bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2025–11–23
fifty-four papers selected by
Christian Frezza, Universität zu Köln
  1. Succinate puts the brakes on de novo purine synthesis.
  2. An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice.
  3. Mitochondrial Transfer Rescues Respiration to Support De Novo Pyrimidine Biosynthesis and Tumor Progression.
  4. Hepatocyte mitochondrial NAD+ content is limiting for liver regeneration.
  5. How one nutrient controls cell size.
  6. FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer.
  7. Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis.
  8. Mitochondrial NAD+ gradient sustained by membrane potential and transport.
  9. Homeostatic control of energy metabolism by monocyte-derived macrophages.
  10. Mitochondrial transfer at the crossroads of cancer, stromal, and immune cells.
  11. Hepatic zonation determines tumorigenic potential of mutant β-catenin.
  12. Glutamine-Dependent Slc25a39-Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment.
  13. SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.
  14. Branched chain amino acids and their aberrant metabolism in cancer.
  15. The mitochondrial protein TMEM177 fine-tunes mammalian cytochrome c oxidase assembly.
  16. Integration and Intersection of Cancer Metabolism with Epigenetic Pathways in Gliomas.
  17. Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models.
  18. Guidelines for T cell nomenclature.
  19. Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.
  20. Quantifying Mitochondrial Metabolism and Metabolic Fluxes in Soft Agar Cultures.
  21. Succinate Dehydrogenase-Deficient Cancer Cells Have Increased Susceptibility to Ym155 Induced DNA Damage.
  22. A unified mechanism for mitochondrial damage sensing in PINK1-Parkin-mediated mitophagy.
  23. SLC7A8 is essential for metabolic fitness and function of Th2 cells.
  24. AMPK opens the door to organelle memory and longevity.
  25. Methionine regulates antitumor function of CD8 + T cells through polyamine synthesis.
  26. Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane.
  27. Unifying regulatory motifs in endocrine circuits.
  28. Metformin inhibits mitochondrial complex I in intestinal epithelium to promote glycemic control.
  29. Dietary protein governs the role of insulin signaling in the postprandial regulation of hepatic mTORC1.
  30. The role and implications of mammalian cellular circadian entrainment.
  31. Retrograde mitochondrial transport regulates mitochondrial biogenesis in zebrafish neurons.
  32. Two decades of FFAR4 biology: From nutrient sensing to therapeutic targeting.
  33. DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency.
  34. Structures of human organellar SPFH protein complexes.
  35. Measuring mitochondrial membrane potential.
  36. The metabolic engine of cognition: microglia-neuron interactions in health, ageing and disease.
  37. Rac1 promotes proximal tubule kidney repair by coupling the actin cytoskeleton to mitochondrial function.
  38. Miniature NAD+-II riboswitches control bacterial genes for nicotinamide salvage and de novo NAD+ biosynthesis.
  39. Targeting the Powerhouse: A Critical Review of Mitochondrial Inhibitors as a Therapeutic Strategy in Lung Cancer.
  40. Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine.
  41. Sequelae and reversal of age-dependent alterations in mitochondrial dynamics via autophagy enhancement in reprogrammed human neurons.
  42. Analysis of Cellular Metabolism Using Flow Cytometry.
  43. Leveraging biochemical covariance to better understand biology.
  44. Tissue expansion-enhanced mass-spectrometry imaging decodes biomolecular landscapes.
  45. Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.
  46. Genetic architecture of the murine red blood cell proteome reveals central role of hemoglobin beta cysteine 93 in maintaining redox balance.
  47. Bacillus subtilis encodes three N-acetylcysteine deacetylase enzymes that can catalyze the final step in S-(2-succino)cysteine breakdown.
  48. Tumour-reactive heterotypic CD8 T cell clusters from clinical samples.
  49. Mitochondria relay cholesterol signal exacerbates osteoarthritis in mice.
  50. Prime editing-installed suppressor tRNAs for disease-agnostic genome editing.
  51. Regulation of intestinal injury via dietary cysteine.
  52. Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy.
  53. The efficacy of longevity interventions in Caenorhabditis elegans is determined by the early life activity of RNA splicing factors.
  54. Glutathionylated DNA adducts accumulate in mitochondrial DNA and are regulated by AP endonuclease 1 and tyrosyl-DNA phosphodiesterase 1.
  1. Mol Cell. 2025 Nov 20. pii: S1097-2765(25)00861-5. [Epub ahead of print]85(22): 4109-4110
    Succinate puts the brakes on de novo purine synthesis.
    Timothy C Kenny, Kıvanç Birsoy.
      In this issue of Molecular Cell, Nengroo et al.1 report that the tricarboxylic acid (TCA) cycle enzyme succinate dehydrogenase (SDH) is essential for de novo purine synthesis, revealing a previously unrecognized metabolic dependency in cancer that can be leveraged therapeutically.
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.020
  2. Nat Commun. 2025 Nov 20. 16(1): 10222
    An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice.
    Eloïse Marques, Stephen P Burr, Alva M Casey, Richard J Stopforth, Chak Shun Yu, Keira Turner, Dane M Wolf, Marisa Dilucca, Vincent Paupe, Suvagata Roy Chowdhury, Victoria J Tyrrell, Robbin Kramer, Yamini M Kanse, Chinmayi Pednekar, Chris A Powell, James B Stewart, Julien Prudent, Michael P Murphy, Michal Minczuk, Valerie B O'Donnell, Clare E Bryant, Patrick F Chinnery, Arthur Kaser, Alexander von Kriegsheim, Dylan G Ryan.
      Impaired mitochondrial bioenergetics in macrophages promotes hyperinflammatory cytokine responses, but whether inherited mtDNA mutations drive similar phenotypes is unknown. Here, we profiled macrophages harbouring a heteroplasmic mitochondrial tRNAAla mutation (m.5019A>G) to address this question. These macrophages exhibit combined respiratory chain defects, reduced oxidative phosphorylation, disrupted cristae architecture, and compensatory metabolic adaptations in central carbon metabolism. Upon inflammatory activation, m.5019A>G macrophages produce elevated type I interferon (IFN), while exhibiting reduced pro-inflammatory cytokines and oxylipins. Mechanistically, suppression of pro-IL-1β and COX2 requires autocrine IFN-β signalling. IFN-β induction is biphasic: an early TLR4-IRF3 driven phase, and a later response involving mitochondrial nucleic acids and the cGAS-STING pathway. In vivo, lipopolysaccharide (LPS) challenge of m.5019A>G mice results in elevated type I IFN signalling and exacerbated sickness behaviour. These findings reveal that a pathogenic mtDNA mutation promotes an imbalanced innate immune response, which has potential implications for the progression of pathology in mtDNA disease patients.
    DOI:  https://doi.org/10.1038/s41467-025-65023-4
  3. Cancer Res. 2025 Nov 17.
    Mitochondrial Transfer Rescues Respiration to Support De Novo Pyrimidine Biosynthesis and Tumor Progression.
    Maria Dubisova, Klara Bohacova, Zuzana Nahacka, Daniel Kraus, Jaromir Novak, Sarka Dvorakova, Petra Brisudova, Natalie Danesova, Saba Selvi, Mariia Hrysiuk, Berwini B Endaya, Panagiotis Botsios, Dan-Diem Thi Le, Monika Novotna, Sona Vodenkova, Jaroslav Truksa, Karel Chalupsky, Krystof Klima, Jan Prochazka, Radislav Sedlacek, Francesco Mengarelli, Patrick Orlando, Luca Tiano, Stepana Boukalova, Michael V Berridge, Renata Zobalova, Jiri Neuzil.
      Cancer cells with severe defects in mitochondrial DNA (mtDNA) can import mitochondria via horizontal mitochondrial transfer (HMT) to restore respiration. Mitochondrial respiration is necessary for the activity of dihydroorotate dehydrogenase (DHODH), an enzyme of the inner mitochondrial membrane that catalyzes the fourth step of de novo pyrimidine synthesis. Here, we investigated the role of de novo synthesis of pyrimidines in driving tumor growth in mtDNA-deficient (ρ0) cells. While ρ0 cells grafted in mice readily acquired mtDNA, this process was delayed in cells transfected with alternative oxidase (AOX), which combines the functions of mitochondrial respiratory complexes III and IV. The ρ0 AOX cells were glycolytic but maintained normal DHODH activity and pyrimidine production. Deletion of DHODH in a panel of tumor cells completely blocked or delayed tumor growth. The grafted ρ0 cells rapidly recruited tumor-promoting/stabilizing cells of the innate immune system, including pro-tumor M2 macrophages, neutrophils, eosinophils, and mesenchymal stromal cells (MSCs). The ρ0 cells recruited MSCs early after grafting, which were potential mitochondrial donors. Grafting MSCs together with ρ0 cancer cells into mice resulted in mitochondrial transfer from MSCs to cancer cells. Overall, these findings indicate that cancer cells with compromised mitochondrial function readily acquire mtDNA from other cells in the tumor microenvironment to restore DHODH-dependent respiration and de novo pyrimidine synthesis. The inhibition of tumor growth induced by blocking DHODH supports targeting pyrimidine synthesis as a potential widely applicable therapeutic approach.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-0737
  4. Nat Metab. 2025 Nov 20.
    Hepatocyte mitochondrial NAD+ content is limiting for liver regeneration.
    Sarmistha Mukherjee, Ricardo A Velázquez Aponte, Caroline E Perry, Won Dong Lee, Kevin A Janssen, Marc Niere, Gabriel K Adzika, Mu-Jie Lu, Hsin-Ru Chan, Xiangyu Zou, Beishan Chen, Nicole Bye, Teresa Xiao, Jin-Seon Yook, Oniel Salik, David W Frederick, Ryan B Gaspar, Khanh V Doan, James G Davis, Joshua D Rabinowitz, Douglas C Wallace, Nathaniel W Snyder, Shingo Kajimura, Xiaolu A Cambronne, Mathias Ziegler, Joseph A Baur.
      Nicotinamide adenine dinucleotide (NAD+) precursor supplementation shows metabolic and functional benefits in rodent models of disease and is being explored as potential therapeutic strategy in humans. However, the wide range of processes that involve NAD+ in every cell and subcellular compartment make it difficult to narrow down the mechanisms of action. Here we show that the rate of liver regeneration is closely associated with the concentration of NAD+ in hepatocyte mitochondria. We find that the mitochondrial NAD+ concentration in hepatocytes of male mice is determined by the expression of the transporter SLC25A51 (MCART1). The heterozygous loss of SLC25A51 modestly decreases mitochondrial NAD+ content in multiple tissues and impairs liver regeneration, whereas the hepatocyte-specific overexpression of SLC25A51 is sufficient to enhance liver regeneration comparably to the effect of systemic NAD+ precursor supplements. This benefit is observed even though NAD+ levels are increased only in mitochondria. Thus, the hepatocyte mitochondrial NAD+ pool is a key determinant of the rate of liver regeneration.
    DOI:  https://doi.org/10.1038/s42255-025-01408-5
  5. Elife. 2025 Nov 19. pii: e109482. [Epub ahead of print]14
    How one nutrient controls cell size.
    Angela Montero, Lydia W S Finley.
      The metabolic fate of a nutrient called pyruvate determines how big cells become.
    Keywords:  D. melanogaster; biochemistry; cell biology; cell growth; chemical biology; genetics; hepatocytes; human; pyruvate metabolism; redox state; translation
    DOI:  https://doi.org/10.7554/eLife.109482
  6. EMBO Rep. 2025 Nov 20.
    FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer.
    Suzan Ber, Ming Yang, Marco Sciacovelli, Shamith Samarajiwa, Khushali Patel, Efterpi Nikitopoulou, Annie Howitt, Simon J Cook, Ashok R Venkitaraman, Christian Frezza, Alessandro Esposito.
      Mutations in KRAS, particularly at codon 12, are frequent in adenocarcinomas of the colon, lungs and pancreas, driving carcinogenesis by altering cell signalling and reprogramming metabolism. However, the specific mechanisms by which different KRAS G12 alleles initiate distinctive patterns of metabolic reprogramming are unclear. Using isogenic panels of colorectal cell lines harbouring the G12A, G12C, G12D and G12V heterozygous mutations and employing transcriptomics, metabolomics, and extensive biochemical validation, we characterise distinctive features of each allele. We demonstrate that cells harbouring the common G12D and G12V oncogenic mutations significantly alter glutamine metabolism and nitrogen recycling through FOXO1-mediated regulation compared to parental lines. Moreover, with a combination of small molecule inhibitors targeting glutamine and glutamate metabolism, we also identify a common vulnerability that eliminates mutant cells selectively. These results highlight a previously unreported mutant-specific effect of KRAS alleles on metabolism and signalling that could be potentially harnessed for cancer therapy.
    Keywords:  Colorectal Cancer; FOXO Signalling; Glutamine Metabolism; Glutamine Synthase; KRAS Mutation
    DOI:  https://doi.org/10.1038/s44319-025-00641-z
  7. bioRxiv. 2025 Sep 29. pii: 2025.09.28.674326. [Epub ahead of print]
    Glutamine antagonism suppresses tumor growth in adrenocortical carcinoma through inhibition of de novo nucleotide biosynthesis.
    Vasileios Chortis, Kleiton Silva Borges, Cong-Hui Yao, Claudio Ribeiro, Luis Fernando Nagano, Mesut Berber, Alessandro Prete, Lukáš Najdekr, Michail E Klontzas, Andris Jankevics, Pedro Vendramini, Jean Lucas Kremer, Liam Kelley, Sathuwarman Raveenthiraraj, Stylianos Tsagarakis, Magdalena Macech, Ivana D Pupovac, Thomas G Papathomas, Betul Haykir, Catherine Winder, Marcus Quinkler, M Conall Dennedy, Grethe Å Ueland, Felix Beuschlein, Antoine Tabarin, Martin Fassnacht, Angela E Taylor, Darko Kastelan, Urszula Ambroziak, Dimitra A Vassiliadi, Katja Kiseljak-Vassiliades, Irina Bancos, Diana L Carlone, Warwick B Dunn, Wiebke Arlt, Marcia C Haigis, David T Breault.
      Dysregulation of cellular metabolism is a hallmark of cancer, which remains poorly understood in adrenocortical carcinoma (ACC). Here, we dissected ACC metabolism by integrating transcriptional profiling from human and mouse ACC, targeted tissue metabolomics from a mouse ACC model, and untargeted serum metabolomics from a large patient cohort, providing cross-species validation of metabolic rewiring in ACC. This study revealed global metabolic dysregulation, involving glutamine-dependent pathways such as non-essential amino-acid and hexosamine biosynthesis, nucleotide metabolism, and glutathione biosynthesis, suggesting glutamine catabolism is a critical metabolic vulnerability in ACC. Treatment with glutamine antagonists 6-Diazo-5-Oxo-L-Norleucine (DON) and JHU-083 elicited robust anti-tumor responses. Mechanistic studies revealed DON's anti-tumor effect was primarily driven by selective inhibition of glutamine-fueled de novo nucleotide biosynthesis. Additionally, DON led to DNA damage, which yielded potent synergism with inhibition of the DNA damage response pathway. Collectively, this work highlights glutamine metabolism as a central metabolic dependency and therapeutic target in ACC.
    DOI:  https://doi.org/10.1101/2025.09.28.674326
  8. Sci Adv. 2025 Nov 21. 11(47): eaea7460
    Mitochondrial NAD+ gradient sustained by membrane potential and transport.
    Shivansh Goyal, Scott N Lyons, Xiaolu A Cambronne.
      SLC25A51 is required for the replenishment of free nicotinamide adenine dinucleotide (oxidized form) (NAD+) into mammalian mitochondria. However, it is not known how SLC25A51 imports this anionic molecule to sustain elevated NAD+ concentrations in the matrix. Understanding this would reveal regulatory mechanisms used to maintain critical bioenergetic gradients for cellular respiration, oxidative mitochondrial reactions, and mitochondrial adenosine triphosphate (ATP) production. In this work, mutational analyses and localized NAD+ biosensors revealed that the mitochondrial membrane potential (ΔΨm) works in concert with charged residues in the carrier's inner pore to enable sustained import of NAD+ against its electrochemical gradient into the matrix. Dissipation of the ΔΨm or mutation of select residues in SLC25A51 led to equilibration of NAD+ from the matrix. Corroborating data were obtained with the structurally distinct mitochondrial NAD+ carrier from Saccharomyces cerevisiae (ScNdt1p) and mitochondrial ATP transport suggesting a shared mechanism of charge compensation and electrogenic transport in these mitochondrial carrier family members.
    DOI:  https://doi.org/10.1126/sciadv.aea7460
  9. EMBO J. 2025 Nov 17.
    Homeostatic control of energy metabolism by monocyte-derived macrophages.
    Rui Martins, Birte Blankehaus, Faouzi Braza, Miguel Mesquita, Pedro Ventura, Sumnima Singh, Sebastian Weis, Maria Pires, Sara Pagnotta, Qian Wu, Sílvia Cardoso, Elisa Jentho, Ana Figueiredo, Pedro Faísca, Ana Nóvoa, Vanessa Alexandra Morais, Stefanie K Wculek, David Sancho, Moises Mallo, Miguel P Soares.
      Multicellular organisms rely on inter-organ communication networks to maintain vital parameters within a dynamic physiological range. Macrophages are central to this homeostatic control system, sensing and responding to deviations of those parameters to sustain organismal homeostasis. Here, we demonstrate that dysregulation of iron (Fe) metabolism, imposed by the deletion of ferritin H chain (FTH) in mouse parenchymal cells, is sensed by monocyte-derived macrophages. In response, monocyte-derived macrophages support tissue function, energy metabolism, and thermoregulation via a mechanism that sustains the mitochondria of parenchymal cells. Mechanistically, FTH supports a transcriptional program promoting mitochondrial biogenesis in macrophages, involving mitochondrial transcription factor A (TFAM). Moreover, FTH sustains macrophage viability and supports intercellular mitochondrial transfer from donor parenchymal cells. In conclusion, monocyte-derived macrophages cross-regulate iron and energy metabolism to support tissue function and organismal homeostasis.
    Keywords:  Ferritin; Homeostasis; Macrophages; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1038/s44318-025-00622-x
  10. Trends Cell Biol. 2025 Nov 15. pii: S0962-8924(25)00245-4. [Epub ahead of print]
    Mitochondrial transfer at the crossroads of cancer, stromal, and immune cells.
    Takamasa Ishino, Yu Inutsuka, Hideki Ikeda, Yosuke Togashi.
      Mitochondria are organelles that are essential for their multiple roles in cell biology, including energy metabolism. Accumulating evidence has revealed that intercellular mitochondrial transfer occurs within the tumor microenvironment (TME). The mitochondrial transfer among the TME components can profoundly affect tumor progression, immune surveillance, and stromal remodeling. Importantly, cancer cells function not only as recipients but also as donors of mitochondria, underscoring the bidirectional nature of this process. This review summarizes the multifaceted roles of mitochondria in cancer cells, immune cells, and stromal cells, with particular emphasis on emerging insights into mitochondrial transfer. In addition, the current implications of mitochondria-targeting therapies and future challenges in this evolving field are highlighted.
    Keywords:  antitumor immunity; cancer; mitochondria; mitochondrial transfer
    DOI:  https://doi.org/10.1016/j.tcb.2025.10.004
  11. Nature. 2025 Nov 19.
    Hepatic zonation determines tumorigenic potential of mutant β-catenin.
    Alexander Raven, Kathryn Gilroy, Hu Jin, Joseph A Waldron, Holly Leslie, June Munro, Holly Hall, Rachel A Ridgway, Catriona A Ford, Doga C Gulhan, Nikola Vlahov, Megan L Mills, Andrew Hartley, Eve Anderson, Sheila Bryson, Nathalie Sphyris, Miryam Müller, Stephanie May, Barbara Cadden, Colin Nixon, Scott H Waddell, Rachel Guest, Luke Boulter, Nick Barker, Hans Clevers, Hao Zhu, Johanna Ivaska, Douglas Strathdee, Crispin J Miller, Nigel B Jamieson, Martin Bushell, Peter J Park, Thomas G Bird, Owen J Sansom.
      Oncogenic mutations in phenotypically normal tissue are common across adult organs1,2. This suggests that multiple events need to converge to drive tumorigenesis and that many processes such as tissue differentiation may protect against carcinogenesis. WNT-β-catenin signalling maintains zonal differentiation during liver homeostasis3,4. However, the CTNNB1 oncogene-encoding β-catenin-is also frequently mutated in hepatocellular carcinoma, resulting in aberrant WNT signalling that promotes cell growth5,6. Here we investigated the antagonistic interplay between WNT-driven growth and differentiation in zonal hepatocyte populations during liver tumorigenesis. We found that β-catenin mutations co-operate with exogenous MYC expression to drive a proliferative translatome. Differentiation of hepatocytes to an extreme zone 3 fate suppressed this proliferative translatome. Furthermore, a GLUL and Lgr5-positive perivenous subpopulation of zone 3 hepatocytes were refractory to WNT-induced and MYC-induced tumorigenesis. However, when mutant CTNNB1 and MYC alleles were activated sporadically across the liver lobule, a subset of mutant hepatocytes became proliferative and tumorigenic. These early lesions were characterized by reduced WNT pathway activation and elevated MAPK signalling, which suppresses zone 3 differentiation. The proliferative lesions were also dependent on IGFBP2-mTOR-cyclin D1 pathway signalling, in which inhibition of either IGFBP2 or mTOR suppressed proliferation and tumorigenesis. Therefore, we propose that zonal identity dictates hepatocyte susceptibility to WNT-driven tumorigenesis and that escaping WNT-induced differentiation is essential for liver cancer.
    DOI:  https://doi.org/10.1038/s41586-025-09733-1
  12. bioRxiv. 2025 Oct 04. pii: 2025.10.02.680066. [Epub ahead of print]
    Glutamine-Dependent Slc25a39-Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment.
    Brian Kelly, Chia-Hua Wu, Kaan I Eskut, Elizabeth McCauley, Sajina Dhungel, Samantha Pavlecic, Grace Bieghler, Jelena Perovanovic, Dean Tantin, Jakub Famulski, Jeramiah Smith, Chintan Kikani.
      Myogenic commitment is a decisive and irreversible step in skeletal muscle regeneration, necessitating proliferating myoblasts to integrate metabolic cues with nuclear transcriptional programs. Among amino acids, glutamine is uniquely positioned to influence this transition by coupling energy production to macromolecule biosynthesis and epigenetic regulation. We reasoned that myoblasts must sense glutamine availability to ensure orderly progression toward commitment, and we tested this by examining the molecular consequences of acute glutamine withdrawal. We find that continued glutamine oxidation is required to sustain glycolysis, maintain mitochondrial fission, and preserve a redox balance that supports progression towards myogenic commitment. In its absence, myoblasts undergo a reductive shift, characterized by mitochondrial elongation, membrane depolarization, and suppression of glycolysis, ultimately leading to growth arrest. Transcriptomic profiling reveals reduced MyoD and MKi67 , accompanied by increased Sprouty1 levels, defining a reversible non-proliferative state that resembles but is distinct from quiescent and reserve cells. We term this state Poised Metabolic Arrest (PMA), a cellular response to glutamine limitation during myogenic progression. Mechanistically, PMA is driven by Nrf2-dependent increased glutathione (GSH) biosynthesis and upregulation of mitochondrial GSH carrier Slc25a39 when glutamine is limited. Depleting mitochondrial glutathione or silencing Slc25a39 forces exit from PMA. However, this premature exit compromises subsequent differentiation potential, indicating PMA serves to preserve differentiation competence when glutamine is limited. Consistent with this, both loss and overexpression of Slc25a39 impair myoblast differentiation in vitro and disrupt regeneration in vivo. Together, these data suggest that a reciprocal Slc25a39-Nrf2 redox axis functions as a nutrient-dependent checkpoint, coupling glutamine availability to mitochondrial remodeling and metabolic reprogramming, necessary to establish irreversible myogenic commitment.
    DOI:  https://doi.org/10.1101/2025.10.02.680066
  13. Nat Commun. 2025 Nov 20. 16(1): 10198
    SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.
    Cecilia Colson, Yujue Wang, James Atherton, Nisha Rani Dahiya, Davood Kharaghani, Xiaoyang Su.
      Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We develop a metabolomic-transcriptomic association analysis, and we find that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrate that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the peroxisome membrane to facilitate GABA production. Taken together, our results reveal a biochemical mechanism where SLC45A4 controls GABA production.
    DOI:  https://doi.org/10.1038/s41467-025-62721-x
  14. Trends Cancer. 2025 Nov 18. pii: S2405-8033(25)00255-9. [Epub ahead of print]
    Branched chain amino acids and their aberrant metabolism in cancer.
    Morgan L Brown, Xuanyan Cai, M Celeste Simon.
      Cancer cells require sufficient nutrients to support biomass generation, rapid proliferation, and survival. Thus, extensive reprogramming of amino acid metabolism is necessary for tumor initiation and progression under strenuous conditions. One metabolic pathway that has garnered attention is branched chain amino acid (BCAA) catabolism, a pathway that is highly altered across malignancies. This review examines current insights into how circulating BCAAs and their aberrant catabolic enzymes impact both cancer cells and the surrounding tumor microenvironment.
    Keywords:  branched chain amino acids; cancer metabolism; nutrient supplementation; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.trecan.2025.10.004
  15. Mitochondrion. 2025 Nov 16. pii: S1567-7249(25)00096-0. [Epub ahead of print] 102099
    The mitochondrial protein TMEM177 fine-tunes mammalian cytochrome c oxidase assembly.
    Jakob D Busch, Thomas Schöndorf, Dusanka Milenkovic, Xinping Li, Rolf Wibom, Joana F Silva-Rodrigues, Roberta Filograna, Camilla Koolmeister, Nils-Göran Larsson, Diana Rubalcava-Gracia.
      The mitochondrial cytochrome c oxidase (COX, complex IV), a multi-subunit protein complex, plays a crucial role in cellular respiration by reducing oxygen to water and simultaneously pumping protons to enable oxidative phosphorylation (OXPHOS). Thus, defects in its assembly can directly affect cellular energy homeostasis. COX20 is an essential chaperone for the core subunit COX2. In human cultured cells, TMEM177 was found to stabilize COX20 and maintain balanced COX2 levels. In mice, TMEM177 was also identified as an interactor of mitochondrial ribosomes. To understand the function of TMEM177 in vivo, we generated Tmem177 knockout mice. Here, we analyze how TMEM177 loss affects mitochondrial gene expression, as well as the activity and assembly of OXPHOS complexes. We found that a small proportion of the knockout mice died perinatally, while surviving knockout mice tended to gain less weight. TMEM177 depletion moderately reduced COX20 levels, but OXPHOS complexes were preserved. Moreover, Tmem177 and Surf1 double knockout mice were born asymptomatic. In conclusion, TMEM177 fine-tunes complex IV assembly by stabilizing COX20 in vivo. Our findings refine the current model of complex IV assembly in mammals.
    Keywords:  Cytochrome c oxidase; Mitochondria; Mitoribosomes; OXPHOS; mtDNA
    DOI:  https://doi.org/10.1016/j.mito.2025.102099
  16. Annu Rev Pathol. 2025 Nov 18.
    Integration and Intersection of Cancer Metabolism with Epigenetic Pathways in Gliomas.
    Siva Kumar Natarajan, Matthew Pun, James Haggerty-Skeans, Sriram Venneti.
      The interplay between metabolomics and epigenetics is a key glioma driver. Both tumor-intrinsic and microenvironmental metabolic cues can shape chromatin. Epigenetic methylation and demethylation are metabolically regulated by S-adenosyl methionine (SAM) (via methionine metabolism) and the TCA-cycle-related metabolite α-ketoglutarate (α-KG), respectively. Additionally, glycolysis and the TCA cycle modulate histone acetylation and lactylation. Gliomas in both adults and children hijack these pathways. Adult isocitrate dehydrogenase (IDH)-wild-type tumors enhance glycolysis via epidermal growth factor receptor to alter chromatin. IDH-mutant gliomas generate D-2-hydroxyglutarate (D-2HG), which inhibits α-KG demethylases to create epigenetic hypermethylation. Pediatric gliomas, including gliomas with lysine-to-methionine mutations at residue 27 of histone H3 and posterior fossa group A ependymomas, can also rewire metabolism to regulate chromatin. These pathways can be targeted for therapeutic development. Inhibiting IDH mutations with vorasidenib lowers D-2HG and is beneficial to patients. Other drugs like ONC201 and metformin can metabolically suppress oncogenic chromatin states in pediatric gliomas. This dynamic cross talk between metabolism and epigenetics not only underpins tumor biology but also presents opportunities for innovative therapeutic strategies.
    DOI:  https://doi.org/10.1146/annurev-pathmechdis-111523-023424
  17. J Clin Invest. 2025 Nov 17. pii: e193370. [Epub ahead of print]135(22):
    Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models.
    Jie Zhao, Xinghao Li, Xinyu Li, Pengfei Ren, Yilan Wu, Hao Gong, Lijian Wu, Junran Huang, Saisai Wang, Ziwei Guo, Mo Chen, Zexian Zeng, Deng Pan.
      Macrophage-mediated phagocytosis plays a critical role in the elimination of cancer cells and shaping antitumor immunity. However, the tumor-intrinsic pathways that regulate cancer cell sensitivity to macrophage-mediated phagocytosis remain poorly defined. In this study, we performed a genome-wide CRISPR screen in murine pancreatic cancer cells cocultured with primary macrophages and identified that disruption of the tumor-intrinsic pyrimidine synthesis pathway enhances phagocytosis. Mechanistically, we discovered that macrophages inhibit the pyrimidine salvage pathway in tumor cells by upregulating Upp1-mediated uridine degradation through cytokines TNF-α and IL-1. This shift increased tumor cells' reliance on de novo pyrimidine synthesis. As a result, tumor cells with impaired de novo pyrimidine synthesis showed depleted UMP and displayed enhanced exposure of phosphatidylserine (PtdSer), a major "eat-me" signal, thereby promoting macrophage-mediated phagocytosis. In multiple pancreatic cancer models, Cad-deficient tumors exhibited markedly reduced tumor burden with increased levels of phagocytosis by macrophages. Importantly, the Cad-mediated suppression of pancreatic cancer was dependent on TAMs and cytokines IL-1 and TNF-α. Pharmacological inhibition of DHODH, which blocks de novo pyrimidine synthesis, similarly decreased tumor burden with enhanced phagocytosis in pancreatic cancer models. These findings highlight the critical role of the tumor-intrinsic pyrimidine synthesis pathway in modulating macrophage-mediated antitumor immunity, with potential therapeutic implications.
    Keywords:  Cancer immunotherapy; Immunology; Innate immunity; Macrophages; Metabolism; Oncology
    DOI:  https://doi.org/10.1172/JCI193370
  18. Nat Rev Immunol. 2025 Nov 18.
    Guidelines for T cell nomenclature.
    David Masopust, Amit Awasthi, Rémy Bosselut, David G Brooks, Marcus Buggert, Kenji Chamoto, Weiguo Cui, Chen Dong, Donna L Farber, Thomas Gebhardt, Carmen Gerlach, Ananda Goldrath, Philip D Greenberg, J Scott Hale, Adrian Hayday, Dirk Homann, Matteo Iannacone, Stephen C Jameson, Marc K Jenkins, Nikhil S Joshi, Susan M Kaech, Axel Kallies, Alice O Kamphorst, Mark H Kaplan, Paul Klenerman, Marco Künzli, Antonio Lanzavecchia, Georg M Lauer, Enrico Lugli, Andrew D Luster, Laura K Mackay, M Juliana McElrath, Scott N Mueller, Zaza Ndhlovu, Thumbi Ndung'u, Pamela S Ohashi, Annette Oxenius, Giuseppe Pantaleo, Marion Pepper, Louis J Picker, Clare F Quarnstrom, Gustavo Reyes-Terán, Mario Roederer, Pamela C Rosato, Gonzalo Salgado-Montes de Oca, Federica Sallusto, Ton N Schumacher, Daniella M Schwartz, Eui-Cheol Shin, Andrew G Soerens, Daniela S Thommen, Vaiva Vezys, João P B Viola, Bruce D Walker, Tania H Watts, Casey T Weaver, E John Wherry, Hai-Hui Xue, Ben Youngblood, Rafi Ahmed.
      Advances in T cell biology have revealed heterogeneity among T cell populations that is not captured by existing general nomenclature. This issue has caused an ad hoc broadening of core T cell subset definitions and the invention of new subset designations that have not been uniformly delineated. To address this issue, in this Consensus Statement, we propose guidelines that serve three goals. First, they advocate that primary research reports define the experimental basis by which relevant subsets are designated in the methods section of each study. Second, they provide standardized definitions for existing subset designations in popular use, and common experimental criteria for defining each subset are noted. Last, they present an alternative 'modular nomenclature' paradigm. The newly proposed modular nomenclature eschews conceptualization of antigen-experienced T cells as belonging to a few idealized subsets, and the nomenclature instead simply indicates individual biological properties present in a T cell population with brief descriptors. Collectively, these guidelines intend to enhance transparency in the literature while facilitating clearer communication of findings and concepts to researchers, students and clinicians.
    DOI:  https://doi.org/10.1038/s41577-025-01238-2
  19. Cell. 2025 Nov 19. pii: S0092-8674(25)01233-4. [Epub ahead of print]
    Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.
    Alexander C Lewis, Emily Gruber, Rheana Franich, Jessica Armstrong, Madison J Kelly, Carlos M Opazo, Yau C Low, Léa Flippe, Kevin Wijanarko, Caitlin L Rowe, Celeste H Mawal, Alexandra Birrell, Joan So, Srimayee Vaidyanathan, Keziah Ting, Liana N Semcesen, Karena Last, Ching-Seng Ang, Giovanna Pomilio, Fiona C Brown, Andrew H Wei, Jason A Powell, Elizabeth S Ng, Ann E Frazier, Kate McArthur, Najoua Lalaoui, David A Stroud, Kristin K Brown, Ricky W Johnstone, Lev M Kats.
      The ubiquitous metabolite heme has diverse enzymatic and signaling functions in most mammalian cells. Through integrated analyses of mouse models, human cell lines, and primary patient samples, we identify de novo heme biosynthesis as a selective dependency in acute myeloid leukemia (AML). The dependency is underpinned by a propensity of AML cells, and especially leukemic stem cells (LSCs), to downregulate heme biosynthesis enzymes (HBEs), which promotes their self-renewal. Inhibition of HBEs causes the collapse of mitochondrial Complex IV and dysregulates the copper-chaperone system, inducing cuproptosis, a form of programmed cell death brought about by the oligomerization of lipoylated proteins by copper. Moreover, we identify pathways that are synthetic lethal with heme biosynthesis, including glycolysis, which can be leveraged for combination strategies. Altogether, our work uncovers a heme rheostat that is connected to gene expression and drug sensitivity in AML and implicates HBE inhibition as a trigger of cuproptosis.
    Keywords:  acute myeloid leukemia; cuproptosis; heme biosynthesis; metabolic vulnerability; metabolism; mitochondrial Complex IV
    DOI:  https://doi.org/10.1016/j.cell.2025.10.028
  20. Methods Mol Biol. 2026 ;2990 127-143
    Quantifying Mitochondrial Metabolism and Metabolic Fluxes in Soft Agar Cultures.
    Birte Dowerg, Fangfang Chen, Thekla Cordes.
      Anchorage-independent cultures provide insights into cell proliferation, differentiation, and tumorigenesis beyond traditional two-dimensional models by mimicking parts of the extracellular matrix (ECM). The soft agar colony formation assay enables cells to proliferate in a three-dimensional manner resulting in metabolic phenotypes that are distinct from traditional monolayer cultures. Here, we established a soft agar colony formation assay with subsequent cell isolation to analyze mitochondrial metabolism, metabolic fluxes, morphology, and gene expression within the same sample. We applied mass spectrometry and tracing approaches to decipher carbon utilization for tricarboxylic acid (TCA) cycle metabolism. We also quantified the alteration of immune-related genes in response to inflammatory stimuli in soft agar cultures that might be relevant to autoimmune diseases, which are frequently associated with inflammatory environments and may contribute insights into chronic inflammation and immune cell survival that parallel tumorigenic processes. Our methodology offers a robust model to better understand cell metabolism and function of anchorage-independent cultures that may contribute to the development of new treatment strategies.
    Keywords:  Anchorage-independent cultures; Extracellular matrix; Mass spectrometry; Metabolic flux; Metabolism; Metabolite extraction; Mitochondria; Soft agar; Stable isotope tracer
    DOI:  https://doi.org/10.1007/978-1-0716-4997-8_11
  21. bioRxiv. 2025 Oct 01. pii: 2025.09.29.679343. [Epub ahead of print]
    Succinate Dehydrogenase-Deficient Cancer Cells Have Increased Susceptibility to Ym155 Induced DNA Damage.
    Qianjin Guo, Sooyeon Lee, Neali Armstrong, Brian Lim, Rebecca C Schugar, David Tomz, Haixia Xu, Anzel Zhen, Leor Needleman, Electron Kebebew, Justin P Annes.
      The hereditary pheochromocytoma and paraganglioma (hPPGL) syndrome is caused by inherited mutations in Succinate Dehydrogenase genes (SDHx). Affected individuals are predisposed to developing pheochromocytomas (Pheo), paragangliomas (PGL), renal cell carcinoma (RCC) and gastrointestinal stromal tumors (GIST). Notably, tumors with succinate dehydrogenase subunit B ( SDHB ) deficiency demonstrate increased metastatic risk, for which treatments remain palliative. Hence, discovering novel therapeutic avenues to improve the prognosis for SDHB -cancer patients is an urgent need. Here we employed human SDHB -deficient UOK269 RCC cells ( SDHB -KO) and isogenic SDHB -reconstituted control cells ( SDHB -WT) to discover SDH-dependent mitochondria-directed cytotoxic agents. Given the reduced ATP-generating capacity of SDHB -KO cells, we hypothesized they would be uniquely sensitive to futile cycle induction with mitochondrial ionophores (2,4-Dinitrophenol (2-DNP), BAM15, Niclosamide, Nitazoxanide). Indeed, these compounds exhibited preferential cytotoxicity toward SDHB -KO cells. However, the chemotherapeutic compound Ym155 demonstrated the most potent and dramatic (five-fold) preferential cytotoxicity towards SDHB -KO cells. Importantly, the SDH-dependent cytotoxicity of Ym155 was validated in both primary human pheochromocytoma cells and mouse pheochromocytoma (MPC) cells. Furthermore, because few SDH-deficient cell lines are available, we buttressed our findings in additional relevant cell lines by modeling SDH-deficiency using chemical SDH enzyme inhibition with 3-nitropropionic acid (3-NPA). We observed a persistent cooperativity between SDH-deficiency and Ym155 cytotoxicity across multiple cell lineages and disease models. Mechanistically, Ym155-induced cytotoxicity was independent of its primary target, Survivin. Instead, SDH-deficiency sensitized cells to Ym155-induced DNA damage. Strikingly, the phenotype of SDH-deficient Ym155 sensitivity was recapitulated by inhibition of the histone demethylase KDM4, a downstream consequence of SDH deficiency. Thus, the accumulation of succinate in SDH-deficient tumors inhibits KDM4 activity, impairs DNA repair and yields enhanced susceptibility to Ym155-induced reactive oxygen species (ROS) generation. The identified intrinsic susceptibilities of SDHB -deficient cancers has the potential to be therapeutically leveraged.
    DOI:  https://doi.org/10.1101/2025.09.29.679343
  22. EMBO J. 2025 Nov 20.
    A unified mechanism for mitochondrial damage sensing in PINK1-Parkin-mediated mitophagy.
    Julia A Thayer, Jennifer D Petersen, Xiaoping Huang, Luiza M Gruel Budet, James Hawrot, Daniel M Ramos, Shiori Sekine, Yan Li, Michael E Ward, Derek P Narendra.
      Damaged mitochondria can be cleared from the cell by mitophagy, using a pathway formed by the recessive Parkinson's disease genes PINK1 and Parkin. Whether the pathway senses diverse forms of mitochondrial damage via a common mechanism, however, remains uncertain. Here, using a novel Parkin reporter in genome-wide screens, we identified that diverse forms of mitochondrial damage converge on loss of mitochondrial membrane potential (MMP) to activate PINK1. Loss of MMP, but not the presequence translocase-associated import motor (PAM), blocked progression of PINK1 import through the translocase of the inner membrane (TIM23), causing it to remain bound to the translocase of the outer membrane (TOM). Ablation of TIM23 was sufficient to arrest PINK1 within TOM, irrespective of MMP. Meanwhile, TOM (including subunit TOMM5) was required for PINK1 retention on the mitochondrial surface. The energy state outside of the mitochondria further modulated the pathway by controlling the rate of new PINK1 synthesis. Together, our findings point to a convergent mechanism of PINK1-Parkin activation by mitochondrial damage: loss of MMP stalls PINK1 import during its transfer from TOM to TIM23.
    Keywords:  Autophagy; Glycolysis; Parkinson’s Disease; Unfolded Protein Response
    DOI:  https://doi.org/10.1038/s44318-025-00604-z
  23. J Exp Med. 2026 Feb 02. pii: e20250439. [Epub ahead of print]223(2):
    SLC7A8 is essential for metabolic fitness and function of Th2 cells.
    Santosh K Panda, Do-Hyun Kim, Pritesh Desai, Shitong Wu, Patrick Fernandes Rodrigues, Raki Sudan, Yizhou Liu, Haerin Jung, Intelly Lee, Susan Gilfillan, Marina Cella, Steven J Van Dyken, Marco Colonna.
      Amino acids are essential for the activation and function of CD4 T helper (Th) cells, which differentiate into Th1, Th2, Th17, and Treg subsets to coordinate immune responses. While specific amino acid transporters have been identified for Th1, Th17, and Tregs, a transporter regulating Th2 cells remains unknown. This study identifies SLC7A8 as a Th2-specific amino acid transporter in the Th compartment. We found that Slc7a8 expression is upregulated in Th2 cells compared with other T helper subsets, and Slc7a8 deficiency impairs Th2 cell proliferation and cytokine production. Furthermore, SLC7A8 was found to be crucial for an effective type 2 immune response to helminth infection and allergen-induced lung inflammation. Mechanistically, Slc7a8 deficiency disrupted Th2 cell metabolism, leading to reduced mTOR activation and, consequently, diminished mitochondrial function along with an impaired c-Myc pathway; these defects cumulatively induced cellular stress that curtailed cell growth and survival. Collectively, these findings highlight a previously unknown role for SLC7A8 in Th2 cells, with potential implications for understanding and treating type 2 immune-related diseases.
    DOI:  https://doi.org/10.1084/jem.20250439
  24. Trends Cell Biol. 2025 Nov 15. pii: S0962-8924(25)00248-X. [Epub ahead of print]
    AMPK opens the door to organelle memory and longevity.
    Arpit Sharma.
      Nutrient sensors serve as sentinels of cellular energy status, relaying metabolic information to effectors that reprogram gene expression. Zhou et al. identified an AMP-activated protein kinase (AMPK)-NUP50 axis through which AMPK stabilizes the nucleoporin NUP50 to activate transcriptional programs promoting lipid catabolism and longevity. This redefines the nuclear pore complex (NPC) as a dynamic hormetic effector coupling energy sensing to transcriptional control.
    Keywords:  AMPK; fasting; longevity; metabolism; nuclear pore complex; organelles
    DOI:  https://doi.org/10.1016/j.tcb.2025.10.005
  25. bioRxiv. 2025 Oct 05. pii: 2025.10.03.680201. [Epub ahead of print]
    Methionine regulates antitumor function of CD8 + T cells through polyamine synthesis.
    Tian Zhao, Gillian A Carleton, Sarah Macpherson, Madison Shiyuk, Joseph Monaghan, Jun Han, Oro Uchenunu, Robert Rottapel, Ralph J DeBerardinis, Kelly M Stewart, Bo-Hyun Kim, Juan Ausió, David R Goodlett, Helena Pětrošová, Kyle D Duncan, Julian J Lum.
      Methionine is an essential amino acid critical for T cell activation. While methionine restriction (MR) combined with immune checkpoint blockade has been shown to enhance T cell function, the impact of methionine on adoptive T cell therapies is largely unexplored. Here, we examined the functionality of T cells under MR and pharmaceutical inhibition of the methionine cycle (MAT2Ai), using primary T cells and a murine adoptive T cell therapy model. In vitro , transient MR or MAT2Ai treatment increased interferon gamma (IFNγ) expression in CD8 + T cells, whereas sustained MR led to the upregulation of T cell exhaustion-associated markers. Mechanistically, transient MR suppressed the polyamine synthesis pathway, and supplementation with polyamines reversed MR-induced IFNγ expression. Genetic ablation of s-adenosylmethionine decarboxylase, an enzyme in the polyamine synthesis pathway, recapitulated the effect of MR, indicating that transient MR enhances T cell function by inhibiting polyamine synthesis. Despite this, transient MR treatment of ovalbumin (OVA)-specific (OT-I) CD8 + T cells prior to adoptive transfer did not improve antitumor efficacy against EG7-OVA tumors in vivo . In contrast, sustained dietary MR accelerated EG7-OVA tumor growth in mice treated with OT-I T cells, demonstrating that methionine availability is essential for the activity of adoptively transferred T cells. These findings suggest that enhancing methionine availability in the tumor microenvironment may improve the efficacy of adoptive T cell therapies.
    DOI:  https://doi.org/10.1101/2025.10.03.680201
  26. bioRxiv. 2025 Oct 02. pii: 2025.09.30.679611. [Epub ahead of print]
    Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane.
    Shiying Huang, Yeun Ju Kim, Xiaofu Cao, Timothy W Bumpus, Mira Sohn, Matthew Tyler Menold, Ryan S Dale, Jin Joo Kang, Saori Uematsu, Shagun Gupta, Shu-Bing Qian, Haiyuan Yu, Tamas Balla, Jeremy M Baskin.
      Cells tightly control the homeostatic levels and subcellular localizations of membrane phospholipids through the regulation of the activities of numerous lipid-metabolizing enzymes and lipid transfer proteins. Yet, the mechanisms by which lipid imbalances are sensed and corrected to establish and maintain homeostasis are, in most cases, unknown. Here we present an expanded view of plasma membrane (PM) phosphoinositide metabolism by revealing an unexpected metabolic connection between two key anionic lipids in this membrane, phosphatidylinositol 4-phosphate (PI4P) and phosphatidic acid (PA). PM pools of PI4P are generated by PI 4-kinase Type IIIα (PI4KIIIα/PI4KA), an essential enzyme whose partial dysfunction leads to numerous hereditary human diseases. We find that depletion of PI4P by pharmacological inhibition of PI4KA increases the activity of phospholipase Ds (PLDs) and the levels of their lipid product, PA, in the PM. Guided by RNA-seq analysis and proximity labeling proteomics, we elucidate how cells connect this PI4P decrease to a compensatory increase in PA levels. Loss of PM PI4P induces a concomitant decrease of phosphatidylserine (PS) levels, and this metabolic rewiring activates a reciprocal relationship between PS synthesis and PLD-mediated PA generation. These metabolic changes also lead to transcriptional and translational upregulation of the small GTPase RhoB, which enhances PLD-mediated PA synthesis and subsequent actin cytoskeletal remodeling. Our study reveals how disease-relevant perturbation of phosphoinositide synthesis induces an integrated response that ultimately boosts levels of PA, a key anionic lipid and metabolic intermediate in phosphoinositide resynthesis.
    DOI:  https://doi.org/10.1101/2025.09.30.679611
  27. Nat Commun. 2025 Nov 21.
    Unifying regulatory motifs in endocrine circuits.
    Moriya Raz, David S Glass, Tomer Milo, Yael Korem Kohanim, Omer Karin, Avichai Tendler, Avi Mayo, Uri Alon.
      Hormone systems, which control diverse physiological functions, have been extensively studied, yet consistent rules underlying these systems remain elusive. Here we identify unifying design principles in human endocrine systems. Available data was found for 43 of 63 systems, and all 43 fall into five classes of circuits. Each class uses distinct regulation circuitry to perform specific dynamical functions: homeostasis, acute input-output response, or adjustable set points. The circuits involve interactions across multiple timescales - minutes to hours for hormone secretion, ultradian and diurnal rhythms, and weeks for changes in endocrine gland mass. The weeks-timescale for gland mass occurs in several circuit classes, including the most complex, which features an intermediate gland, the pituitary. We analyze this circuit in detail and identify tradeoffs between endocrine amplification, buffering of hypersecreting tumors, and response times. These unifying principles reveal how circuit structure maps to function and contribute to the emerging field of systems endocrinology.
    DOI:  https://doi.org/10.1038/s41467-025-65924-4
  28. bioRxiv. 2025 Oct 02. pii: 2025.10.02.678294. [Epub ahead of print]
    Metformin inhibits mitochondrial complex I in intestinal epithelium to promote glycemic control.
    Zachary L Sebo, Ram P Chakrabarty, Rogan A Grant, Karis B D'Alessandro, Alec R Koss, Jenna L E Blum, Shawn M Davidson, Colleen R Reczek, Navdeep S Chandel.
      Metformin is a therapeutically versatile biguanide drug primarily prescribed for type II diabetes. Despite its extensive use, the mechanisms underlying many of its clinical effects, including attenuated postprandial glucose excursions, elevated intestinal glucose uptake, and increased production of lactate, Lac-Phe and GDF15, remain unclear. Here, we map these and other clinical effects of metformin to intestine-specific mitochondrial complex I inhibition. Using human metabolomic data and an orthogonal genetics approach in male mice, we demonstrate that metformin suppresses citrulline synthesis, a metabolite generated exclusively by small intestine mitochondria, and increases GDF15 by inhibiting the mitochondrial respiratory chain at complex I. This inhibition co-opts the intestines to function as a glucose sink, driving uptake of excess glucose and converting it to lactate and Lac-Phe. Notably, the glucose-lowering effect of another biguanide, phenformin, and berberine, a structurally unrelated nutraceutical, similarly depends on intestine-specific mitochondrial complex I inhibition, underscoring a shared therapeutic mechanism.
    DOI:  https://doi.org/10.1101/2025.10.02.678294
  29. bioRxiv. 2025 Oct 03. pii: 2025.10.01.679861. [Epub ahead of print]
    Dietary protein governs the role of insulin signaling in the postprandial regulation of hepatic mTORC1.
    Krystle C Kalafut, Yann Cormerais, Madi Y Cissé, Samuel C Lapp, Karen E Inouye, Gökhan S Hotamışlıgil, Brendan D Manning.
      The nutrient-sensing mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway controls cellular and organismal growth and metabolism, while aberrant activation is linked to human disease, including metabolic disease. Cellular studies have established several regulatory mechanisms influencing mTORC1 activation, but the physiological signals that control mTORC1 at the organismal and tissue levels are less well defined. mTORC1 is dynamically regulated by fasting and feeding in metabolic tissues, with both nutrients and insulin proposed to activate mTORC1 in response to feeding. Here, a liver-specific mouse model that disconnects mTORC1 activation from AKT-mediated TSC2 phosphorylation is employed. This genetic mouse model demonstrates that AKT-mediated TSC2 phosphorylation is the predominant mechanism of hepatic mTORC1 induction by insulin but is dispensable for activation by feeding. Furthermore, dietary protein is critical and dictates the insulin-responsiveness of hepatic mTORC1 signaling. Contrary to dogma, hepatic mTORC1 signaling was not elevated in response to diet-induced obesity associated with the phenotypes of type-2 diabetes, including hyperinsulinemia, systemic insulin resistance, and hyperglycemia, and blocking hepatic AKT-TSC-mTORC1 signaling did not prevent these metabolic impairments. Evidence is also provided supporting a role for glucagon in hepatic mTORC1 suppression during fasting. This study reveals a hierarchy of physiological signals regulating hepatic mTORC1.
    DOI:  https://doi.org/10.1101/2025.10.01.679861
  30. FEBS Lett. 2025 Nov 20.
    The role and implications of mammalian cellular circadian entrainment.
    Priya Crosby.
      The ability to align circadian phase to specific cues, or 'entrainment', is a defining feature of a circadian rhythm. Entrainment is critical for useful circadian function, as it enables organisms to determine the specific time of day to perform temporally restricted behavioural and physiological activities, ranging from sleep to cell division. While mammals have long been known to entrain their circadian rhythm, recent work has shed light on how this is achieved in every single cell, all of which maintain their own individual circadian oscillation. Here I will highlight the current understanding of how the major entraining cues of light, feeding and temperature are communicated to cells to alter their phase. Knowledge of the mechanisms of cellular entrainment has the capacity to impact both fundamental understanding of circadian rhythms and our application of cellular circadian research to real-world problems, including shift work.
    Keywords:  PERIOD; cell biology; cell signalling; circadian; entrainment
    DOI:  https://doi.org/10.1002/1873-3468.70223
  31. bioRxiv. 2025 Oct 01. pii: 2025.09.29.679307. [Epub ahead of print]
    Retrograde mitochondrial transport regulates mitochondrial biogenesis in zebrafish neurons.
    Angelica E Lang, Chris Stein, Catherine M Drerup.
      To maintain a healthy mitochondrial population in a long-lived cell like a neuron, mitochondria must be continuously replenished through the process of mitochondrial biogenesis. Because the majority of mitochondrial proteins are nuclear encoded, mitochondrial biogenesis requires nuclear sensing of mitochondrial population health and function. This can be a challenge in a large, compartmentalized cell like a neuron in which a large portion of the mitochondrial population is in neuronal compartments far from the nucleus. Using in vivo assessments of mitochondrial biogenesis in zebrafish neurons, we determined that mitochondrial transport between distal axonal compartments and the cell body is required for sustained mitochondrial biogenesis. Estrogen-related receptor transcriptional activation links transport with mitochondrial gene expression. Together, our data support a role for retrograde feedback between axonal mitochondria and the nucleus for regulation of mitochondrial biogenesis in neurons.
    DOI:  https://doi.org/10.1101/2025.09.29.679307
  32. Cell Rep. 2025 Nov 15. pii: S2211-1247(25)01358-0. [Epub ahead of print]44(11): 116586
    Two decades of FFAR4 biology: From nutrient sensing to therapeutic targeting.
    Yulin Kong, DaYoung Oh, Shenglong Zhu.
      Free fatty acid receptor 4 (FFAR4; also known as GPR120) serves as a key lipid-sensing G-protein-coupled receptor that mediates the physiological actions of long-chain fatty acids, particularly omega-3 polyunsaturated fatty acids. Over the past two decades, studies of FFAR4 have revealed its pivotal role in metabolic regulation, inflammation resolution, and energy balance. This review integrates recent advances from structural biology, physiology, and translational research to provide an updated framework of FFAR4 biology. In particular, we highlight new cryo-electron microscopy-based insights into receptor activation and ligand recognition; the expanding roles of FFAR4 in non-metabolic systems, such as the central nervous system and kidney; and recent progress in the clinical development of selective FFAR4 agonists. By bridging molecular mechanisms with therapeutic translation, this review offers a comprehensive perspective on FFAR4's functions in health and disease.
    Keywords:  CP: metabolism; CP: molecular biology; FFAR4; GPR120; biased agonism; metabolic homeostasis; nutrient sensing; therapeutic targeting
    DOI:  https://doi.org/10.1016/j.celrep.2025.116586
  33. Cancer Discov. 2025 Nov 20.
    DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency.
    Thomas Köhnke, Daiki Karigane, Eleanor Hilgart, Amy C Fan, Kensuke Kayamori, Masashi Miyauchi, Cailin T Collins, Fabian P Suchy, Athreya Rangavajhula, Yang Feng, Yusuke Nakauchi, Eduardo Martinez-Montes, Jonas L Fowler, Kyle M Loh, Hiromitsu Nakauchi, Michael A Koldobskiy, Andrew P Feinberg, Ravindra Majeti.
      Genetic mutations are being thoroughly mapped in human cancers, yet a fundamental question in cancer biology is whether such mutations are functionally required for cancer initiation, maintenance of established cancer, or both. Here, we study this question in the context of human acute myeloid leukemia (AML), where DNMT3AR882 missense mutations often arise early, in pre-leukemic clonal hematopoiesis, and corrupt the DNA methylation landscape to initiate leukemia. We developed CRISPR-based methods to directly correct DNMT3AR882 mutations in leukemic cells obtained from patients. Surprisingly, DNMT3AR882 mutations were largely dispensable for disease maintenance. Replacing DNMT3AR882 mutants with wild-type DNMT3A did not impair the ability of AML cells to engraft in vivo, and minimally altered DNA methylation. Taken together, DNMT3AR882 mutations are initially necessary for AML initiation, but are largely dispensable for disease maintenance. The notion that initiating oncogenes differ from those that maintain cancer has important implications for cancer evolution and therapy.
    DOI:  https://doi.org/10.1158/2159-8290.CD-24-1604
  34. Nat Commun. 2025 Nov 17. 16(1): 10064
    Structures of human organellar SPFH protein complexes.
    Jingjing Gao, Dawafuti Sherpa, Nikita Kupko, Haruka Chino, Jianwei Zeng, Sichen Shao.
      Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are found in all kingdoms of life and in multiple eukaryotic organelles. SPFH proteins assemble into homo- or hetero-oligomeric rings that form domed structures. Most SPFH assemblies also abut a cellular membrane, where they are implicated in diverse functions ranging from membrane organization to protein quality control. However, the precise architectures of different SPFH complexes remain unclear. Here, we report single-particle cryo-EM structures of the endoplasmic reticulum (ER)-resident Erlin1/2 complex and the mitochondrial prohibitin (PHB1/2) complex, revealing assemblies of 13 heterodimers of Erlin1 and Erlin2 and 11 heterodimers of PHB1 and PHB2, respectively. We also describe key interactions underlying the architecture of each complex and conformational heterogeneity of the PHB1/2 complex. Our findings elucidate the distinct stoichiometries and properties of human organellar SPFH complexes and highlight common principles of SPFH complex organization.
    DOI:  https://doi.org/10.1038/s41467-025-65078-3
  35. EMBO J. 2025 Nov 17.
    Measuring mitochondrial membrane potential.
    Oscar Tovar-Ferrero, Javier Rubio, Antonio Zorzano, Guillermo Martínez-Corrales, Marc Liesa.
      
    DOI:  https://doi.org/10.1038/s44318-025-00632-9
  36. Nat Metab. 2025 Nov 21.
    The metabolic engine of cognition: microglia-neuron interactions in health, ageing and disease.
    Evridiki Asimakidou, Stefano Pluchino, Bianca Ambrogina Silva, Luca Peruzzotti-Jametti.
      Cognitive impairment is associated with perturbations of fine-tuned neuroimmune interactions. At the molecular level, alterations in cellular metabolism can compromise brain function, driving structural damage and cognitive deficits. In this Review, we focus on the bidirectional interactions between microglia, the brain-resident immune cells and neurons to dissect the metabolic determinants of brain resilience and cognition. We first outline these metabolic pathways during development and adult life. Then, we delineate how these processes are perturbed in ageing, as well as in metabolic, neuroinflammatory and neurodegenerative disorders. By doing so, we provide a mechanistic understanding of the metabolic pathways relevant to cognitive function in health and disease, thus paving the way for novel therapeutic targets based on the emerging field of neuroimmunometabolism.
    DOI:  https://doi.org/10.1038/s42255-025-01409-4
  37. Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2504565122
    Rac1 promotes proximal tubule kidney repair by coupling the actin cytoskeleton to mitochondrial function.
    Olga M Viquez, Meiling Melzer, Shensen Li, Matthew Tantengco, Xinyu Dong, Eric Sha, Jeffery Huang, Evan S Krystofiak, Rachel C Hart, Wentian Luo, Christian Warren, Al-Borhan Bayazid, Richard Zhang, Ryoichi Bessho, Volker H Haase, Cord Brakebusch, Takanari Inoue, Craig Brooks, Matthew H Wilson, Andrew S Terker, Juan P Arroyo, Ambra Pozzi, Roy Zent, Fabian Bock.
      The kidney proximal tubule (PT) is a specialized polarized epithelium that functions as a high capacity resorptive machine. PT cells are exquisitely sensitive to ischemia due to their high metabolic rate. The small GTPase Rac1 regulates epithelial function by promoting polarity through its effects on the actin cytoskeleton. We show that Rac1, in the setting of the recovery of the PT from ischemic injury, plays a critical role in reconstituting cellular bioenergetics by promoting actin cytoskeleton formation around damaged mitochondria. This mechanism removes damaged mitochondria through mitophagy and preserves PT metabolic capacity and reabsorption function. Loss of Rac1 causes intracellular lipid accumulation, energy depletion, and PT cell atrophy. Thus, Rac1 promotes the repair of PT cells by enhancing mitochondrial bioenergetics, rather than by regulating cell polarity via a mechanism that links the actin cytoskeleton to metabolic demands and cell morphology.
    Keywords:  actin cytoskeleton; kidney repair; mitochondria
    DOI:  https://doi.org/10.1073/pnas.2504565122
  38. RNA. 2025 Nov 17. pii: rna.080744.125. [Epub ahead of print]
    Miniature NAD+-II riboswitches control bacterial genes for nicotinamide salvage and de novo NAD+ biosynthesis.
    Christopher G King, Kenny P Cheng, Ronald R Breaker.
      Nicotinamide adenine dinucleotide (NAD) is a ubiquitous enzyme cofactor that serves as a carrier of hydride ions for metabolic oxidation-reduction reactions. NAD is also sometimes used as a source of activated adenosine monophosphate (AMP) for adenylation reactions or as a precursor of ADP-ribose upon removal of nicotinamide. Many bacterial riboswitch classes are known to sense nucleotide-derived enzyme cofactors, but NAD is one of several ancient cofactors that have few or no known riboswitch representatives. Two rare riboswitch classes, named NAD+-I and NAD+-II, have been reported that regulate genes relevant to NAD biosynthesis and transport. However, these RNAs exhibit unusual functional and structural properties. Here we report that miniature NAD+-II riboswitches, named mini-NAD+-II, are more abundant and widespread than the longer RNAs that were used to defined the original consensus model for this class. The newfound examples are commonly found within lactic acid bacteria, which are notable for varied metabolic fermentation strategies used to maintain sufficient NAD+. Furthermore, the simple H-type pseudoknot core of mini-NAD+-II aptamers is similar to that of class I preQ1 riboswitch (preQ1-I) aptamers. Thus, H-type pseudoknots might serve as a versatile architecture for the natural or synthetic construction of ligand-binding aptamers.
    Keywords:  aptamer; gene control; nicotinamide adenine dinucleotide; prequeosine; pseudoknot
    DOI:  https://doi.org/10.1261/rna.080744.125
  39. Eur J Pharmacol. 2025 Nov 18. pii: S0014-2999(25)01136-7. [Epub ahead of print] 178382
    Targeting the Powerhouse: A Critical Review of Mitochondrial Inhibitors as a Therapeutic Strategy in Lung Cancer.
    Woo Hyun Park.
      Lung cancer therapy is constrained by profound intrinsic and acquired resistance to targeted therapies and immunotherapy. To overcome this, a new therapeutic paradigm is emerging that targets the unique metabolic and survival dependencies of cancer cells. Mitochondria, the central hubs of metabolism, cell death, and signaling, represent a critical vulnerability. This review provides a new conceptual framework for understanding and targeting mitochondrial pathways in lung cancer. First, this review outlines the key "mitochondrial hallmarks" of lung cancer that create therapeutic windows, emphasizing the critical role of metabolic heterogeneity. Second, it provides a novel, mechanism-based classification of mitochondrial inhibitors into four major classes: (1) electron transport chain (ETC) inhibitors, (2) metabolic enzyme modulators, (3) apoptosis pathway modulators, and (4) mitochondrial quality control (MQC) disruptors. Third, this review critically analyzes the molecular mechanisms by which these inhibitors activate regulated cell death pathways (apoptosis, ferroptosis) and, most importantly, their potential in overcoming therapeutic resistance to standard-of-care. Fourth, it explores the mechanisms of mitochondrial crosstalk within the tumor microenvironment (TME), including intercellular transfer via tunneling nanotubes. Finally, this review presents a systematic review of the clinical landscape, synthesizing data from preclinical models and ongoing clinical trials. This review concludes by highlighting key limitations and future perspectives, positioning MQC and the mitochondrial unfolded protein response (UPRmt) as next-generation targets to improve patient outcomes.
    Keywords:  Ferroptosis; Lung Cancer; Mitochondria; Mitochondrial Inhibitors; Mitochondrial Quality Control (MQC); Therapeutic Resistance
    DOI:  https://doi.org/10.1016/j.ejphar.2025.178382
  40. Genome Res. 2025 Nov 17. pii: gr.281058.125. [Epub ahead of print]
    Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine.
    Sarah Leichter, Kami Ahmad, Steve Henikoff.
      Aging compromises intestinal integrity, yet the chromatin changes driving this decline remain unclear. Polycomb-mediated repression is essential for silencing developmental genes, but this regulatory mechanism becomes dysregulated with age. Although shifts in Polycomb regulation within intestinal stem cells have been linked to gut aging, the Polycomb landscape of differentiated cell types remains unexplored. Differentiated cells comprise the majority of the gut epithelium and directly impact both tissue and whole organismal aging. Using single-cell chromatin profiling of the Drosophila intestine, we identify cell type-specific chromatin landscape changes during aging. We find that old enterocytes aberrantly repress genes essential for transmembrane transport and chitin metabolism, contributing to intestinal barrier decline - an example of antagonistic pleiotropy in a regenerative tissue. Barrier decline leads to derepression of JAK/STAT ligands in all cell types and increased proliferation of aging stem cells, with elevated RNA Polymerase II (RNAPII) at S-phase-dependent histone genes. Specific upregulation of histone genes during aging stem cell proliferation resembles RNAPII hypertranscription of histone genes in aggressive human cancers. Our work reveals that misregulation of the Polycomb-mediated H3K27me3 histone modification in differentiated cells during aging not only underlies tissue decline but also mirrors transcriptional changes in cancer, suggesting a common mechanism linking aging and cancer progression.
    DOI:  https://doi.org/10.1101/gr.281058.125
  41. bioRxiv. 2025 Oct 02. pii: 2025.10.02.680077. [Epub ahead of print]
    Sequelae and reversal of age-dependent alterations in mitochondrial dynamics via autophagy enhancement in reprogrammed human neurons.
    Eva Klinman, Ji-Sun Kwon, Roland E Dolle, Stephen C Pak, Gary A Silverman, David H Perlmutter, Andrew S Yoo.
      How aging of human neurons affects dynamics of essential organelle such as mitochondria and autophagosomes remains largely unknown. MicroRNA-induced directly reprogrammed neurons (miNs) derived from adult fibroblasts retain age-associated signatures of the donor, enabling the study of age-dependent features in human neurons, including longitudinal isogenic samples. Transcriptomic analysis revealed that neurons derived from elderly individuals are characterized by gene expression changes associated with the regulation of autophagosomes, lysosomes, and mitochondria, compared to young counterparts. To clarify these changes at the cellular level, we performed live-cell imaging of cellular organelles in miNs from donors of different ages. Older donor miNs exhibit decreased mitochondrial membrane potential, which surprisingly co-occurs with a significant increase in mitochondrial fission and fusion events. We posit that the increased fission and fusion of mitochondria may reflect age-dependent compensation for impaired mitochondrial turnover, perhaps due to changes in autophagy. We subsequently identified a significant decrease in autophagosome acidification in neurons derived from individuals >65 years compared to younger donors, and a corresponding age-dependent reduction in neuritic lysosomes resulting in fewer lysosomes available to acidify autophagosomes. This age-dependent deficit in autolysosome flux was rescued by chemically promoting autophagosome generation, which also reversed the age-dependent increase in mitochondrial fission and fusion and improved mitochondrial health. Together, this work reveals a mechanism by which aging reduces autophagic flux secondary to a loss of neuritic lysosomes, resulting in in mitochondria-intrinsic mechanisms to avoid loss of energy production.
    DOI:  https://doi.org/10.1101/2025.10.02.680077
  42. Methods Mol Biol. 2026 ;2990 119-125
    Analysis of Cellular Metabolism Using Flow Cytometry.
    Christos Aronis, Matteo Villa.
      The understanding that cellular metabolism underlines the differentiation, activation, and function of immune cells has opened new avenues to modulate immunity. Here, we describe a method to analyze cellular metabolism using the quintessential immunological technique: flow cytometry. We analyze single cell suspensions, by combining the staining of surface immune cell markers and nutrient transporters, with the staining using metabolic dyes, to readout surrogates of metabolic pathway utilization with cell subset resolution.
    Keywords:  Cellular metabolism; Flow cytometry; Metabolic dyes; Single cell analysis; Surface nutrient transporters
    DOI:  https://doi.org/10.1007/978-1-0716-4997-8_10
  43. Mol Cell. 2025 Nov 20. pii: S1097-2765(25)00892-5. [Epub ahead of print]85(22): 4114-4115
    Leveraging biochemical covariance to better understand biology.
    Emeline Joulia, Christian M Metallo.
      In a recent Nature article, Xiao et al.1 report development of a metabolite-protein covariation architecture (MPCA) database from a diversity outbred mouse cohort that facilitates the deciphering of metabolite-protein relationships in liver and brown adipose tissue (BAT). Using these correlations, the authors describe a role for LRRC58 in controlling cysteine-taurine metabolism.
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.031
  44. Nat Rev Mol Cell Biol. 2025 Nov 17.
    Tissue expansion-enhanced mass-spectrometry imaging decodes biomolecular landscapes.
    Lang Ding.
      
    DOI:  https://doi.org/10.1038/s41580-025-00931-3
  45. Cell Rep. 2025 Nov 13. pii: S2211-1247(25)01229-X. [Epub ahead of print]44(11): 116458
    Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.
    Vinayak V Viswanadham, Sonia N Kim, Emre Caglayan, Ryan N Doan, Yanmei Dou, Sara Bizzotto, Sattar Khoshkhoo, August Yue Huang, Rebecca Yeh, Brian H Chhouk, Alex Truong, Kathleen M Chappell, Marc Beaudin, Alison Barton, Shyam K Akula, Yifan Zhao, Lariza Rento, Michael Lodato, Ryan A Szeto, Javier Ganz, Pengpeng Li, Jessica W Tsai, Robert Sean Hill, Peter J Park, Christopher A Walsh.
      The human cerebral cortex is specialized into regions, but little is known about how human cellular lineages shape cortical regional variation and neuronal cell-type distribution during development. Here, we map single-cell lineages of human cortical regions and neuronal subtypes using >1,000 somatic single-nucleotide variants (sSNVs) identified from deep bulk whole-genome sequencing and analyzed over 25 regions and >72,000 single cells. In the fronto-parietal cortex, sSNVs are rarely restricted, marking neuron-generating clones that disperse into neighboring regions. In contrast, the primary visual cortex harbors 30%-70% more sSNVs than the neighboring secondary visual cortex. Clones at this border exhibit more restricted dispersion, suggesting late developmental lineage segregation. Single-nucleus sSNV and whole-transcriptome analysis reveal glutamatergic neuron clones with modest regional restrictions that share low-mosaic sSNVs with some GABAergic neurons, suggesting a recent dorsal cortical progenitor. Our analysis reveals human-specific cortical lineage patterns, regional differences in clonal patterns, and late divergence of some glutamatergic/GABAergic lineages.
    Keywords:  CP: genomics; CP: neuroscience; cortical development; glutamatergic neurons; interneurons; lineage tracing; single-cell transcriptomics; somatic mutations; spatial genomics; visual cortex
    DOI:  https://doi.org/10.1016/j.celrep.2025.116458
  46. Cell Genom. 2025 Nov 19. pii: S2666-979X(25)00325-8. [Epub ahead of print] 101069
    Genetic architecture of the murine red blood cell proteome reveals central role of hemoglobin beta cysteine 93 in maintaining redox balance.
    Gregory R Keele, Monika Dzieciatkowska, Ariel M Hay, Matthew Vincent, Callan O'Connor, Daniel Stephenson, Julie A Reisz, Travis Nemkov, Kirk C Hansen, Grier P Page, James C Zimring, Gary A Churchill, Angelo D'Alessandro.
      Red blood cells (RBCs) transport oxygen but accumulate oxidative damage over time, reducing function in vivo and during storage, critical for transfusions. To explore the genetics of RBC resilience, we profiled proteins, metabolites, and lipids from fresh and stored RBCs from 350 genetically diverse mice. Our analysis identified over 6,000 quantitative trait loci (QTLs). Compared to other tissues, the prevalence of trans genetic effects over cis ones reflects the absence of de novo protein synthesis in anucleated RBCs. QTL hotspots at Hbb, Hba, Mon1a, and (storage-specific) Steap3 linked ferroptosis to hemolysis. Proteasome QTLs clustered at multiple loci, underscoring the importance of degrading oxidized proteins. Post-translational modification (PTM) QTLs mapped predominantly to hemoglobins, including cysteine residues. The loss of reactive C93 in humanized mice (hemoglobulin beta [HBB] C93A) disrupted redox balance, glutathione pools, glutathionylation, and redox PTMs. These findings highlight genetic regulation of RBC oxidation, with implications for transfusion biology and oxidative-stress-dependent hemolytic disorders.
    Keywords:  Diversity Outbred mice; PTM QTL; blood transfusion; erythrocyte; hematology; hemoglobin; oxidative stress; pQTL; storage lesion
    DOI:  https://doi.org/10.1016/j.xgen.2025.101069
  47. J Biol Chem. 2025 Nov 17. pii: S0021-9258(25)02806-6. [Epub ahead of print] 110954
    Bacillus subtilis encodes three N-acetylcysteine deacetylase enzymes that can catalyze the final step in S-(2-succino)cysteine breakdown.
    Anthony J Zmuda, Andrew J Toensing, Katie B Wissbroecker, Thomas D Niehaus.
      Succination occurs when the TCA cycle intermediate fumarate reacts with cellular thiols, such as cysteine, yielding the damaged metabolite S-(2-succino)cysteine (2SC). Increased fumarate levels result in global succination of thiol-containing macromolecule and metabolites, which has been implicated in many human diseases. 2SC is a chemically stable molecule, however, enzymatic breakdown pathways have been identified in prokaryotes that involve N-acetylation of 2SC followed by a breakdown step that results in release of the succino- moiety and N-acetylcysteine (NAC). NAC must be metabolized to cysteine to be assimilated, but enzymes catalyzing NAC deacetylation had hitherto not been thoroughly characterized. Here, we describe three enzymes in Bacillus subtilis, ScmP, YhaA, and YtnL, that all possess high NAC deacetylase activity in vitro. All three enzymes are metal-dependent hydrolases that are most active with cobalt and show remarkable specificity to NAC compared to structurally related acetylated small molecules. Growth assays demonstrated that these genes are functionally redundant in B. subtilis, and growth on NAC is only severely compromised when all three genes are knocked out of the genome. Together, our biochemical and genetic studies complete the functional characterization of the three step 2SC degradation pathway in B. subtilis.
    Keywords:  Bacillus; acetylation; bacterial metabolism; biodegradation; enzyme catalysis; post‐translational modification (PTM)
    DOI:  https://doi.org/10.1016/j.jbc.2025.110954
  48. Nature. 2025 Nov 19.
    Tumour-reactive heterotypic CD8 T cell clusters from clinical samples.
    Sofía Ibáñez-Molero, Johanna Veldman, Juan Simon Nieto, Joleen J H Traets, Austin George, Kelly Hoefakker, Anita Karomi, Rolf Harkes, Bram van den Broek, Su Min Pack, Liselotte Tas, Nils L Visser, Susan E van Hal-van Veen, Paula Alóndiga-Mérida, Maartje Alkemade, Iris M Seignette, Renaud Tissier, Marja Nieuwland, Martijn van Baalen, Joanna Poźniak, Erik Mul, Simon Tol, Sofia Stenqvist, Lisa M Nilsson, Jonas A Nilsson, John B A G Haanen, Winan J van Houdt, Daniel S Peeper.
      Emerging evidence suggests a correlation between CD8+ T cell-tumour cell proximity and anti-tumour immune response1,2. However, it remains unclear whether these cells exist as functional clusters that can be isolated from clinical samples. Here, using conventional and imaging flow cytometry, we show that from 21 out of 21 human melanoma metastases, we could isolate heterotypic clusters, comprising CD8+ T cells interacting with one or more tumour cells and/or antigen-presenting cells (APCs). Single-cell RNA-sequencing analysis revealed that T cells from clusters were enriched for gene signatures associated with tumour reactivity and exhaustion. Clustered T cells exhibited increased TCR clonality indicative of expansion, whereas TCR-matched T cells showed more exhaustion and co-modulation when conjugated to APCs than when conjugated to tumour cells. T cells that were expanded from clusters ex vivo exerted on average ninefold increased killing activity towards autologous melanomas, which was accompanied by enhanced cytokine production. After adoptive cell transfer into mice, T cells from clusters showed improved patient-derived melanoma control, which was associated with increased T cell infiltration and activation. Together, these results demonstrate that tumour-reactive CD8+ T cells are enriched in functional clusters with tumour cells and/or APCs and that they can be isolated and expanded from clinical samples. Typically excluded by single-cell gating in flow cytometry, these distinct heterotypic T cell clusters are a valuable source to decipher functional tumour-immune cell interactions and may also be therapeutically explored.
    DOI:  https://doi.org/10.1038/s41586-025-09754-w
  49. Nat Commun. 2025 Nov 19. 16(1): 10123
    Mitochondria relay cholesterol signal exacerbates osteoarthritis in mice.
    Yiyang Ma, Yidan Pang, Chenglong Liu, Yuchen Tian, Kaiwen Zheng, Meng Yao, Xiaofeng Liu, Ruomu Cao, Yiwei Zhao, Zhikai Zheng, Weitao Jia, Daoyu Zhu, Hao Peng, Dajiang Du, Xinhua Qu, Chuan-Ju Liu, Pei Yang, Yigang Huang, Changqing Zhang, Junjie Gao.
      Osteoarthritis (OA) is the most common joint disease characterized by joint inflammation and cartilage deterioration. Though disrupted cholesterol metabolism has been implicated in the pathogenesis of OA, the underlying mechanisms remains unclear. Here we demonstrate that increased cholesterol in joint is a crucial activator of the cGAS-STING pathway in cartilage during OA. Subchondral osteocytes, which contact with blood vessel and cartilage, increase their uptake of cholesterol and transfer mitochondria to cartilage to trigger its inflammatory pathway. This process is mediated by increased cytosolic mitochondrial DNA (mtDNA) in chondrocytes, and is further amplified through enhanced mitochondrial transfer between chondrocytes. Mechanistically, we identify a mitochondrial subpopulation in osteocytes that enriched in Nudt8, which act as a key regulator of metabolic-inflammatory crosstalk. Nudt8 alters cholesterol metabolism by degrading coenzyme A, leading to an accumulation of cytosolic mtDNA and subsequent activation of the cGAS-STING pathway in chondrocytes. Pharmacological targeting osteocyte mitochondrial Nudt8 by supplementing pantethine ameliorate inflammation in cartilage and joint pain in OA mice, offering a potential therapeutic strategy for OA.
    DOI:  https://doi.org/10.1038/s41467-025-65689-w
  50. Nature. 2025 Nov 19.
    Prime editing-installed suppressor tRNAs for disease-agnostic genome editing.
    Sarah E Pierce, Steven Erwood, Keyede Oye, Meirui An, Nicholas Krasnow, Emily Zhang, Aditya Raguram, Davis Seelig, Mark J Osborn, David R Liu.
      Precise genome-editing technologies such as base editing1,2 and prime editing3 can correct most pathogenic gene variants, but their widespread clinical application is impeded by the need to develop new therapeutic agents for each mutation. For diseases that are caused by premature stop codons, suppressor tRNAs (sup-tRNAs) offer a more general strategy. Existing approaches to use sup-tRNAs therapeutically, however, require lifelong administration4,5 or show modest potency, necessitating potentially toxic overexpression. Here we present prime editing-mediated readthrough of premature termination codons (PERT), a strategy to rescue nonsense mutations in a disease-agnostic manner by using prime editing to permanently convert a dispensable endogenous tRNA into an optimized sup-tRNA. Iterative screening of thousands of variants of all 418 human tRNAs identified tRNAs with the strongest sup-tRNA potential. We optimized prime editing agents to install an engineered sup-tRNA at a single genomic locus without overexpression and observed efficient readthrough of premature termination codons and protein rescue in human cell models of Batten disease, Tay-Sachs disease and cystic fibrosis. In vivo delivery of a single prime editor that converts an endogenous mouse tRNA into a sup-tRNA extensively rescued disease pathology in a model of Hurler syndrome. PERT did not induce detected readthrough of natural stop codons or cause significant transcriptomic or proteomic changes. Our findings suggest the potential of disease-agnostic therapeutic genome-editing approaches that require only a single composition of matter to treat diverse genetic diseases.
    DOI:  https://doi.org/10.1038/s41586-025-09732-2
  51. Trends Immunol. 2025 Nov 19. pii: S1471-4906(25)00286-8. [Epub ahead of print]
    Regulation of intestinal injury via dietary cysteine.
    Francesco Siracusa, Nicola Gagliani.
      Chi and colleagues revealed that dietary cysteine enhances intestinal stem cell (ISC) regeneration, driving coenzyme A (CoA) synthesis and expansion of intraepithelial (IEL) CD8αβ+ T cells that secrete IL-22. This epithelial-immune crosstalk potentiates ISC repair after injury, highlighting a metabolism-immune axis linking cysteine sensing to tissue regeneration.
    DOI:  https://doi.org/10.1016/j.it.2025.11.003
  52. Cell. 2025 Nov 19. pii: S0092-8674(25)01235-8. [Epub ahead of print]
    Macrophage-targeted immunocytokine leverages myeloid, T, and NK cell synergy for cancer immunotherapy.
    Michelle von Locquenghien, Pascale Zwicky, Ken Xie, Diego Adhemar Jaitin, Fadi Sheban, Adam Yalin, Florian Uhlitz, Chamutal Gur, Reut Sharet Eshed, Eyal David, Kfir Mazuz, Caroline Jennings Marin, Ankita Sankar, Devin Mediratta, Roberto Avellino, Assaf Weiner, Ido Amit.
      Tumor-associated macrophages (TAMs) expressing the myeloid checkpoint TREM2 are key immunosuppressive cells in the tumor microenvironment (TME), driving tumor progression and contributing to poor prognosis in cancer patients. Due to their pivotal role, TAMs have emerged as a promising target for immunotherapies. However, current TAM-targeting monotherapies show limited efficacy, highlighting the need for strategies engaging multiple immune modalities. Here, we developed myeloid-targeted immunocytokines and natural killer (NK)/T cell enhancers (MiTEs) harnessing myeloid and lymphoid synergy for immunotherapy. MiTEs are trans-acting immunocytokines with tumor-specific activation, allowing dual targeting of TAMs and lymphocytes by TREM2 antagonism and cytotoxic effector cell activation through interleukin (IL)-2. To avoid off-target toxicities, MiTEs contain an IL-2 masking moiety, which is cleaved by a TAM-specific protease. MiTEs demonstrate high efficacy in preclinical tumor models through extensive immune reprogramming spanning TAM, T, and NK cell compartments. MiTEs show transformative potential for treating solid cancers by inducing potent multi-axis anti-tumor immunity while minimizing toxicities.
    Keywords:  T and NK cell synergy; TME-conditional IL-2; TREM2; cancer immunotherapy; cytokines; myeloid checkpoints; myeloid-targeted immunocytokine; single-cell genomics; synthetic immunology; tumor-associated macrophages; tumor-microenvironment modulation
    DOI:  https://doi.org/10.1016/j.cell.2025.10.030
  53. PLoS Biol. 2025 Nov 21. 23(11): e3003504
    The efficacy of longevity interventions in Caenorhabditis elegans is determined by the early life activity of RNA splicing factors.
    Sneha Dutta, Maria Camila Perez Matos, Caroline Heintz, Ayse Sena Mutlu, Mary Piper, Meeta Mistry, Arpit Sharma, Christopher S Morrow, Hannah Smith, Porsha Howell, Rohan Sehgal, Anne Lanjuin, Meng C Wang, William B Mair.
      Geroscience aims to target the aging process to extend healthspan. However, even isogenic individuals show heterogeneity in natural aging rate and responsiveness to pro-longevity interventions, limiting translational potential. Using RNAseq analysis of young, isogenic, subpopulations of Caenorhabditis elegans selected solely on the basis of the splicing pattern of an in vivo minigene reporter that is predictive of future life expectancy, we find a strong correlation in young animals between predicted life span and alternative splicing of mRNAs related to lipid metabolism. The activity of two RNA splicing factors, Reversed Polarity-1 (REPO-1) and Splicing Factor 1 (SFA-1), early in life is necessary for C. elegans response to specific longevity interventions and leads to context-specific changes to fat content that is mirrored by knockdown of their direct target POD-2/ACC1. Moreover, POD-2/ACC1 is required for the same longevity interventions as REPO-1/SFA-1. In addition, early inhibition of REPO-1 renders animals refractory to late onset suppression of the TORC1 pathway. Together, we propose that splicing factor activity establishes a cellular landscape early in life that enables responsiveness to specific longevity interventions and may explain variance in efficacy between individuals.
    DOI:  https://doi.org/10.1371/journal.pbio.3003504
  54. Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2509312122
    Glutathionylated DNA adducts accumulate in mitochondrial DNA and are regulated by AP endonuclease 1 and tyrosyl-DNA phosphodiesterase 1.
    Yu Hsuan Chen, Martin Esparza Sanchez, Ta I Hung, Jin Tang, Wenyan Xu, Jiekai Yin, Yinsheng Wang, Chia-En A Chang, Huimin Zhang, Junjie Chen, Linlin Zhao.
      Mitochondrial DNA (mtDNA) is crucial for cellular energy production, metabolism, and signaling. Its dysfunction is implicated in various diseases, including mitochondrial disorders, neurodegeneration, and diabetes. mtDNA is susceptible to damage by endogenous and environmental factors; however, unlike nuclear DNA (nDNA), mtDNA lesions do not necessarily lead to an increased mutation load in mtDNA. Instead, mtDNA lesions have been implicated in innate immunity and inflammation. Here, we report a type of mtDNA damage: glutathionylated DNA (GSH-DNA) adducts. These adducts are formed from abasic (AP) sites, key intermediates in base excision repair, or from alkylation DNA damage. Using mass spectrometry, we quantified the GSH-DNA lesion in both nDNA and mtDNA and found its significant accumulation in mtDNA of two different human cell lines, with levels one or two orders of magnitude higher than in nDNA. The formation of GSH-DNA adducts is influenced by TFAM and polyamines, and their levels are regulated by repair enzymes AP endonuclease 1 (APE1) and tyrosyl-DNA phosphodiesterase 1 (TDP1). The accumulation of GSH-DNA adducts is associated with the downregulation of several ribosomal and complex I subunit proteins and the upregulation of proteins related to redox balance and mitochondrial dynamics. Molecular dynamics (MD) simulations revealed that the GSH-DNA lesion stabilizes the TFAM-DNA binding, suggesting shielding effects from mtDNA transactions. Collectively, this study provides critical insights into the formation, regulation, and biological effects of GSH-DNA adducts in mtDNA. Our findings underscore the importance of understanding how these lesions may contribute to innate immunity and inflammation.
    Keywords:  DNA damage; DNA repair; GSH; PRDX6; TFAM
    DOI:  https://doi.org/10.1073/pnas.2509312122
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