ (nicotinamide adenine dinucleotide), revealing a tetrameric organization with distinct structural features. We discover that the amino (N)- and carboxyl (C)-terminal tails of NADK have opposing effects on its enzymatic activity and cellular NADP(H) levels. Specifically, the C-terminal region is critical for NADK activity, whereas the N-terminal region exhibits an inhibitory role. This study highlights molecular insights into the regulation of a vital enzyme governing NADP(H) production.
    DOI:  https://doi.org/10.1126/sciadv.ads2664
  40. Nat Rev Cancer. 2025 Jan 20.
    Metabolic interplays between the tumour and the host shape the tumour macroenvironment.
    Patricia Altea-Manzano, Amanda Decker-Farrell, Tobias Janowitz, Ayelet Erez.
      Metabolic reprogramming of cancer cells and the tumour microenvironment are pivotal characteristics of cancers, and studying these processes offer insights and avenues for cancer diagnostics and therapeutics. Recent advancements have underscored the impact of host systemic features, termed macroenvironment, on facilitating cancer progression. During tumorigenesis, these inherent features of the host, such as germline genetics, immune profile and the metabolic status, influence how the body responds to cancer. In parallel, as cancer grows, it induces systemic effects beyond the primary tumour site and affects the macroenvironment, for example, through inflammation, the metabolic end-stage syndrome of cachexia, and metabolic dysregulation. Therefore, understanding the intricate metabolic interplay between the tumour and the host is a growing frontier in advancing cancer diagnosis and therapy. In this Review, we explore the specific contribution of the metabolic fitness of the host to cancer initiation, progression and response to therapy. We then delineate the complex metabolic crosstalk between the tumour, the microenvironment and the host, which promotes disease progression to metastasis and cachexia. The metabolic relationships among the host, cancer pathogenesis and the consequent responsive systemic manifestations during cancer progression provide new perspectives for mechanistic cancer therapy and improved management of patients with cancer.
    DOI:  https://doi.org/10.1038/s41568-024-00786-4
  41. Bioessays. 2025 Jan 19. e202400203
    Mechanisms of Lipid-Associated Macrophage Accrual in Metabolically Stressed Adipose Tissue.
    Isabel Reinisch, Sarah Enzenhofer, Andreas Prokesch.
      Adipose tissue (AT) inflammation, a hallmark of the metabolic syndrome, is triggered by overburdened adipocytes sending out immune cell recruitment signals during obesity development. An AT immune landscape persistent throughout weight loss and regain constitutes an immune-obesogenic memory that hinders long-term weight loss management. Lipid-associated macrophages (LAMs) are emerging as major players in diseased, inflamed metabolic tissues and may be key contributors to an obesogenic memory in AT. Our previous study found that LAM abundance increases with weight loss via intermittent fasting (IF) in obese mice, which is driven by adipocyte p53 signalling. However, the specific signals causing LAM accumulation in AT under IF remain unknown. In this piece, we hypothesise on a range of adipocyte-secreted signals that can harbor immune-attractive features upon fasting/refeeding cycles. We highlight possible mechanisms including cell death signalling, matrikines, and other damage-associated molecular patterns (DAMPs), as well as adipo(-cyto)kines, lipid mediators, metabolites, extracellular vesicles, and epigenetic rewiring. Finally, we consider how advances in mechanisms of AT LAM recruitment gleaned from preclinical models might be translatable to long-term weight management in humans. Thus, we provide vantage points to study signals driving monocyte recruitment, polarisation towards LAMs, and LAM retention, to harness the therapeutic potential of modulating AT LAM levels by impacting the immune-obesogenic memory in metabolic disease.
    Keywords:  adipose; lipid‐associated macrophages; metabolic syndrome; metaflammation; obesity
    DOI:  https://doi.org/10.1002/bies.202400203
  42. Nat Metab. 2025 Jan 20.
    Aldolase A: the broker of glycolysis.
    Luiza Martins Nascentes Melo, Feyza Cansiz, Alpaslan Tasdogan.
      
    DOI:  https://doi.org/10.1038/s42255-024-01202-9
  43. Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230344
    Chronic CRYPTOCHROME deficiency enhances cell-intrinsic antiviral defences.
    Christine T Major-Styles, Jack Munns, Aiwei Zeng, Michael Vanden Oever, John S O'Neill, Rachel S Edgar.
      The within-host environment changes over circadian time and influences the replication and severity of viruses. Genetic knockout of the circadian transcription factors CRYPTOCHROME 1 and CRYPTOCHROME 2 (CRY1-/-/CRY2-/-; CKO) leads to altered protein homeostasis and chronic activation of the integrated stress response (ISR). The adaptive ISR signalling pathways help restore cellular homeostasis by downregulating protein synthesis in response to endoplasmic reticulum overloading or viral infections. By quantitative mass spectrometry analysis, we reveal that many viral recognition proteins and type I interferon (IFN) effectors are significantly upregulated in lung fibroblast cells from CKO mice compared with wild-type (WT) mice. This basal 'antiviral state' restricts the growth of influenza A virus and is governed by the interaction between proteotoxic stress response pathways and constitutive type I IFN signalling. CKO proteome composition and type I IFN signature were partially phenocopied upon sustained depletion of CRYPTOCHROME (CRY) proteins using a small-molecule CRY degrader, with modest differential gene expression consistent with differences seen between CKO and WT cells. Our results highlight the crosstalk between circadian rhythms, cell-intrinsic antiviral defences and protein homeostasis, providing a tractable molecular model to investigate the interface of these key contributors to human health and disease.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.
    Keywords:  CRYPTOCHROME; circadian rhythms; integrated stress response; interferon; protein homeostasis; virus
    DOI:  https://doi.org/10.1098/rstb.2023.0344
  44. Cell. 2025 Jan 14. pii: S0092-8674(24)01379-5. [Epub ahead of print]
    Long somatic DNA-repeat expansion drives neurodegeneration in Huntington's disease.
    Robert E Handsaker, Seva Kashin, Nora M Reed, Steven Tan, Won-Seok Lee, Tara M McDonald, Kiely Morris, Nolan Kamitaki, Christopher D Mullally, Neda R Morakabati, Melissa Goldman, Gabriel Lind, Rhea Kohli, Elisabeth Lawton, Marina Hogan, Kiku Ichihara, Sabina Berretta, Steven A McCarroll.
      In Huntington's disease (HD), striatal projection neurons (SPNs) degenerate during midlife; the core biological question involves how the disease-causing DNA repeat (CAG)n in the huntingtin (HTT) gene leads to neurodegeneration after decades of biological latency. We developed a single-cell method for measuring this repeat's length alongside genome-wide RNA expression. We found that the HTT CAG repeat expands somatically from 40-45 to 100-500+ CAGs in SPNs. Somatic expansion from 40 to 150 CAGs had no apparent cell-autonomous effect, but SPNs with 150-500+ CAGs lost positive and then negative features of neuronal identity, de-repressed senescence/apoptosis genes, and were lost. Our results suggest that somatic repeat expansion beyond 150 CAGs causes SPNs to degenerate quickly and asynchronously. We conclude that in HD, at any one time, most neurons have an innocuous but unstable HTT gene and that HD pathogenesis is a DNA process for almost all of a neuron's life.
    Keywords:  CAG; DNA repeats; Huntington’s disease; neurodegeneration; repeat instability; single-nucleus RNA-seq; somatic expansion; striatal projection neurons; triplet repeat disorders
    DOI:  https://doi.org/10.1016/j.cell.2024.11.038
  45. Appl Environ Microbiol. 2025 Jan 22. e0142224
    Effects of vitamin B12 supply on cellular processes of the facultative vitamin B12 consumer Vibrio campbellii.
    Luna-Agrippina Groon, Stefan Bruns, Leon Dlugosch, Heinz Wilkes, Gerrit Wienhausen.
      Vitamin B12 (cobalamin, herein B12) is a key cofactor for most organisms being involved in essential metabolic processes. In microbial communities, B12 is often scarce, largely because only few prokaryotes can synthesize B12 de novo and are thus considered B12-prototrophs. B12-auxotrophy is mostly manifested by the absence of the B12-independent methionine synthase, MetE. Here, we focus on bacteria that we classified as facultative B12 consumers as they encode both B12-independent and -dependent (MetH) methionine synthases yet largely cannot synthesize B12 de novo. The genus Vibrio belongs to this group, and our work shows that upon B12 supply growth of Vibrio campbellii is accelerated and autoinducer-2 (AI-2) concentrations are enhanced. We speculate that methionine synthesis efficiency, dependent on B12 availability, is linked to AI-2 synthesis. The precursor for AI-2 synthesis is S-adenosyl-L-homocysteine (SAH), which in turn requires methionine as a precursor. In almost all Vibrio species studied, btuF (B12-binding protein), which is required for B12 uptake, and cobD (Adenosylcobinamide-phosphate synthase), which enables remodeling of B12-like compounds, are encoded on the same operon as pfs (or mtnN, Adenosylhomocysteine nucleosidase), the first enzyme in the two-step AI-2 synthesis reaction. Transcriptomic analyses show that virulence factors, such as toxin synthesis, fimbriae formation, and activation of the type-6 secretion system, which have been shown to be regulated by quorum sensing via AI-2, are significantly upregulated in V. campbellii when B12 is available. Our results demonstrate that V. campbellii is a facultative B12 consumer and indicate that B12 availability affects AI-2 levels and thus potentially virulence factor regulation.IMPORTANCEMetabolites play a key role in microbial metabolism and communication. While vitamin B12 is an essential cofactor for important enzymatic reactions, autoinducer-2 mediates interspecies signaling and can regulate the expression of genes that are crucial for virulence and survival. In our study, we hypothesize and present findings how these two important metabolites are linked in Vibrio species. Vibrio campbellii grows without B12 but at an accelerated rate when B12 is present, and we detect higher AI-2 values in cultures with B12 amendment. Transcriptome analyses show how vitamin B12 availability significantly upregulates gene expression of virulence factors such as toxin synthesis, fimbrial formation, and activation of the type-6 secretion system in V. campbellii.
    Keywords:  Gammaproteobacteria; Vibrio campbellii; Vibrionales; autoinducer-2; facultative vitamin B12 consumer; methionine; virulence factor; vitamin B12
    DOI:  https://doi.org/10.1128/aem.01422-24
  46. Trends Cell Biol. 2025 Jan 20. pii: S0962-8924(24)00283-6. [Epub ahead of print]
    Current and future perspectives of lysine lactylation in cancer.
    Sijia Li, Lixia Dong, Kui Wang.
      Lactate, a glycolytic intermediate, has a crucial role in cancer metabolism and microenvironment remodeling. Recently, researchers found that lactate mediates lysine lactylation, a novel protein post-translational modification (PTM). Here, we summarize the mechanism and role of lysine lactylation in cancer, and discuss the potential of targeting lysine lactylation in cancer therapy.
    Keywords:  cancer; lactate; lactylation; tumor metabolism; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.tcb.2024.12.015
  47. FEBS J. 2025 Jan 21.
    Succinate receptor 1 signaling mutually depends on subcellular localization and cellular metabolism.
    Aenne-Dorothea Liebing, Philipp Rabe, Petra Krumbholz, Christian Zieschang, Franziska Bischof, Angela Schulz, Susan Billig, Claudia Birkemeyer, Thanigaimalai Pillaiyar, Mikel Garcia-Marcos, Robert Kraft, Claudia Stäubert.
      Succinate is a pivotal tricarboxylic acid cycle metabolite but also specifically activates the Gi- and Gq-coupled succinate receptor 1 (SUCNR1). Contradictory roles of succinate and succinate-SUCNR1 signaling include reports about its anti- or pro-inflammatory effects. The link between cellular metabolism and localization-dependent SUCNR1 signaling qualifies as a potential cause for the reported conflicts. To systematically address this connection, we used a diverse set of methods, including several bioluminescence resonance energy transfer-based biosensors, dynamic mass redistribution measurements, second messenger and kinase phosphorylation assays, calcium imaging, and metabolic analyses. Different cellular metabolic states were mimicked using glucose (Glc) or glutamine (Gln) as available energy substrates to provoke differential endogenous succinate (SUC) production. We show that SUCNR1 signaling, localization, and metabolism are mutually dependent, with SUCNR1 showing distinct spatial and energy substrate-dependent Gi and Gq protein activation. We found that Gln-consumption associated with a higher rate of oxidative phosphorylation causes increased extracellular SUC concentrations, accompanied by a higher rate of SUCNR1 internalization, reduced miniGq protein recruitment to the plasma membrane, and lower Ca2+ signals. In Glc, under basal conditions, SUCNR1 causes stronger Gq than Gi protein activation, while the opposite is true upon stimulation with an agonist. In addition, SUCNR1 specifically interacts with miniG proteins in endosomal compartments. In THP-1 cells, polarized to M2-like macrophages, endogenous SUCNR1-mediated Gi signaling stimulates glycolysis, while Gq signaling inhibits the glycolytic rate. Our results suggest that the metabolic context determines spatially dependent SUCNR1 signaling, which in turn modulates cellular energy homeostasis and mediates adaptations to changes in SUC concentrations.
    Keywords:  SUCNR1; macrophages; metabolism; signal transduction; succinate
    DOI:  https://doi.org/10.1111/febs.17407
  48. Nature. 2025 Jan 22.
    CD45-PET is a robust, non-invasive tool for imaging inflammation.
    Ali Salehi Farid, Jennifer E Rowley, Harris H Allen, Isabella G Kruger, Soheil Tavakolpour, Kyle Neeley, Min Cong, Haneyeh Shahbazian, Niki Dorafshani, Achraf Berrada, Alexander C MacDonagh, Robert F Padera, Pedro Brugarolas, Alan B Packard, Matthew W Rosenbaum, Sanjay Divakaran, Marcelo F Di Carli, Mohammad Rashidian.
      Imaging inflammation holds immense potential for advancing the diagnosis, treatment and prognosis of many conditions1-3. The lack of a specific and sensitive positron emission tomography (PET) probe to detect inflammation is a critical challenge. To bridge this gap, we present CD45-PET imaging, which detects inflammation with exceptional sensitivity and clarity in several preclinical models. Notably, the intensity of the CD45-PET signal correlates robustly with the severity of disease in models of inflammatory lung and bowel diseases, outperforming 18F-fluorodeoxyglucose PET, the most widely used imaging modality for inflammation globally. Longitudinal CD45-PET imaging further enables precise monitoring of dynamic changes in tissue-specific inflammatory profiles. Finally, we developed a human CD45-PET probe for clinical translation that effectively detects human immune cells in a humanized mouse model. CD45-PET imaging holds substantial clinical promise, offering a tool for guiding diagnostic and therapeutic decisions for inflammatory diseases through a precise, whole-body assessment of the inflammation profiles of individual patients.
    DOI:  https://doi.org/10.1038/s41586-024-08441-6
  49. Aging Cell. 2025 Jan 21. e14483
    Aging and Cancer-Inextricably Linked Across the Lifespan.
    James DeGregori, Katherine J Seidl, Monty Montano.
      Aging (as old man wind) alters the trajectory of cancer (dangerous seas) through changes in the immune system and metabolism (among many others), leading to altered cancer epidemiology, pathogenesis, and therapeutic responses, as represented by the research areas (boats)-artwork by Michael DeGregori.
    DOI:  https://doi.org/10.1111/acel.14483
  50. Evol Med Public Health. 2025 ;13(1): 1-4
    Rethinking cancer evolution: from genetic mutations to complex information systems in tumor reversion.
    Mesut Tez.
      Cancer research has historically focused on the somatic mutation theory, viewing cancer as a consequence of genetic mutations. However, this perspective has limitations in explaining phenomena like tumor reversion and cancer heterogeneity. This paper introduces an alternative approach: viewing cancer as a complex information-processing system shaped by its microenvironment. By integrating historical data on tumor reversion and insights into evolutionary dynamics, I propose a reframing of cancer biology. This process-oriented perspective highlights the role of cellular plasticity and adaptive behaviors, offering new pathways for therapeutic development.
    Keywords:  cancer; evolution; genetic; information systems; mutations
    DOI:  https://doi.org/10.1093/emph/eoae032
  51. Sci Adv. 2025 Jan 24. 11(4): eadu5787
    Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.
    Felix Kraus, Yuchen He, Sharan Swarup, Katherine A Overmyer, Yizhi Jiang, Johann Brenner, Cristina Capitanio, Anna Bieber, Annie Jen, Nicole M Nightingale, Benton J Anderson, Chan Lee, Joao A Paulo, Ian R Smith, Jürgen M Plitzko, Steven P Gygi, Brenda A Schulman, Florian Wilfling, Joshua J Coon, J Wade Harper.
      Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multiomic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lysophosphatidylcholine species and multilamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.
    DOI:  https://doi.org/10.1126/sciadv.adu5787
  52. J Dermatol Sci. 2025 Jan 09. pii: S0923-1811(25)00002-7. [Epub ahead of print]
    Aberrant fumarate metabolism links interferon release in diffuse systemic sclerosis.
    Thomas Steadman, Steven O'Reilly.
       BACKGROUND: Systemic Sclerosis (SSc) is an idiopathic rheumatic inflammatory disease that is characterised by inflammation and skin fibrosis. Type I interferon is significantly elevated in the disease.
    OBJECTIVE: The objective of this study is to determine the role of the TCA cycle metabolite fumarate in SSc.
    METHODS: CD14 + cells were isolated from 12 SSc patients and healthy controls. Fumarate hydratase and Interferon dependant genes were quantified by qPCR. In vitro inhibition of STING using a small molecule STING inhibitor and enforced mitophagy was induced in vitro and IFN-β release was quantified. VDAC1 inhibitor was used to determine the role of mt DNA release in IFN-β induction. In whole skin biopsies fumarate and succinate was quantified.
    RESULTS: Fumarate Hydratase is significantly reduced in SSc monocytes. Type I interferon is also elevated in monocytes from SSc donors compared to controls. The mitochondrial-specific stress marker GDF-15 was significantly elevated in SSc monocytes. Blockade of the cGAS-STING pathway chemically reduced interferon-β release and induced mitophagy also retarded release of the cytokine in response to LPS stimulation. Inhibition of VDAC1 mitigated IFN-β, as did the depletion of mitochondria in cells. Furthermore, the itaconate derivative 4-octyl itaconate reduced IFN-β induction in SSc monocytes, that was downstream of mitochondrial nucleic acid release. Fumarate, but not succinate was elevated in whole skin biopsies.
    CONCLUSION: Fumarate metabolism links interferon release in SSc and may underlie the aberrant expression of interferon in SSc via cytosolic DNA released from mitochondria.
    Keywords:  CGAS; DNA; Fibrosis; Fumarate hydratase; Interferon; STING; Systemic sclerosis
    DOI:  https://doi.org/10.1016/j.jdermsci.2025.01.002
  53. Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230483
    PERspectives on circadian cell biology.
    Andrei Mihut, John S O'Neill, Carrie L Partch, Priya Crosby.
      Daily rhythms in the activities of PERIOD proteins are critical to the temporal regulation of mammalian physiology. While the molecular partners and genetic circuits that allow PERIOD to effect auto-repression and regulate transcriptional programmes are increasingly well understood, comprehension of the time-resolved mechanisms that allow PERIOD to conduct this daily dance is incomplete. Here, we consider the character and controversies of this central mammalian clock protein with a focus on its intrinsically disordered nature.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.
    Keywords:  PERIOD/ PER; biomolecular condensation/ phase separation; cellular clock; circadian rhythm; intrinsically disordered regions (IDRs); post-translational modification
    DOI:  https://doi.org/10.1098/rstb.2023.0483
  54. Science. 2025 Jan 24. 387(6732): eadn7277
    Lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension.
    Lloyd D Harvey, Mona Alotaibi, Yi-Yin Tai, Ying Tang, Hee-Jung J Kim, Neil J Kelly, Wei Sun, Chen-Shan C Woodcock, Sanya Arshad, Miranda K Culley, Wadih El Khoury, Rong Xie, Yassmin Al Aaraj, Jingsi Zhao, Neha Hafeez, Rashmi J Rao, Siyi Jiang, Vinny Negi, Anna Kirillova, Dror Perk, Annie M Watson, Claudette M St Croix, Donna B Stolz, Ji Young Lee, Mary Hongying Cheng, Manling Zhang, Samuel Detmer, Edward Guzman, Rajith S Manan, Rajan Saggar, Kathleen J Haley, Aaron B Waxman, Satoshi Okawa, Tae-Hwi Schwantes-An, Michael W Pauciulo, Bing Wang, Amy Webb, Caroline Chauvet, Daniel G Anderson, William C Nichols, Ankit A Desai, Robert Lafyatis, S Mehdi Nouraie, Haodi Wu, Jeffrey G McDonald, Susan Cheng, Ivet Bahar, Thomas Bertero, Raymond L Benza, Mohit Jain, Stephen Y Chan.
      Vascular inflammation regulates endothelial pathophenotypes, particularly in pulmonary arterial hypertension (PAH). Dysregulated lysosomal activity and cholesterol metabolism activate pathogenic inflammation, but their relevance to PAH is unclear. Nuclear receptor coactivator 7 (NCOA7) deficiency in endothelium produced an oxysterol and bile acid signature through lysosomal dysregulation, promoting endothelial pathophenotypes. This oxysterol signature overlapped with a plasma metabolite signature associated with human PAH mortality. Mice deficient for endothelial Ncoa7 or exposed to an inflammatory bile acid developed worsened PAH. Genetic predisposition to NCOA7 deficiency was driven by single-nucleotide polymorphism rs11154337, which alters endothelial immunoactivation and is associated with human PAH mortality. An NCOA7-activating agent reversed endothelial immunoactivation and rodent PAH. Thus, we established a genetic and metabolic paradigm that links lysosomal biology and oxysterol processes to endothelial inflammation and PAH.
    DOI:  https://doi.org/10.1126/science.adn7277
  55. J Physiol Sci. 2024 ;pii: S1880-6546(24)00088-X. [Epub ahead of print]74(1): 1
    Identification of three distinct cell populations for urate excretion in human kidneys.
    Yoshihiko M Sakaguchi, Pattama Wiriyasermkul, Masaya Matsubayashi, Masaki Miyasaka, Nau Sakaguchi, Yoshiki Sahara, Minoru Takasato, Kaoru Kinugawa, Kazuma Sugie, Masahiro Eriguchi, Kazuhiko Tsuruya, Hiroki Kuniyasu, Shushi Nagamori, Eiichiro Mori.
      In humans, uric acid is an end-product of purine metabolism. Urate excretion from the human kidney is tightly regulated by reabsorption and secretion. At least eleven genes have been identified as human renal urate transporters. However, it remains unclear whether all renal tubular cells express the same set of urate transporters. Here, we show renal tubular cells are divided into three distinct cell populations for urate handling. Analysis of healthy human kidneys at single-cell resolution revealed that not all tubular cells expressed the same set of urate transporters. Only 32% of tubular cells were related to both reabsorption and secretion, while the remaining tubular cells were related to either reabsorption or secretion at 5% and 63%, respectively. These results provide physiological insight into the molecular function of the transporters and renal urate handling on single-cell units. Our findings suggest that three different cell populations cooperate to regulate urate excretion from the human kidney, and our proposed framework is a step forward in broadening the view from the molecular to the cellular level of transport capacity.
    Keywords:  Gout; Human kidney; Single nucleus RNA-sequencing; Solute carriers; Transporter; Uric acid
    DOI:  https://doi.org/10.1186/s12576-023-00894-0
  56. Cell Rep. 2025 Jan 21. pii: S2211-1247(24)01575-4. [Epub ahead of print]44(2): 115224
    Redox proteomics reveal a role for peroxiredoxinylation in stress protection.
    Gerhard Seisenbacher, Zrinka Raguz Nakic, Eva Borràs, Eduard Sabidó, Uwe Sauer, Eulalia de Nadal, Francesc Posas.
      The redox state of proteins is essential for their function and guarantees cell fitness. Peroxiredoxins protect cells against oxidative stress, maintain redox homeostasis, act as chaperones, and transmit hydrogen peroxide signals to redox regulators. Despite the profound structural and functional knowledge of peroxiredoxins action, information on how the different functions are concerted is still scarce. Using global proteomic analyses, we show here that the yeast peroxiredoxin Tsa1 interacts with many proteins of essential biological processes, including protein turnover and carbohydrate metabolism. Several of these interactions are of a covalent nature, and we show that failure of peroxiredoxinylation of Gnd1 affects its phosphogluconate dehydrogenase activity and impairs recovery upon stress. Thioredoxins directly remove TSA1-formed mixed disulfide intermediates, thus expanding the role of the thioredoxin-peroxiredoxin redox cycle pair to buffer the redox state of proteins.
    Keywords:  CP: Molecular biology; Tsa1; oxidative stress; peroxiredoxins; redox biology; stress
    DOI:  https://doi.org/10.1016/j.celrep.2024.115224
  57. Cancer Cell. 2025 Jan 13. pii: S1535-6108(24)00483-5. [Epub ahead of print]
    A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer.
    Amelia Acha-Sagredo, Pietro Andrei, Kalum Clayton, Emma Taggart, Carlotta Antoniotti, Chloé A Woodman, Hassnae Afrache, Constance Fourny, Maria Armero, Hafsa Kaja Moinudeen, Mary Green, Nisha Bhardwaj, Anna Mikolajczak, Maria Rodriguez-Lopez, Marg Crawford, Emma Connick, Steven Lim, Philip Hobson, Josep Linares, Ekaterina Ignatova, Diana Pelka, Elizabeth C Smyth, Nikolaos Diamantis, Dominika Sosnowska, Martina Carullo, Paolo Ciraci, Francesca Bergamo, Rossana Intini, Emma Nye, Patricia Barral, Michele Mishto, James N Arnold, Sara Lonardi, Chiara Cremolini, Elisa Fontana, Manuel Rodriguez-Justo, Francesca D Ciccarelli.
      Fewer than 50% of metastatic deficient mismatch repair (dMMR) colorectal cancer (CRC) patients respond to immune checkpoint inhibition (ICI). Identifying and expanding this patient population remains a pressing clinical need. Here, we report that an interferon-high immunophenotype locally enriched in cytotoxic lymphocytes and antigen-presenting macrophages is required for response. This immunophenotype is not exclusive to dMMR CRCs but comprises a subset of MMR proficient (pMMR) CRCs. Single-cell spatial analysis and in vitro cell co-cultures indicate that interferon-producing cytotoxic T cells induce overexpression of antigen presentation in adjacent macrophages and tumor cells, including MHC class II invariant chain CD74. dMMR CRCs expressing high levels of CD74 respond to ICI and a subset of CD74 high pMMR CRC patients show better progression free survival when treated with ICI. Therefore, CD74 abundance can identify the constitutive interferon-high immunophenotype determining clinical benefit in CRC, independently of tumor mutational burden or MMR status.
    Keywords:  CD74; antigen presentation; colorectal cancer; immunotherapy; interferon; marker of response; patient stratification; spatial transcriptomics; tumor immune microenvironment
    DOI:  https://doi.org/10.1016/j.ccell.2024.12.008
  58. Sci Signal. 2025 Jan 21. 18(870): eadv9441
    Bypassing senescence.
    Annalisa M VanHook.
      A metabolic switch enables hepatocytes in damaged livers to escape senescence and form tumors.
    DOI:  https://doi.org/10.1126/scisignal.adv9441
  59. Autophagy. 2025 Jan 19.
    Mammalian nucleophagy: process and function.
    Fujian Ji, Enyong Dai, Rui Kang, Daniel J Klionsky, Tong Liu, Yu Hu, Daolin Tang, Kun Zhu.
      The nucleus is a highly specialized organelle that houses the cell's genetic material and regulates key cellular activities, including growth, metabolism, protein synthesis, and cell division. Its structure and function are tightly regulated by multiple mechanisms to ensure cellular integrity and genomic stability. Increasing evidence suggests that nucleophagy, a selective form of autophagy that targets nuclear components, plays a critical role in preserving nuclear integrity by clearing dysfunctional nuclear materials such as nuclear proteins (lamins, SIRT1, and histones), DNA-protein crosslinks, micronuclei, and chromatin fragments. Impaired nucleophagy has been implicated in aging and various pathological conditions, including cancer, neurodegeneration, autoimmune disorders, and neurological injury. In this review, we focus on nucleophagy in mammalian cells, discussing its mechanisms, regulation, and cargo selection, as well as evaluating its therapeutic potential in promoting human health and mitigating disease.
    Keywords:  Autophagy; disease; micronucleus; nuclear quality control; nucleophagy
    DOI:  https://doi.org/10.1080/15548627.2025.2455158
  60. Dev Cell. 2025 Jan 20. pii: S1534-5807(24)00757-3. [Epub ahead of print]60(2): 171-173
    Plasticity in metastatic colorectal cancer.
    Frederick J H Whiting, Trevor A Graham.
      Genetic mutations cause colorectal cancer (CRC) initiation, but their contribution to metastasis and therapy resistance is less clear. In a recent issue of Nature, Moorman et al.1 use single-cell transcriptome sequencing to map the changes in cancer cell state (cell phenotypes) that occur through CRC progression.
    DOI:  https://doi.org/10.1016/j.devcel.2024.12.018
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