bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2025–02–16
29 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Redefining phenotypic intratumor heterogeneity of pancreatic ductal adenocarcinoma: a bottom-up approach.
  2. Extracellular vesicles from the lung pro-thrombotic niche drive cancer-associated thrombosis and metastasis via integrin beta 2.
  3. Look Beyond Plasma Membrane Biophysics: Revealing Considerable Variability of the Dipole Potential Between Plasma and Organelle Membranes of Living Cells.
  4. Concurrent Inhibition of the RAS-MAPK Pathway and PIKfyve is a Therapeutic Strategy for Pancreatic Cancer.
  5. Intercellular adhesion boots collective cell migration through elevated membrane tension.
  6. KRAS mutation status integrated with RNA subtyping improves prognostic modeling in FOLFIRINOX-treated metastatic pancreatic cancer.
  7. Aging, cancer, and autophagy: connections and therapeutic perspectives.
  8. Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues.
  9. Addressing persistent challenges in digital image analysis of cancer tissue: resources developed from a hackathon.
  10. Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy.
  11. Intrinsic electrical activity drives small-cell lung cancer progression.
  12. Neuronal mimicry in tumors: lessons from neuroscience to tackle cancer.
  13. Analyzing the Cholesteryl Ester Fraction in Lipid Droplets with a Polarity-Ultrasensitive Fluorescence Lifetime Probe.
  14. Bafilomycin A1 induces colon cancer cell death through impairment of the endolysosome system dependent on iron.
  15. Identification of intratumoral bacteria that enhance breast tumor metastasis.
  16. HBimmCue: A Versatile Fluorescent Probe for Multi-Scale Imaging of Lipid Polarity and Membrane Order in Inner Mitochondrial Membrane.
  17. Assessing acute pancreatitis: A novel method combining live cell imaging with tissue damage evaluation.
  18. TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis.
  19. Early detection of pancreatic cancer by a high-throughput protease-activated nanosensor assay.
  20. Txnip deficiency causes a susceptibility to acute cold stress with brown fat dysfunction in mice.
  21. A polarity-sensitive fluorescent probe for visualizing lipid droplets in ferroptosis, cuproptosis, and autophagy.
  22. A relative metabolic flux analysis model of glucose anaplerosis.
  23. Adhesion-regulated dynamics of cells.
  24. The LC3-interacting region of NBR1 is a protein interaction hub enabling optimal flux.
  25. Segment Anything for Microscopy.
  26. Cellpose3: one-click image restoration for improved cellular segmentation.
  27. Intracellular signalling in arterial chemoreceptors during acute hypoxia and glucose deprivation: role of ATP.
  28. Converging mechanism of UM171 and KBTBD4 neomorphic cancer mutations.
  29. Directing autophagy to degrade cell surface receptors.
  1. J Pathol. 2025 Feb 11.
    Redefining phenotypic intratumor heterogeneity of pancreatic ductal adenocarcinoma: a bottom-up approach.
    Marc Hilmi, Flore Delecourt, Jérôme Raffenne, Taib Bourega, Nelson Dusetti, Juan Iovanna, Yuna Blum, Magali Richard, Cindy Neuzillet, Anne Couvelard, Matthieu Tihy, Louis de Mestier, Vinciane Rebours, Rémy Nicolle, Jérôme Cros.
      Pancreatic ductal adenocarcinoma (PDAC) tumor interpatient heterogeneity has been well described with two major prognostic subtypes (classical and basal-like). An important intrapatient heterogeneity has been reported but has not yet been studied extensively due to the lack of standardized, reproducible, and easily accessible high-throughput methods. We built an immunohistochemical (IHC) tool capable of differentiating RNA-defined classical and basal-like tumors by selecting relevant antibodies using a multistep process. The successive stages of (i) an in silico selection from a literature review and a bulk transcriptome analysis of 309 PDACs, (ii) a tumor-specific selection from 30 patient-derived xenografts and single-cell data, followed by (iii) the validation on tissue microarrays in 50 PDAC were conducted. We used our final IHC panel on two independent cohorts of resected PDAC (n = 95, whole-slide, n = 148, tissue microarrays) for external validation. After digitization and registration of pathology slides, we performed a tile-based analysis in tumor areas to identify relevant marker combinations. Sequential marker selection led to the following panel: GATA6, CLDN18, TFF1, MUC16, S100A2, KRT17, PanBasal. Four different phenotypes were identified: one classical, one intermediate (KRT17+), and two basal-like (MUC16+ versus S100A2+) with specific biological properties. The presence of a minor basal contingent drastically reduced overall survival [hazard ratio (HR) = 1.90, p = 0.03], even in classical predominant PDACs. Analysis of preneoplastic lesions suggested that pancreatic carcinogenesis might follow a progressive evolution from classical toward a basal through an early intermediate phenotype. In conclusion, our IHC panel redefined and easily assessed the high degree of intra- and intertumoral heterogeneity of PDAC. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
    Keywords:  image analysis; molecular subtypes; pancreatic ductal adenocarcinoma; tumoral heterogeneity
    DOI:  https://doi.org/10.1002/path.6398
  2. Cell. 2025 Feb 10. pii: S0092-8674(25)00094-7. [Epub ahead of print]
    Extracellular vesicles from the lung pro-thrombotic niche drive cancer-associated thrombosis and metastasis via integrin beta 2.
    Serena Lucotti, Yusuke Ogitani, Candia M Kenific, Jacob Geri, Young Hun Kim, Jinghua Gu, Uthra Balaji, Linda Bojmar, Lee Shaashua, Yi Song, Michele Cioffi, Pernille Lauritzen, Oveen M Joseph, Tetsuhiko Asao, Paul M Grandgenett, Michael A Hollingsworth, Christopher Peralta, Alexandra E Pagano, Henrik Molina, Harry B Lengel, Elizabeth G Dunne, Xiaohong Jing, Madeleine Schmitter, Lucia Borriello, Thomas Miller, Haiying Zhang, Yevgeniy Romin, Katia Manova, Doru Paul, H Lawrence Remmel, Eileen M O'Reilly, William R Jarnagin, David Kelsen, Sharon M Castellino, Lisa Giulino-Roth, David R Jones, John S Condeelis, Virginia Pascual, James B Bussel, Nancy Boudreau, Irina Matei, David Entenberg, Jacqueline F Bromberg, Diane M Simeone, David Lyden.
      Cancer is a systemic disease with complications beyond the primary tumor site. Among them, thrombosis is the second leading cause of death in patients with certain cancers (e.g., pancreatic ductal adenocarcinoma [PDAC]) and advanced-stage disease. Here, we demonstrate that pro-thrombotic small extracellular vesicles (sEVs) are secreted by C-X-C motif chemokine 13 (CXCL13)-reprogrammed interstitial macrophages in the non-metastatic lung microenvironment of multiple cancers, a niche that we define as the pro-thrombotic niche (PTN). These sEVs package clustered integrin β2 that dimerizes with integrin αX and interacts with platelet-bound glycoprotein (GP)Ib to induce platelet aggregation. Blocking integrin β2 decreases both sEV-induced thrombosis and lung metastasis. Importantly, sEV-β2 levels are elevated in the plasma of PDAC patients prior to thrombotic events compared with patients with no history of thrombosis. We show that lung PTN establishment is a systemic consequence of cancer progression and identify sEV-β2 as a prognostic biomarker of thrombosis risk as well as a target to prevent thrombosis and metastasis.
    Keywords:  cancer; cancer metastasis; cancer-associated thrombosis; extracellular vesicles; integrin beta 2; platelets; pro-thrombotic niche
    DOI:  https://doi.org/10.1016/j.cell.2025.01.025
  3. Int J Mol Sci. 2025 Jan 22. pii: 889. [Epub ahead of print]26(3):
    Look Beyond Plasma Membrane Biophysics: Revealing Considerable Variability of the Dipole Potential Between Plasma and Organelle Membranes of Living Cells.
    Mate Szabo, Bence Cs Szabo, Kitti Kurtan, Zoltan Varga, Gyorgy Panyi, Peter Nagy, Florina Zakany, Tamas Kovacs.
      Due to the lack of measurement techniques suitable for examining compartments of intact, living cells, membrane biophysics is almost exclusively investigated in the plasma membrane despite the fact that its alterations in intracellular organelles may also contribute to disease pathogenesis. Here, we employ a novel, easy-to-use, confocal microscopy-based approach utilizing F66, an environment-sensitive fluorophore in combination with fluorescent organelle markers and quantitative image analysis to determine the magnitude of the molecular order-related dipole potential in the plasma membrane and intracellular organelles of various tumor and neural cell lines. Our comparative analysis demonstrates considerable intracellular variations of the dipole potential that may be large enough to modulate protein functions, with an inward decreasing gradient on the route of the secretory/endocytic pathway (plasma membrane >> lysosome > Golgi > endoplasmic reticulum), whereas mitochondrial membranes are characterized by a dipole potential slightly larger than that of lysosomes. Our approach is suitable and sensitive enough to quantify membrane biophysical properties selectively in intracellular compartments and their comparative analysis in intact, living cells, and, therefore, to identify the affected organelles and potential therapeutic targets in diseases associated with alterations in membrane lipid composition and thus biophysics such as tumors, metabolic, neurodegenerative, or lysosomal storage disorders.
    Keywords:  Golgi; endoplasmic reticulum; fluorescence microscopy; intracellular organelles; lysosome; membrane biophysics; membrane dipole potential; mitochondrion
    DOI:  https://doi.org/10.3390/ijms26030889
  4. Cancer Res. 2025 Feb 11.
    Concurrent Inhibition of the RAS-MAPK Pathway and PIKfyve is a Therapeutic Strategy for Pancreatic Cancer.
    Jonathan M DeLiberty, Mallory K Roach, Clint A Stalnecker, Ryan Robb, Elyse G Schechter, Noah L Pieper, Khalilah E Taylor, Lily M Pita, Runying Yang, Scott Bang, Kristina Drizyte-Miller, Sarah E Ackermann, Sheila R Nicewarner Peña, Elisa Baldelli, Sophia M Min, David H Drewry, Emanuel F Petricoin, John P Morris, Channing J Der, Adrienne D Cox, Kirsten L Bryant.
      Pancreatic ductal adenocarcinoma (PDAC) is characterized by KRAS- and autophagy-dependent growth. Inhibition of the KRAS-RAF-MEK-ERK pathway enhances autophagic flux and dependency, and concurrent treatment with the nonspecific autophagy inhibitor chloroquine (CQ) and ERK-MAPK pathway inhibitors can synergistically block PDAC growth. However, CQ is limited in terms of specificity and potency. To find alternative anti-autophagy strategies, here we performed a CRISPR-Cas9 loss-of-function screen in PDAC cell lines that identified the lipid kinase PIKfyve as a growth-promoting gene. PIKfyve inhibition by the small molecule apilimod resulted in durable growth suppression, with much greater potency than CQ treatment. PIKfyve inhibition caused lysosomal dysfunction, reduced autophagic flux, and led to the accumulation of autophagy-related proteins. Furthermore, PIKfyve inhibition blocked the compensatory increases in autophagic flux associated both with MEK inhibition and with direct RAS inhibition. Accordingly, combined inhibition of PIKfyve and the RAS-MAPK pathway showed robust growth suppression across a panel of KRAS-mutant PDAC models. Growth suppression was due, in part, to potentiated cell cycle arrest and induction of apoptosis following loss of IAP proteins. These findings indicate that concurrent inhibition of RAS and PIKfyve is a synergistic, cytotoxic combination that may represent a therapeutic strategy for PDAC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-1757
  5. Nat Commun. 2025 Feb 12. 16(1): 1588
    Intercellular adhesion boots collective cell migration through elevated membrane tension.
    Brent M Bijonowski, Jongkwon Park, Martin Bergert, Christina Teubert, Alba Diz-Muñoz, Milos Galic, Seraphine V Wegner.
      In multicellular systems, the migration pattern of individual cells critically relies on the interactions with neighboring cells. Depending on the strength of these interactions, cells either move as a collective, as observed during morphogenesis and wound healing, or migrate individually, as it is the case for immune cells and fibroblasts. Mediators of cell-cell adhesions, such as cadherins coordinate collective dynamics by linking the cytoskeleton of neighboring cells. However, whether intercellular binding alone triggers signals that originate from within the plasma membrane itself, remains unclear. Here, we address this question through artificial photoswitchable cell-cell adhesions that selectively connect adjacent plasma membranes without linking directly to cytoskeletal elements. We find that these intercellular adhesions are sufficient to achieve collective cell migration. Linking adjacent cells increases membrane tension, which activates the enzyme phospholipase D2. The resulting increase in phosphatidic acid, in turn, stimulates the mammalian target of rapamycin, a known actuator of collective cell migration. Collectively, these findings introduce a membrane-based signaling axis as promotor of collective cell dynamics, which is independent of the direct coupling of cell-cell adhesions to the cytoskeleton.
    DOI:  https://doi.org/10.1038/s41467-025-56941-4
  6. Med. 2025 Feb 04. pii: S2666-6340(25)00028-5. [Epub ahead of print] 100601
    KRAS mutation status integrated with RNA subtyping improves prognostic modeling in FOLFIRINOX-treated metastatic pancreatic cancer.
    Marjolein F Lansbergen, Mark P G Dings, Jan Koster, Mariette Labots, Emile D Kerver, Anouk Jochems, Marjolein Y V Homs, Judith de Vos-Geelen, Mathijs P Hendriks, Michael W T Tanck, Johanna W Wilmink, Hanneke W M van Laarhoven, Maarten F Bijlsma.
       BACKGROUND: First-line chemotherapy (5-fluorouracil, leucovorin, irinotecan, and oxaliplatin [FOLFIRINOX]) benefits few patients with metastatic pancreatic ductal adenocarcinoma (mPDAC). Prognostic markers for treatment-related survival are needed. This study validated the added benefit of whole-genome sequencing (WGS) to transcriptome-based classification in modeling FOLFIRINOX-related survival.
    METHODS: Patients with mPDAC planning to start FOLFIRINOX were included in a prospective nationwide cohort. Pretreatment biopsies were submitted to WGS and RNA sequencing. Samples of non-FOLFIRINOX-treated patients were included for exploratory analyses.
    FINDINGS: WGS was performed in biopsies from 108 FOLFIRINOX-treated patients and 51 non-FOLFIRINOX-treated patients. 12% of the tumors were KRAS wild type. These tumors had more targetable alterations (42% vs. 17%) and were associated with a longer median overall survival (mOS) than KRAS mutant tumors (7.8 months in KRAS mutant vs. 17.7 months in wild-type tumors, p = 0.0024). Transcriptome-based clustering revealed a tumor subgroup showing low classical and basal-like gene expression, enriched for KRAS wild-type status (p < 0.0001), a so-called "classifier-negative" subtype. The gene expression of these classifier-negative tumors correlated with neural-like signatures. For patients with a homologous recombination-deficient (HRD) tumor, mOS was not increased (8.0 months in homologous recombination-proficient [HRP] vs. 13.3 months in HRD tumors, p = 0.21).
    CONCLUSIONS: KRAS wild-type tumors are a distinct PDAC subgroup with a better prognosis. Consequently, KRAS status assessment before transcriptome-based subtyping can stratify patients into three prognostic molecular subgroups (KRAS wild type, KRAS mutant classical, and KRAS mutant basal like). This integrative way of classification should be validated prior to incorporation in diagnostic practice.
    FUNDING: ZonMw "Good Use of Medicine" program (848101012).
    Keywords:  DNA mutation; FOLFIRINOX; KRAS gene; RNA sequencing; Translation to patients; chemotherapy; pancreatic cancer; pancreatic ductal adenocarcinoma; prognostic biomarkers; subtype; whole-genome sequencing
    DOI:  https://doi.org/10.1016/j.medj.2025.100601
  7. Front Mol Biosci. 2024 ;11 1516789
    Aging, cancer, and autophagy: connections and therapeutic perspectives.
    Begoña Zapatería, Esperanza Arias.
      Aging and cancer are intricately linked through shared molecular processes that influence both the onset of malignancy and the progression of age-related decline. As organisms age, cellular stress, genomic instability, and an accumulation of senescent cells create a pro-inflammatory environment conducive to cancer development. Autophagy, a cellular process responsible for degrading and recycling damaged components, plays a pivotal role in this relationship. While autophagy acts as a tumor-suppressive mechanism by preventing the accumulation of damaged organelles and proteins, cancer cells often exploit it to survive under conditions of metabolic stress and treatment resistance. The interplay between aging, cancer, and autophagy reveals key insights into tumorigenesis, cellular senescence, and proteostasis dysfunction. This review explores the molecular connections between these processes, emphasizing the potential for autophagy-targeted therapies as strategies that could be further explored in both aging and cancer treatment. Understanding the dual roles of autophagy in suppressing and promoting cancer offers promising avenues for therapeutic interventions aimed at improving outcomes for elderly cancer patients while addressing age-related deterioration.
    Keywords:  aging; autopaghy; cancer; proteostasis; therapeutics
    DOI:  https://doi.org/10.3389/fmolb.2024.1516789
  8. Nat Commun. 2025 Feb 12. 16(1): 1579
    Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues.
    IMAXT Grand Challenge Consortium
      Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines an innovative membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validate the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supports the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrate the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yields ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.
    DOI:  https://doi.org/10.1038/s41467-025-56641-z
  9. Mol Oncol. 2025 Feb 10.
    Addressing persistent challenges in digital image analysis of cancer tissue: resources developed from a hackathon.
    Sandhya Prabhakaran, Clarence Yapp, Gregory J Baker, Johanna Beyer, Young Hwan Chang, Allison L Creason, Robert Krueger, Jeremy Muhlich, Nathan Heath Patterson, Kevin Sidak, Damir Sudar, Adam J Taylor, Luke Ternes, Jakob Troidl, Xie Yubin, Artem Sokolov, Darren R Tyson.
      The National Cancer Institute (NCI) supports numerous research consortia that rely on imaging technologies to study cancerous tissues. To foster collaboration and innovation in this field, the Image Analysis Working Group (IAWG) was created in 2019. As multiplexed imaging techniques grow in scale and complexity, more advanced computational methods are required beyond traditional approaches like segmentation and pixel intensity quantification. In 2022, the IAWG held a virtual hackathon focused on addressing challenges in analyzing complex, high-dimensional datasets from fixed cancer tissues. The hackathon addressed key challenges in three areas: (1) cell type classification and assessment, (2) spatial data visualization and translation, and (3) scaling image analysis for large, multi-terabyte datasets. Participants explored the limitations of current automated analysis tools, developed potential solutions, and made significant progress during the hackathon. Here we provide a summary of the efforts and resultant resources and highlight remaining challenges facing the research community as emerging technologies are integrated into diverse imaging modalities and data analysis platforms.
    Keywords:  artifact removal; artifacts; cancer; computational scalability; domain representation; image analysis
    DOI:  https://doi.org/10.1002/1878-0261.13783
  10. Nat Methods. 2025 Feb 12.
    Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy.
    Stephan Daetwyler, Hanieh Mazloom-Farsibaf, Felix Y Zhou, Dagan Segal, Etai Sapoznik, Bingying Chen, Jill M Westcott, Rolf A Brekken, Gaudenz Danuser, Reto Fiolka.
      Most biological processes, from development to pathogenesis, span multiple time and length scales. While light-sheet fluorescence microscopy has become a fast and efficient method for imaging organisms, cells and subcellular dynamics, simultaneous observations across all these scales have remained challenging. Moreover, continuous high-resolution imaging inside living organisms has mostly been limited to a few hours, as regions of interest quickly move out of view due to sample movement and growth. Here, we present a self-driving, multiresolution light-sheet microscope platform controlled by custom Python-based software, to simultaneously observe and quantify subcellular dynamics in the context of entire organisms in vitro and in vivo over hours of imaging. We apply the platform to the study of developmental processes, cancer invasion and metastasis, and we provide quantitative multiscale analysis of immune-cancer cell interactions in zebrafish xenografts.
    DOI:  https://doi.org/10.1038/s41592-025-02598-2
  11. Nature. 2025 Feb 12.
    Intrinsic electrical activity drives small-cell lung cancer progression.
    Paola Peinado, Marco Stazi, Claudio Ballabio, Michael-Bogdan Margineanu, Zhaoqi Li, Caterina I Colón, Min-Shu Hsieh, Shreoshi Pal Choudhuri, Victor Stastny, Seth Hamilton, Alix Le Marois, Jodie Collingridge, Linus Conrad, Yinxing Chen, Sheng Rong Ng, Margaret Magendantz, Arjun Bhutkar, Jin-Shing Chen, Erik Sahai, Benjamin J Drapkin, Tyler Jacks, Matthew G Vander Heiden, Maksym V Kopanitsa, Hugh P C Robinson, Leanne Li.
      Elevated or ectopic expression of neuronal receptors promotes tumour progression in many cancer types1,2; neuroendocrine (NE) transformation of adenocarcinomas has also been associated with increased aggressiveness3. Whether the defining neuronal feature, namely electrical excitability, exists in cancer cells and impacts cancer progression remains mostly unexplored. Small-cell lung cancer (SCLC) is an archetypal example of a highly aggressive NE cancer and comprises two major distinct subpopulations: NE cells and non-NE cells4,5. Here we show that NE cells, but not non-NE cells, are excitable, and their action potential firing directly promotes SCLC malignancy. However, the resultant high ATP demand leads to an unusual dependency on oxidative phosphorylation in NE cells. This finding contrasts with the properties of most cancer cells reported in the literature, which are non-excitable and rely heavily on aerobic glycolysis. Additionally, we found that non-NE cells metabolically support NE cells, a process akin to the astrocyte-neuron metabolite shuttle6. Finally, we observed drastic changes in the innervation landscape during SCLC progression, which coincided with increased intratumoural heterogeneity and elevated neuronal features in SCLC cells, suggesting an induction of a tumour-autonomous vicious cycle, driven by cancer cell-intrinsic electrical activity, which confers long-term tumorigenic capability and metastatic potential.
    DOI:  https://doi.org/10.1038/s41586-024-08575-7
  12. Cancer Metastasis Rev. 2025 Feb 11. 44(1): 31
    Neuronal mimicry in tumors: lessons from neuroscience to tackle cancer.
    Hanan Bloomer, Haley B Dame, Savannah R Parker, Madeleine J Oudin.
      Cellular plasticity and the ability to avoid terminal differentiation are hallmarks of cancer. Here, we review the evidence that tumor cells themselves can take on properties of neurons of the central nervous system, which can regulate tumor growth and metastasis. We discuss recent evidence that axon guidance molecules and regulators of electrical activity and synaptic transmission, such as ion channels and neurotransmitters, can drive the oncogenic and invasive properties of tumor cells from a range of cancers. We also review how FDA-approved treatments for neurological disorders are being tested in pre-clinical models and clinical trials for repurposing as anti-cancer agents, offering the potential for new therapies for cancer patients that can be accessed more quickly.
    Keywords:  Axon guidance; Drug repurposing; Ion channels; Metastasis; Neuron; Synapse
    DOI:  https://doi.org/10.1007/s10555-025-10249-3
  13. Anal Chem. 2025 Feb 12.
    Analyzing the Cholesteryl Ester Fraction in Lipid Droplets with a Polarity-Ultrasensitive Fluorescence Lifetime Probe.
    Sijia Lu, Yanyan Zhao, Diankai Liu, Zixu He, He Li, Wei Zhang, Xiaohua Li, Huimin Ma, Wen Shi.
      Quantifying the lipid composition of cellular lipid droplets (LDs) in situ is challenging but crucial for understanding lipid metabolic diseases. Here, we propose a fluorescence lifetime imaging method based on a polarity-sensitive probe (LD660) for analyzing the lipid composition of the LDs. The probe emits strong fluorescence at 660 nm only in apolar LD environments, with dielectric constants of 2-4, and outperforms Nile red in LD imaging. Importantly, the fluorescence lifetime of LD660 increases with the incremental fraction of cholesteryl ester in neutral lipid mixtures. Using fluorescence lifetime microscopy with LD660, we imaged and quantified the cholesteryl ester fractions of LDs in cells and tissues. It is found that macrophages and surrounding hepatocytes in fatty liver diseases show significantly higher cholesteryl ester contents than other hepatocytes. This finding suggests that cholesteryl ester may serve as a potential indicator of the degree of hepatic steatosis.
    DOI:  https://doi.org/10.1021/acs.analchem.4c06472
  14. Sci Rep. 2025 Feb 12. 15(1): 5148
    Bafilomycin A1 induces colon cancer cell death through impairment of the endolysosome system dependent on iron.
    Dong Hwa Min, Dasom Kim, Seung Taek Hong, Joohee Kim, Min Jung Kim, Seung-Hae Kwon, Aeree Kim, Ji-Yun Lee.
      The late endolysosomal compartment plays a crucial role in cancer cell metabolism by regulating lysosomal activity, essential for cell proliferation, and the degradation of cellular components during the final stages of autophagy. Modulating late endolysosomal function represents a new target for cancer therapy. In this study, we investigated the effects of bafilomycin A1 (BA1), a vacuolar H+-ATPase inhibitor, on colon cancer and normal colon fibroblasts (CCD-18Co) cells. We found that very low concentrations (~ 2 nM) of BA1 selectively induced cell death in colon cancer cells. This cytotoxicity was associated with lysosomal stress response and dysregulation of iron homeostasis. BA1 treatment resulted in significant alterations to the endolysosomal system, including an increased number and size of lysosomes, lysosomal membrane permeabilization, and autophagy flux blockade. These changes were accompanied by endoplasmic reticulum stress and lipid droplet accumulation. Furthermore, BA1 decreased intracellular Fe2+ levels, as measured using FerroOrange. Notably, iron (III)-citrate supplementation rescued cells from BA1-induced death. These findings suggest that BA1-induced endolysosomal dysfunction impairs iron homeostasis, ultimately leading to colon cancer cell death. Our results highlight the potential of targeting endolysosomal function and iron homeostasis as novel therapeutic strategies for colon cancer, paving the way for more selective and effective treatments.
    Keywords:  Autophagy; Bafilomycin A1; Colorectal cancer; Endolysosome; Iron
    DOI:  https://doi.org/10.1038/s41598-025-89127-5
  15. mBio. 2025 Feb 11. e0359524
    Identification of intratumoral bacteria that enhance breast tumor metastasis.
    Zachary J Gerbec, Antonio Serapio-Palacios, Avril Metcalfe-Roach, Zakhar Krekhno, Haggai Bar-Yoseph, Sarah E Woodward, Jorge Pena-Díaz, Oksana Nemirovsky, Shannon Awrey, Sebastian H Moreno, Sean Beatty, Esther Kong, Nina Radisavljevic, Mihai Cirstea, Shawn Chafe, Paul C McDonald, Sam Aparicio, B Brett Finlay, Shoukat Dedhar.
      The central, mortality-associated hallmark of cancer is the process of metastasis. It is increasingly recognized that bacteria influence multiple facets of cancer progression, but the extent to which tumor microenvironment-associated bacteria control metastasis in cancer is poorly understood. To identify tumor-associated bacteria and their role in metastasis, we utilized established murine models of non-metastatic and metastatic breast tumors to identify bacteria capable of driving metastatic disease. We found several species of the Bacillus genus that were unique to metastatic tumors, and found that breast tumor cells cultured with a Bacillus bacterium isolated from metastatic tumors, Bacillus thermoamylovorans, produced nearly 3× the metastatic burden as control cells or cells cultured with bacteria from non-metastatic breast tumors. We then performed targeted metabolomics on tumor cells cultured with different bacterial species and found that B. thermoamylovorans differentially regulated tumor cell metabolite profiles compared to bacteria isolated from non-metastatic tumors. Using these bacteria, we performed de novo sequencing and tested for the presence of genes that were unique to the bacterium isolated from metastatic tumors in a patient population to provide a proof-of-concept for identifying how specific bacterial functions are associated with the metastatic process in cancer independent of bacterial species. Together, our data directly demonstrate the ability of specific bacteria to promote metastasis through interaction with cancer cells.
    IMPORTANCE: Metastasis is a major barrier to long-term survival for cancer patients, and therapeutic options for patients with aggressive, metastatic forms of breast cancer remain limited. It is therefore critical to understand the differences between non-metastatic and metastatic disease to identify potential methods for slowing or even stopping metastasis. In this work, we identify a bacterial species present with metastatic breast tumors capable of increasing the metastatic capabilities of tumor cells. We isolated and sequenced this bacteria, as well as a control species which failed to promote metastasis, and identified specific bacterial genes that were unique to the metastasis-promoting species. We tested for the presence of these bacterial genes in patient tumor samples and found they were more likely to be associated with mortality. We also identified enrichment of specific bacterial functions, providing insight into possible sources of bacteria-driven increases in the metastatic potential of multiple cancer types.
    Keywords:  Bacillus; cancer; intratumoral bacteria; metastasis; tumor microbiome
    DOI:  https://doi.org/10.1128/mbio.03595-24
  16. Adv Sci (Weinh). 2025 Feb 09. e2414343
    HBimmCue: A Versatile Fluorescent Probe for Multi-Scale Imaging of Lipid Polarity and Membrane Order in Inner Mitochondrial Membrane.
    Shu Gao, Jing Sun, Yiwei Hou, Xichuan Ge, Ming Shi, Hongxi Zheng, Yan Zhang, Meiqi Li, Baoxiang Gao, Peng Xi.
      Mitochondrial membrane environmental dynamics are crucial for understanding function, yet high-resolution observation remains challenging. Here, HBimmCue is introduced as a fluorescent probe localized to inner mitochondrial membrane (IMM) that reports lipid polarity and membrane order changes, which correlate with cellular respiration levels. Using HBimmCue and fluorescence lifetime imaging microscopy (FLIM), IMM lipid heterogeneity is uncovered across scales, from nanoscale structures within individual mitochondria to mouse pre-implantation embryos. At the sub-organelle level, stimulated emission depletion (STED)-FLIM imaging highlights nanoscale polarity variations within the IMM. At the sub-cellular and cellular level, reduced IMM lipid polarity is observed in damaged mitochondria marked for lysosomal degradation and distinct IMM lipid distributions are identified in neurons and disease models. Additionally, metabolic dysfunction associated with oocytes aging and metabolic reprogramming from zygote to blastocyst is detected. Together, the work demonstrates the broad applicability of HBimmCue, offering a new paradigm for investigating lipid polarity and respiration level at multiple scales.
    Keywords:  HBimmCue; fluorescence lifetime imaging microscopy; inner mitochondrial membrane; lipid polarity
    DOI:  https://doi.org/10.1002/advs.202414343
  17. Histol Histopathol. 2025 Feb 04. 18882
    Assessing acute pancreatitis: A novel method combining live cell imaging with tissue damage evaluation.
    Polona Kovačič, Maša Skelin Klemen, Eva Paradiž Leitgeb, Viktória Venglovecz, Lóránd Kiss, Gabriella Mihalekné Fűr, Andraž Stožer, Jurij Dolenšek.
      Acute pancreatitis (AP) is a sudden inflammation of the exocrine part of the pancreas, resulting in self-digestion and destruction of exocrine tissue. The intricate relationship between exocrine and endocrine functions is pivotal, as damage to acinar cells can affect endocrine cell function and vice versa. However, our understanding of these interactions remains limited. An effective strategy for investigating pancreatic cells involves the utilization of live in-situ acute mouse pancreas tissue slice preparations, combined with noninvasive fluorescent calcium labeling of endocrine or exocrine cells, and subsequent analysis using confocal laser scanning microscopy. Nevertheless, this approach encounters inherent conflicts with conventional methodologies employed to histologically assess the severity of tissue damage due to AP in the model. Traditional methods involve fixing and staining tissue samples with hematoxylin and eosin, thereby precluding live-cell imaging. In this study, our objective was to introduce an innovative method utilizing a commercial fluorescence Live/Dead assay that enables calcium imaging and tissue damage assessment in the same sample. This approach was validated against the classical histological grading of AP severity, and we found a good correlation between the classical histological grading method and the in-situ approach employing the Live/Dead assay. The primary advantage of our novel approach lies in its capacity to enable timely and efficient live-cell imaging together with damage assessment in the same tissue, thereby enabling the study of functional consequences of structural damage at the cellular level and reducing the number of animals required for experimentation.
    DOI:  https://doi.org/10.14670/HH-18-882
  18. BMC Bioinformatics. 2025 Feb 08. 26(1): 44
    TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis.
    Masahiro Ono.
       BACKGROUND: Fluorescent Timer proteins, which display time-dependent changes in their emission spectra, are invaluable for analyzing the temporal dynamics of cellular events at the single-cell level. We previously developed the Timer-of-cell-kinetics-and-activity (Tocky) tools, utilizing a specific Timer protein, Fast-FT, to monitor temporal changes in cellular activities. Despite their potential, the analysis of Timer fluorescence in flow cytometry is frequently compromised by variability in instrument settings and the absence of standardized preprocessing methods. The development and implementation of effective data preprocessing methods remain to be achieved.
    RESULTS: In this study, we introduce the R package that automates the data preprocessing of Timer fluorescence data from flow cytometry experiments for quantitative analysis at single-cell level. Our aim is to standardize Timer data analysis to enhance reproducibility and accuracy across different experimental setups. The package includes a trigonometric transformation method to elucidate the dynamics of Fluorescent Timer proteins. We have identified the normalization of immature and mature Timer fluorescence data as essential for robust analysis, clarifying how this normalization affects the analysis of Timer maturation. These preprocessing methods are all encapsulated within the TockyPrep package.
    CONCLUSIONS: TockyPrep is available for distribution via GitHub at https://github.com/MonoTockyLab/TockyPrep , providing tools for data preprocessing and basic visualization of Timer fluorescence data. This toolkit is expected to enhance the utility of experimental systems utilizing Fluorescent Timer proteins, including the Tocky tools.
    Keywords:  Data preprocessing; Flow Cytometry; Fluorescent Timer Protein; Nr4a3-Tocky; Tocky
    DOI:  https://doi.org/10.1186/s12859-025-06058-8
  19. Sci Transl Med. 2025 Feb 12. 17(785): eadq3110
    Early detection of pancreatic cancer by a high-throughput protease-activated nanosensor assay.
    Jose L Montoya Mira, Arnaud Quentel, Ranish K Patel, Dove Keith, Megan Sousa, Jessica Minnier, Benjamin R Kingston, Larry David, Sadik C Esener, Rosalie C Sears, Charles D Lopez, Brett C Sheppard, Utkan Demirci, Melissa H Wong, Jared M Fischer.
      Pancreatic ductal adenocarcinoma (PDAC) is among the top causes of cancer-related death. Patients are frequently diagnosed in the more advanced stages when effective treatment options are limited; however, earlier detection of PDAC by liquid biopsy may expand treatment options and improve survival outcomes. Here, we developed a noninvasive detection assay for PDAC based on serum protease activity to leverage the increase in cancer-associated protease activity in the peripheral blood of patients with PDAC. We screened a series of protease-cleavable peptide probes for the discrimination of PDAC samples versus healthy controls and noncancerous pancreatic disease. We identified a single MMP-sensitive probe, which could distinguish PDAC from controls with 79 ± 6% accuracy. We further developed this probe into a rapid magnetic nanosensor assay, termed PAC-MANN, that measures serum protease cleavage of a target-probe nanosensor with a simple fluorescent readout. In a longitudinal cohort of patients undergoing surgical removal of the primary tumor, the probe cleavage signal was reduced by 16 ± 24% after surgery. In a separate blinded retrospective study, the PAC-MANN assay identified PDAC samples with 98% specificity and 73% sensitivity across all stages and distinguished 100% of patients with noncancer pancreatic disease relative to patients with PDAC. The PAC-MANN assay combined with the clinical biomarker CA 19-9 was 85% sensitive for detection of stage I PDAC with 96% specificity. Therefore, the PAC-MANN assay is a rapid, high-throughput method that uses small blood volumes with the potential to enhance early PDAC detection, specifically among individuals at high risk of developing PDAC.
    DOI:  https://doi.org/10.1126/scitranslmed.adq3110
  20. J Biol Chem. 2025 Feb 11. pii: S0021-9258(25)00141-3. [Epub ahead of print] 108293
    Txnip deficiency causes a susceptibility to acute cold stress with brown fat dysfunction in mice.
    Meng Zou, Katsuya Tanabe, Kikuko Amo-Shiinoki, Daisuke Kohno, Syota Kagawa, Hideki Shirasawa, Kenji Ikeda, Akihiko Taguchi, Yasuharu Ohta, Shigeru Okuya, Tetsuya Yamada, Tadahiro Kitamura, Hiroshi Masutani, Yukio Tanizawa.
      Mammals adaptively regulate energy metabolism in response to environmental changes such as starvation and cold circumstances. Thioredoxin-interacting protein (Txnip), known as a redox regulator, serves as a nutrient sensor regulating energy homeostasis. Txnip is essential for mice to adapt to starvation, but its role in adapting to cold circumstances remains unclear. Here, we identified Txnip as a pivotal factor for maintaining non-shivering thermogenesis in mice. Txnip protein levels in brown adipose tissue (BAT) were upregulated by the acute cold exposure. Txnip-deficient (Txnip-/-) mice acclimated to thermoneutrality (30°C) exhibited significant BAT enlargement and triglyceride accumulation with downregulation of BAT signature and metabolic gene expression. Upon acute cold exposure (5°C), Txnip-/- mice showed a rapid decline in BAT surface temperatures with the failure of increasing metabolic respiration, developing lethal hypothermia. The BAT dysfunction and cold susceptibility in Txnip-/- mice were corrected by acclimation to 16°C, protecting the mice from life-threatening hypothermia. Transcriptomic and metabolomic analysis using dissected BAT revealed that despite preserving glycolysis, the BAT of Txnip-/- mice failed to activate the catabolism of branched-chain amino acids and fatty acids in response to acute cold stress. These findings illustrate that Txnip is required for maintaining basal BAT function and ensuring cold-induced thermogenesis.
    Keywords:  Thioredoxin-interacting protein; brown adipose tissue; cold stress; metabolism; thermogenesis
    DOI:  https://doi.org/10.1016/j.jbc.2025.108293
  21. Spectrochim Acta A Mol Biomol Spectrosc. 2025 Feb 03. pii: S1386-1425(25)00160-X. [Epub ahead of print]332 125854
    A polarity-sensitive fluorescent probe for visualizing lipid droplets in ferroptosis, cuproptosis, and autophagy.
    Yang Lv, Haoyu Jin, Zhe Liu, Na Li, Ye-Xin Liao, Jianliang Shen, Ji-Ting Hou.
      Dynamics of lipid droplets (LDs) in various pathological processes provides important information about lipid metabolism during theses biological processes, while only a few reports focused on this field. In this work, a benzothiazine-fused coumarin chromophore BCLD with strong fluorescence in low-polarity environment is described. It is confirmed that cyclization-induced rigidification might be a promising approach to enhance the LDs specificity of phenothiazine-based strucutres.The probe is found to enter cells through a clathrin-mediated endocytosis, and is able to monitor LDs variations in living cells, especially during various pathological processes. It is found that obvious increase in polarity of LDs during ferroptosis and cuproptosis was visualized while a dramatic decrease in the number of LDs was recorded during autophagy, indicating different lipid metabolism manners and LD dynamics in these pathological processes. This work supports the potentials of LDs as markers for drug design targeting ferroptosis, cuproptosis, and autophagy.
    Keywords:  Fluorescent dyes; Lipid droplets; Pathological processes; Polarity sensing
    DOI:  https://doi.org/10.1016/j.saa.2025.125854
  22. Arch Biochem Biophys. 2025 Feb 06. pii: S0003-9861(25)00043-8. [Epub ahead of print] 110330
    A relative metabolic flux analysis model of glucose anaplerosis.
    Heesoo Jeong, Nathaniel M Vacanti.
      Glucose provides substrate for the predominant anaplerotic pathway which involves the activity of pyruvate carboxylase (PC). PC-mediated anaplerosis has been extensively studied as a metabolic regulator in glycolytic cells during tumorigenesis and metastasis. Herein, inaccuracies in established methods to measure relative intracellular flux through PC are highlighted and a compartmentalized condensed metabolic network (CCMN) is used to resolve the total malate pool into relative contributions from PC and other sources by metabolic flux analysis (MFA) with [U-13C6]glucose tracing. Performance of the CCMN method is evaluated in breast cancer cell lines that are exposed to small molecules targeting metabolism. Across conditions and cell lines, the CCMN approach yields results nearest to an accepted gold-standard methodology, using [3-13C]glucose, or even exposes the gold standard's limitations. The CCMN method does not require a separate experiment with a much more costly and generally less informative metabolic tracer, such as [3-13C]glucose, and in some cases, may outperform its application.
    Keywords:  breast cancer; metabolic flux; pyruvate carboxylase; stable-isotope tracing; systems biology
    DOI:  https://doi.org/10.1016/j.abb.2025.110330
  23. Biophys J. 2025 Feb 11. pii: S0006-3495(25)00027-X. [Epub ahead of print]
    Adhesion-regulated dynamics of cells.
    Shu-Yi Sun, Xindong Chen, Bo Li, Xi-Qiao Feng.
      A wide variety of dynamic behaviors of cells are closely associated with the active contraction of the cytoskeleton and the cell-substrate adhesion. By inhibiting cell-substrate adhesion, here we experimentally show that an isolated cell exhibits diverse morphological geometries and dynamic behaviors on different adhesion-inhibiting substrates. A biochemomechanical tensegrity model of cytoskeletons is adopted to elucidate the biophysical mechanisms underlying the spontaneous dynamic behaviors of isolated cells. Theoretical analysis shows that the dynamic behaviors of cells depend on the intrinsic active contraction of cytoskeletons and the adherent condition. Combining living cell experiments and numerical simulations, we find that cells may transform from oscillation mode to protrusion mode and then to spreading mode due to the increase of the adhesion force threshold. Furthermore, for oscillating cells, two characteristic patterns, including global oscillation and traveling wave, are captured. These findings highlight the role of environmental adherent properties in mediating cellular spatiotemporal dynamics.
    DOI:  https://doi.org/10.1016/j.bpj.2025.01.014
  24. J Cell Biol. 2025 Apr 07. pii: e202407105. [Epub ahead of print]224(4):
    The LC3-interacting region of NBR1 is a protein interaction hub enabling optimal flux.
    Brian J North, Amelia E Ohnstad, Michael J Ragusa, Christopher J Shoemaker.
      During autophagy, toxic cargo is encapsulated by autophagosomes and trafficked to lysosomes for degradation. NBR1, an autophagy receptor targeting ubiquitinated aggregates, serves as a model for studying the multivalent, heterotypic interactions of cargo-bound receptors. Here, we find that three critical NBR1 partners-ATG8-family proteins, FIP200, and TAX1BP1-each bind to distinct, overlapping determinants within a short linear interaction motif (SLiM). To explore whether overlapping SLiMs extend beyond NBR1, we analyzed >100 LC3-interacting regions (LIRs), revealing that FIP200 and/or TAX1BP1 binding to LIRs is a common phenomenon and suggesting LIRs as protein interaction hotspots. Phosphomimetic peptides demonstrate that phosphorylation generally enhances FIP200 and ATG8-family binding but not TAX1BP1, indicating differential regulation. In vivo, LIR-mediated interactions with TAX1BP1 promote optimal NBR1 flux by leveraging additional functionalities from TAX1BP1. These findings reveal a one-to-many binding modality in the LIR motif of NBR1, illustrating the cooperative mechanisms of autophagy receptors and the regulatory potential of multifunctional SLiMs.
    DOI:  https://doi.org/10.1083/jcb.202407105
  25. Nat Methods. 2025 Feb 12.
    Segment Anything for Microscopy.
    Anwai Archit, Luca Freckmann, Sushmita Nair, Nabeel Khalid, Paul Hilt, Vikas Rajashekar, Marei Freitag, Carolin Teuber, Genevieve Buckley, Sebastian von Haaren, Sagnik Gupta, Andreas Dengel, Sheraz Ahmed, Constantin Pape.
      Accurate segmentation of objects in microscopy images remains a bottleneck for many researchers despite the number of tools developed for this purpose. Here, we present Segment Anything for Microscopy (μSAM), a tool for segmentation and tracking in multidimensional microscopy data. It is based on Segment Anything, a vision foundation model for image segmentation. We extend it by fine-tuning generalist models for light and electron microscopy that clearly improve segmentation quality for a wide range of imaging conditions. We also implement interactive and automatic segmentation in a napari plugin that can speed up diverse segmentation tasks and provides a unified solution for microscopy annotation across different microscopy modalities. Our work constitutes the application of vision foundation models in microscopy, laying the groundwork for solving image analysis tasks in this domain with a small set of powerful deep learning models.
    DOI:  https://doi.org/10.1038/s41592-024-02580-4
  26. Nat Methods. 2025 Feb 12.
    Cellpose3: one-click image restoration for improved cellular segmentation.
    Carsen Stringer, Marius Pachitariu.
      Generalist methods for cellular segmentation have good out-of-the-box performance on a variety of image types; however, existing methods struggle for images that are degraded by noise, blurring or undersampling, all of which are common in microscopy. We focused the development of Cellpose3 on addressing these cases and here we demonstrate substantial out-of-the-box gains in segmentation and image quality for noisy, blurry and undersampled images. Unlike previous approaches that train models to restore pixel values, we trained Cellpose3 to output images that are well segmented by a generalist segmentation model, while maintaining perceptual similarity to the target images. Furthermore, we trained the restoration models on a large, varied collection of datasets, thus ensuring good generalization to user images. We provide these tools as 'one-click' buttons inside the graphical interface of Cellpose as well as in the Cellpose API.
    DOI:  https://doi.org/10.1038/s41592-025-02595-5
  27. J Physiol. 2025 Feb 12.
    Intracellular signalling in arterial chemoreceptors during acute hypoxia and glucose deprivation: role of ATP.
    María Torres-López, Patricia González-Rodríguez, Olalla Colinas, Hee-Sool Rho, Hortensia Torres-Torrelo, Antonio Castellano, Lin Gao, Patricia Ortega-Sáenz, José López-Barneo.
      The carotid body (CB) is the main oxygen (O2) sensing organ that mediates reflex hyperventilation and increased cardiac output in response to hypoxaemia. Acute O2 sensing is an intrinsic property of CB glomus cells, which contain special mitochondria to generate signalling molecules (NADH and H2O2) that modulate membrane K+ channels in response to lowered O2 tension (hypoxia). In parallel with these membrane-associated events, glomus cells are highly sensitive to mitochondrial electron transport chain (ETC) inhibitors. It was suggested that a decrease in oxidative production of ATP is a critical event mediating hypoxia-induced cell depolarization. Here, we show that rotenone [an inhibitor of mitochondrial complex (MC) I] activates rat and mouse glomus cells but abolishes their responsiveness to hypoxia. Rotenone does not prevent further activation of the cells by cyanide (a blocker of MCIV) or glucose deprivation. Responsiveness to glucose deprivation is enhanced in O2-insenstive glomus cells with genetic disruption of MCI. These findings suggest that acute O2 sensing requires a functional MCI but that a decrease in intracellular ATP, presumably produced by the simultaneous inhibition of MCI and MCIV, is not involved in hypoxia signalling. In support of this concept, ATP levels in single glomus cells were unaltered by hypoxia, but rapidly declined following exposure of the cells to low glucose or to inhibitors of oxidative phosphorylation. These observations indicate that a reduction in intracellular ATP does not participate in physiological acute O2 sensing. However, local decreases in ATP of glycolytic origin may contribute to low glucose signalling in glomus cells. KEY POINTS: The carotid body contains oxygen-sensitive glomus cells with specialized mitochondria that generate signalling molecules (NADH and H2O2) to inhibit membrane K+ channels in response to hypoxia. Glomus cells are highly sensitive to electron transport chain (ETC) blockers. It was suggested that a decrease in intracellular ATP is the main signal inducing K+ channel inhibition and depolarization in response to hypoxia or ETC blockade. Rotenone, an inhibitor of mitochondrial complex (MC) I, activates glomus cells but abolishes their responsiveness to hypoxia. However, rotenone does not prevent further activation of glomus cells by cyanide (an MCIV blocker) or glucose deprivation. Single-cell ATP levels were unaltered by hypoxia, but decreased rapidly following exposure of glomus cells to 0 mM glucose or inhibitors of oxidative phosphorylation. A reduction in intracellular ATP does not participate in signalling acute hypoxia. However, it may contribute to hypoglycaemia signalling in glomus cells.
    Keywords:  H2O2; NADH; TASK3 channels; acute oxygen sensing; carotid body glomus cells; cytosolic ATP; electron transport chain inhibitors; glucose sensing; hypoxia; mitochondria‐to‐membrane signalling
    DOI:  https://doi.org/10.1113/JP287130
  28. Nature. 2025 Feb 12.
    Converging mechanism of UM171 and KBTBD4 neomorphic cancer mutations.
    Xiaowen Xie, Olivia Zhang, Megan J R Yeo, Ceejay Lee, Ran Tao, Stefan A Harry, N Connor Payne, Eunju Nam, Leena Paul, Yiran Li, Hui Si Kwok, Hanjie Jiang, Haibin Mao, Jennifer L Hadley, Hong Lin, Melissa Batts, Pallavi M Gosavi, Vincenzo D'Angiolella, Philip A Cole, Ralph Mazitschek, Paul A Northcott, Ning Zheng, Brian B Liau.
      Cancer mutations can create neomorphic protein-protein interactions to drive aberrant function1,2. As a substrate receptor of the CULLIN3-RING E3 ubiquitin ligase complex, KBTBD4 is recurrently mutated in medulloblastoma3, the most common embryonal brain tumour in children4. These mutations impart gain-of-function to KBTBD4 to induce aberrant degradation of the transcriptional corepressor CoREST5. However, their mechanism remains unresolved. Here we establish that KBTBD4 mutations promote CoREST degradation through engaging HDAC1/2 as the direct target of the mutant substrate receptor. Using deep mutational scanning, we chart the mutational landscape of the KBTBD4 cancer hotspot, revealing distinct preferences by which insertions and substitutions can promote gain-of-function and the critical residues involved in the hotspot interaction. Cryo-electron microscopy analysis of two distinct KBTBD4 cancer mutants bound to LSD1-HDAC1-CoREST reveals that a KBTBD4 homodimer asymmetrically engages HDAC1 with two KELCH-repeat β-propeller domains. The interface between HDAC1 and one of the KBTBD4 β-propellers is stabilized by the medulloblastoma mutations, which insert a bulky side chain into the HDAC1 active site pocket. Our structural and mutational analyses inform how this hotspot E3-neosubstrate interface can be chemically modulated. First, we unveil a converging shape-complementarity-based mechanism between gain-of-function E3 mutations and a molecular glue degrader, UM171. Second, we demonstrate that HDAC1/2 inhibitors can block the mutant KBTBD4-HDAC1 interface and proliferation of KBTBD4-mutant medulloblastoma cells. Altogether, our work reveals the structural and mechanistic basis of cancer mutation-driven neomorphic protein-protein interactions.
    DOI:  https://doi.org/10.1038/s41586-024-08533-3
  29. Nat Rev Drug Discov. 2025 Feb 10.
    Directing autophagy to degrade cell surface receptors.
    M Teresa Villanueva.
      
    Keywords:  Biotechnology; Cancer; Chemical biology; Drug discovery
    DOI:  https://doi.org/10.1038/d41573-025-00026-w
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