bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2025–05–25
48 papers selected by
Kıvanç Görgülü, Technical University of Munich



  1. Nature. 2025 May 21.
      To grow at distant sites, metastatic cells must overcome major challenges posed by the unique cellular and metabolic composition of secondary organs1. Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that metastasizes to the liver and lungs. Despite evidence of metabolic reprogramming away from the primary site, the key drivers that dictate the ability of PDAC cells to colonize the liver or lungs and survive there remain undefined. Here we identified PCSK9 as predictive of liver versus lung colonization by integrating metastatic tropism data of human PDAC cell lines2, in vivo metastasis modelling in mice and gene expression correlation analysis. PCSK9 negatively regulates low density lipoprotein (LDL)-cholesterol import and, accordingly, PCSK9-low PDAC cells preferentially colonize LDL-rich liver tissue. LDL-cholesterol taken up by liver-avid PCSK9-low cells supports activation of pro-growth mTORC1 activation at the lysosome, and through conversion into the signalling oxysterol, 24(S)-hydroxycholesterol, reprogrammes the microenvironment to release nutrients from neighbouring hepatocytes. Conversely, PCSK9-high, lung-avid PDAC cells rely on transcriptional upregulation of the distal cholesterol synthesis pathway to generate intermediates-7-dehydrocholesterol and 7-dehydrodesmosterol-with protective action against ferroptosis, a vulnerability in the oxygen-rich microenvironment of the lung. Increasing the amount of PCSK9 redirected liver-avid cells to the lung whereas ablating PCSK9 drove lung-avid cells to the liver, thereby establishing PCSK9 as necessary and sufficient for secondary organ site preference. Our studies reveal PCSK9-driven differential utilization of the distal cholesterol synthesis pathway as a key and potentially actionable driver of metastatic growth in PDAC.
    DOI:  https://doi.org/10.1038/s41586-025-09017-8
  2. Nat Biomed Eng. 2025 May 20.
      Cell density, the ratio of cell mass to volume, is an indicator of molecular crowding and a fundamental determinant of cell state and function. However, existing density measurements lack the precision or throughput to quantify subtle differences in cell states, particularly in primary samples. Here we present an approach for measuring the density of 30,000 single cells per hour by integrating fluorescence exclusion microscopy with a suspended microchannel resonator. This approach achieves a precision of 0.03% (0.0003 g ml-1) for cells larger than 12 μm in diameter. In human lymphocytes, we discover that cell density and its variation decrease as cells transition from quiescence to a proliferative state, suggesting that the level of molecular crowding decreases and becomes more regulated upon entry into the cell cycle. Using a pancreatic cancer patient-derived xenograft model, we find that the ex vivo density response of primary tumour cells to drug treatment can predict the in vivo tumour growth response. Our method reveals unexpected behaviour in molecular crowding during cell state transitions and suggests density as a biomarker for functional precision medicine.
    DOI:  https://doi.org/10.1038/s41551-025-01408-6
  3. Cell Mol Gastroenterol Hepatol. 2025 May 20. pii: S2352-345X(25)00077-3. [Epub ahead of print] 101536
       BACKGROUND & AIMS: Pancreatitis is an inflammatory disease of the exocrine pancreas and a known risk factor for pancreatic ductal adenocarcinoma (PDAC). Previously, we identified HMG-box transcription factor 1 (HBP1) as a potential master transcription factor (TF) in the early progression of PDAC, with its expression associated with poor patient survival, underscoring its significance in pancreatic disease. However, the functional role of HBP1 in the onset and progression of acute pancreatitis (AP) remains unknown.
    METHODS: We examined HBP1 expression in human pancreatitis samples and a cerulein-induced AP mouse model. Pancreatic-specific conditional HBP1 knockout mice, with or without an oncogenic Kras mutation, were generated and compared to their littermate controls. Spatial transcriptomics and multiplexed protein assays, histological analysis, and immunostaining were utilized to characterize pathological changes. Findings from mouse models were validated using inducible HBP1-overexpressing human pancreatic ductal epithelial cells.
    RESULTS: HBP1 was upregulated in pancreatic exocrine cells in human chronic pancreatitis and mouse acute pancreatitis, with its expression in human chronic pancreatitis correlating with cancer presence. Pancreatic HBP1 ablation disrupted acinar homeostasis by impairing autophagic flux and exacerbating inflammation following injury. In the presence of oncogenic KRAS, HBP1 ablation delayed the formation of pancreatic intraepithelial neoplasia (PanIN), the precursor to PDAC, and slowed its progression to higher-grade lesions.
    CONCLUSIONS: HBP1 upregulation in pancreatitis mitigates pancreatic inflammatory injury; however, in the presence of oncogenic KRAS, it facilitates PanIN progression. Thus, HBP1 serves as a critical regulator in both pancreatitis and early pancreatic neoplasia, representing a potential therapeutic target for intervening pancreatitis and PanIN progression.
    Keywords:  HMG box-containing protein 1 (HBP1); PanINs initiation; and autophagy; pancreatic injury; pancreatitis
    DOI:  https://doi.org/10.1016/j.jcmgh.2025.101536
  4. Autophagy Rep. 2024 ;3(1): 2383088
      The KEAP1 (kelch like ECH associated protein 1)- NFE2L2/NRF2 (NFE2 like bZIP transcription factor 2) pathway is a major antioxidative stress pathway that contributes to cellular homeostasis. KEAP1 acts as a sensor and attenuates degradation of the transcription factor NRF2, which induces gene expression for a network of enzymes involved in the antioxidant response. When cells are exposed to various electrophiles and reactive oxidative species, they modify one or more selective cysteine residues in KEAP1, resulting in conformational changes that disable its NRF2-inhibitory function. In addition to this redox-dependent pathway, SQSTM1/p62 (sequestosome 1), which is a selective autophagy receptor for ubiquitinated proteins and a driver of liquid-liquid phase separation (LLPS) upon binding to ubiquitinated proteins, competitively inhibits the binding between KEAP1 and NRF2, thereby disabling the NRF2-repressive function of KEAP1. Our study showed that phase-separated SQSTM1/p62 bodies are phosphorylated by ULK1 (Unc-51 like autophagy activating kinase 1) and that KEAP1 is retained in the SQSTM1/p62 body, resulting in NRF2-activation in a redox-independent manner.
    Keywords:  Autophagy; KEAP1; LLPS; NRF2; p62
    DOI:  https://doi.org/10.1080/27694127.2024.2383088
  5. Transl Oncol. 2025 May 17. pii: S1936-5233(25)00152-4. [Epub ahead of print]57 102421
       BACKGROUND: Emerging evidence suggests that chemotherapy can accumulate senescent-like cells within tumor tissues, a phenomenon linked to therapy resistance. The aim of this study is to analyze the senescence-like state of after-treatment persistent cells associated with KRAS mutational status to offer a therapeutic strategy to target these cells in pancreatic ductal adenocarcinoma (PDAC).
    EXPERIMENTAL DESIGN: Three commercial cell lines and five patient-derived primary cell cultures with different KRAS statuses were studied following gemcitabine treatment. Senescence-like status was assessed using SA-β-gal, together with cell cycle regulators such as p21. Additionally, KRAS mutations were modulated using MRTX1133 and AMG-510, and the signaling pathways ERK and AKT were analyzed and modulated in vitro. Finally, p21 expression, associated with the senescence-like state, on patient outcomes and treatment response was analyzed in publicly available bulk RNA-seq and single-nucleus datasets.
    RESULTS: We observed an overexpression of p21 alongside an increase in SA-β-gal signal in response to gemcitabine treatment, indicating the induction of a senescence-like state. Specific inhibition of KRAS G12D or G12C mutations reduced SA-β-gal signal and sensitized PDAC cells to gemcitabine. Moreover, ERK inhibition but not AKT inhibition decreased SA-β-gal signal. Additionally, we characterized p21 expression levels in relation to patient outcomes and found that they are modulated by treatment.
    CONCLUSIONS: This dual-targeted therapeutic strategy holds promises for overcoming the challenges posed by KRAS-driven cancers, particularly in addressing the formidable obstacle of pancreatic cancer.
    Keywords:  Gemcitabine; MRTX1133; Mutated KRAS; PDAC; Resistance; Senescence-like
    DOI:  https://doi.org/10.1016/j.tranon.2025.102421
  6. Pancreas. 2025 May 23.
       OBJECTIVE: Identify how surgical resection of pancreatic ductal adenocarcinoma (PDAC) affects systemic minimal residual disease (MRD).
    METHODS: Pancreatic tumors were generated by orthotopic implantation of tumor cells into the pancreas of immunocompetent mice. Tumor resection was carried out via distal pancreatectomy and splenectomy. Liver metastases and microenvironment immune changes were analyzed in resected vs. non-resected mice.
    RESULTS: Resection was accompanied by proliferative expansion of liver metastases and an increase in hepatic metastatic burden. Postoperative immune changes predominantly manifested as a time-dependent increase in eosinophils and decrease in neutrophils. The postoperative hepatic eosinophilia was protective of further metastatic progression. The parenchymal findings were detectable in the circulation, and the trends observed in the mouse model modeled those seen in PDAC patients postoperatively.
    CONCLUSION: Collectively, we describe a preclinical resection model that offers a means to investigate MRD. Using this model, we delineated effects of surgical resection on metastatic outgrowth and uncovered a protective link between the postoperative hepatic eosinophilia and further metastatic progression.
    Keywords:  eosinophils; immune reprogramming; liver metastasis; pancreatic ductal adenocarcinoma; pancreatic neoplasm; surgical stress
    DOI:  https://doi.org/10.1097/MPA.0000000000002516
  7. Autophagy Rep. 2024 ;3(1): 2412916
      Much is still unknown about microautophagy and its regulators. In our recent paper, one such regulator of microautophagy, the lipid kinase PIKfyve, is described. Previously it was found that treating cells with agents like lysomotropic drugs or proton ionophores, which alter lysosomal osmotic potential and pH, leads to a form of microautophagy that selectively degrades transmembrane proteins. Induction of this type of microautophagy is linked to a lysosomal stress response that involves the targeting of macroautophagy proteins, like ATG8s, to the lysosome membrane, through a mechanism called CASM. We found that CASM-induced microautophagy turns over ATG8s and other lysosomal membrane proteins, and requires PIKfyve activity functioning downstream of ATG8 lipidation. The lysosome biogenesis transcription factor TFEB is induced in parallel to microautophagy, in a CASM-dependent, but PIKfyve-independent manner. These findings demonstrate that stressors that engage CASM cause selective turnover by microautophagy that is coordinated with lysosome biogenesis through a mechanism that is separable through PIKfyve.
    Keywords:  ATG8; CASM; LC3; PIKfyve; TFEB; TRPML1; autophagy; lysosome; microautophagy
    DOI:  https://doi.org/10.1080/27694127.2024.2412916
  8. Database (Oxford). 2025 Apr 21. pii: baaf028. [Epub ahead of print]2025
      Understanding protein subcellular localization and its dynamic changes is crucial for elucidating cellular function and disease mechanisms, particularly under stress conditions, where protein localization changes can modulate cellular responses. Currently available databases provide insights into protein localization under steady-state conditions; however, stress-related dynamic localization changes remain poorly understood. Here, we present the Localizatome, a comprehensive database that captures stress-induced protein localization dynamics in living cells. Using an original high-throughput microscopy system and machine learning algorithms, we analysed the localization patterns of 10 287 fluorescent protein-fused human proteins in HeLa cells before and after exposure to oxidative stress. Our analysis revealed that 1910 proteins exhibited oxidative stress-dependent localization changes, particularly forming distinct foci. Among them, there were stress granule assembly factors and autophagy-related proteins, as well as components of various signalling pathways. Subsequent characterization identified some specific amino acid motifs and intrinsically disordered regions associated with stress-induced protein redistribution. The Localizatome provides open access to these data through a web-based interface, supporting a wide range of studies on cellular stress response and disease mechanisms. Database URL https://localizatome.embrys.jp/.
    DOI:  https://doi.org/10.1093/database/baaf028
  9. Cell. 2025 May 15. pii: S0092-8674(25)00511-2. [Epub ahead of print]
      Phosphatidylinositol 3-kinase (PI3K) signaling is both the effector pathway of insulin and among the most frequently activated pathways in human cancer. In murine cancer models, the efficacy of PI3K inhibitors is dramatically enhanced by a ketogenic diet, with a proposed mechanism involving dietary suppression of insulin. Here, we confirm profound diet-PI3K anticancer synergy but show that it is, surprisingly, unrelated to diet macronutrient composition. Instead, the diet-PI3K interaction involves microbiome metabolism of ingested phytochemicals. Specifically, murine ketogenic diet lacks the complex spectrum of phytochemicals found in standard chow, including the soy phytochemicals soyasaponins. We find that soyasaponins are converted by the microbiome into inducers of hepatic cytochrome P450 enzymes, and thereby lower PI3K inhibitor blood levels and anticancer activity. A high-carbohydrate, low-phytochemical diet synergizes with PI3K inhibition to treat cancer in mice, as do antibiotics that curtail the gut microbiome. Thus, diet impacts anticancer drug activity through phytochemical-microbiome-liver interactions.
    Keywords:  PI3Ki; breast cancer; cytochrome P450; diet and cancer treatment; gut-liver axis; microbiome metabolites; pancreatic cancer; pharmacokinetics; phytochemicals; soyasaponins
    DOI:  https://doi.org/10.1016/j.cell.2025.04.041
  10. Nat Commun. 2025 May 16. 16(1): 4570
      Skin is a regulatory hub for energy expenditure and metabolism, and alteration of lipid metabolism enzymes in skin impacts thermogenesis and obesogenesis in mice. Here we show that thermal properties of skin are highly reactive to diet: within three days, a high fat diet reduces heat transfer through skin. In contrast, a dietary manipulation that prevents obesity accelerates energy loss through skins. We find that skin is the largest target for dietary fat delivery, and that dietary triglyceride is assimilated by epidermis and dermal white adipose tissue, persisting for weeks after feeding. With caloric-restriction, mouse skins thin and assimilation of circulating lipids decreases. Using multi-modal lipid profiling, keratinocytes and sebocytes are implicated in lipid changes, which correlate with thermal function. We propose that skin should be routinely included in physiological studies of lipid metabolism, given the size of the skin lipid reservoir and its adaptable functionality.
    DOI:  https://doi.org/10.1038/s41467-025-59869-x
  11. Nat Chem. 2025 May 22.
      The plasticity of living cell membranes relies on complex metabolic networks fueled by cellular energy. These metabolic processes exert direct control over membrane properties such as lipid composition and morphological plasticity, which are essential for cellular functions. Despite notable progress in the development of artificial systems mimicking natural membranes, the realization of synthetic membranes capable of sustaining metabolic cycles remains a challenge. Here we present an abiotic phospholipid metabolic network that generates and maintains dynamic artificial cell membranes. Chemical coupling agents drive the in situ synthesis of transiently stable non-canonical phospholipids, leading to the formation and maintenance of phospholipid membranes. We find that phospholipid metabolic cycles can drive lipid self-selection, favouring the enrichment of specific lipid species. Moreover, we demonstrate that controlling lipid metabolism can induce reversible membrane phase transitions, facilitating lipid mixing between distinct populations of artificial membranes. Our work demonstrates that a simple lipid metabolic network can drive dynamic behaviour in artificial membranes, offering insights into mechanisms for engineering functional synthetic compartments.
    DOI:  https://doi.org/10.1038/s41557-025-01829-5
  12. Curr Opin Cell Biol. 2025 May 15. pii: S0955-0674(25)00069-9. [Epub ahead of print]95 102531
      The pH balance between extracellular and intracellular space is crucial for a multitude of cellular processes. Real-time observation of pH fluctuations in the range 4-9 in live cells and tissues in a sensitive, non-invasive manner has become feasible with advances in pH quantification by organic dyes, genetically encoded fluorescent proteins, and DNA-based probes. We discuss mechanisms through which pH affects cell cycle, transcription, senescence, neurotransmission, glycolipid-lectin driven endocytosis, tissue remodelling, immune responses, and GPCR signalling. Growth factor-stimulated acidification of the extracellular space notably triggers enzymatic reactions like desialylation at the plasma membrane that control processes involving cell migration and bone resorption. Research into the role of pH in cellular physiology continues to be a fertile ground for discovery that underscores its fundamental importance.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102531
  13. Autophagy. 2025 May 20.
      Macroautophagy (hereafter autophagy), a major intracellular catabolic process, is evolutionarily conserved from yeasts to mammals, and is associated with a broad range of human diseases. Autophagy is morphologically characterized by the formation of double-membrane autophagosomes. ATG9A, a multi-spanning transmembrane protein and lipid scramblase, is a core component of the autophagy machinery that complements membrane sources and equilibrates lipids across membrane bilayers. Here, we report that palmitoyltransferase ZDHHC5 is indispensable for autophagosome nucleation and subsequent autophagosome formation. Upon autophagy induction, ZDHHC5 is internalized from the plasma membrane into intracellular compartments via clathrin-mediated endocytosis. This enzyme activates ATG9A S-palmitoylation at cysteine 155/156, which orchestrates the interaction of ATG9A with the heterotetrameric adaptor protein complex family member AP4E1/AP-4ε and subsequent trafficking from the trans-Golgi network to endosomal compartments. Functionally, impairment of ATG9A S-palmitoylation results in defects in autophagy initiation and autophagosome formation. These findings identify a regulatory mechanism that coordinates ATG9A-binding with AP4E1 and vesicular trafficking events through ATG9A S-palmitoylation by ZDHHC5, thereby ensuring the spatiotemporal fidelity of membrane trafficking and maintenance of autophagic homeostasis.
    Keywords:  AP4E1; Trans-golgi network; ZDHHC5; autophagosome formation; clathrin-mediated endocytosis; membrane trafficking
    DOI:  https://doi.org/10.1080/15548627.2025.2509376
  14. Autophagy Rep. 2023 ;2(1): 2256599
      ATG9A is an important membrane protein in mammalian macroautophagy. The formation of autophagosomes and phagophores is blocked in atg9a KO cells. However, it remains possible that residual membrane formation activity exists in these cells. These precursor structures that precede phagophores are, if they exist, rare and may be difficult to find. Here, we introduce the modified volume correlative light and electron microscopy (CLEM) method to analyze these structures three-dimensionally. In addition to target proteins, mitochondria were labeled as a landmark for precise correlation of slice images by a confocal fluorescence microscope and a focused ion beam scanning electron microscope. We found phagophores and small membrane vesicles near SQSTM1/p62 aggregates in atg9a KO cells, indicating that phagophores could be formed in atg9a-deficient cells, although they were immature and inefficient. Furthermore, we found that RB1CC1/FIP200-positive structures formed clusters around SQSTM1/p62 with ferritin and TAX1BP1. Taken together, our method contributes to the understanding of undiscovered fine structures. Abbreviations: CLEM: correlative light and electron microscopy; EM: electron microscopy; ER: endoplasmic reticulum; FIB-SEM: focused ion beam scanning electron microscopy; FM: fluorescence microscopy; GFP: green fluorescent protein; KO: knock out; MEF: mouse embryonic fibroblast; PBS: phosphate-buffered saline; ROI: region of interest; SEM: scanning electron microscopy.
    Keywords:  3D-CLEM; FIB-SEM; autophagosome; autophagy; electron microscopy; isolation membrane
    DOI:  https://doi.org/10.1080/27694127.2023.2256599
  15. NPJ Syst Biol Appl. 2025 May 22. 11(1): 52
      Collective cell migration is central to processes like development and cancer metastasis. While mechanisms of collective motility are increasingly understood, their classification remains incomplete. Here, we study the migration of small cell chains, namely cohesive pairs. Experiments with Dictyostelium discoideum (Dd) revealed two motility modes: the individual contributor (IC) mode, where each cell generates its own traction dipole, and the supracellular (S) mode, characterized by a single dipole. Dd pairs favored the IC mode, while Madin-Darby canine kidney (MDCK) doublets predominantly used the S mode. A 2D biophysical model recapitulated many experimental observations; the IC mode emerged naturally in ameboid Dd doublets when both cells exerted similar traction stresses, while the S mode dominated with stronger leaders. Contrary to amebas, MDCK-like cell chains showed a bias towards the IC mode when increasing cell-cell adhesion. Extending the model to longer chains, we show its potential for understanding emergent migration patterns across cell types and scales.
    DOI:  https://doi.org/10.1038/s41540-025-00529-7
  16. Nat Commun. 2025 May 22. 16(1): 4771
      Kinases regulate cellular processes and are essential for understanding cellular function and disease. To investigate the regulatory state of a kinase, numerous methods have been developed to infer kinase activities from phosphoproteomics data using kinase-substrate libraries. However, few phosphorylation sites can be attributed to an upstream kinase in these libraries, limiting the scope of kinase activity inference. Moreover, inferred activities vary across methods, necessitating evaluation for accurate interpretation. Here, we present benchmarKIN, an R package enabling comprehensive evaluation of kinase activity inference methods. Alongside classical perturbation experiments, benchmarKIN introduces a tumor-based benchmarking approach utilizing multi-omics data to identify highly active or inactive kinases. We used benchmarKIN to evaluate kinase-substrate libraries, inference algorithms and the potential of adding predicted kinase-substrate interactions to overcome the coverage limitations. Our evaluation shows most computational methods perform similarly, but the choice of library impacts the inferred activities with a combination of manually curated libraries demonstrating superior performance in recapitulating kinase activities. Additionally, in the tumor-based evaluation, adding predicted targets from NetworKIN further boosts the performance. We then demonstrate how kinase activity inference aids characterize kinase inhibitor responses in cell lines. Overall, benchmarKIN helps researchers to select reliable methods for identifying deregulated kinases.
    DOI:  https://doi.org/10.1038/s41467-025-59779-y
  17. Nat Commun. 2025 May 19. 16(1): 4652
      The tumor microenvironment (TME) influences cancer cell metabolism and survival. However, how immune and stromal cells respond to metabolic stress in vivo, and how nutrient limitations affect therapy, remains poorly understood. Here, we introduce Dual Ribosome Profiling (DualRP) to simultaneously monitor translation and ribosome stalling in multiple tumor cell populations. DualRP reveals that cancer-fibroblast interactions trigger an inflammatory program that reduces amino acid shortages during glucose starvation. In immunocompetent mice, we show that serine and glycine are essential for optimal T cell function and that their deficiency impairs T cell fitness. Importantly, immune checkpoint blockade therapy imposes amino acid restrictions specifically in T cells, demonstrating that therapies create distinct metabolic demands across TME cell types. By mapping codon-resolved ribosome stalling in a cell‑type‑specific manner, DualRP uncovers metabolic crosstalk that shapes translational programs. DualRP thus offers a powerful, innovative approach for dissecting tumor cell metabolic interplay and guiding combined metabolic-immunotherapeutic strategies.
    DOI:  https://doi.org/10.1038/s41467-025-59986-7
  18. Autophagy Rep. 2024 ;3(1): 2326241
      Autophagy is considered a target for cancer treatment, although few compounds manipulating this process have been added to the anticancer arsenal in humans. Pharmacological manipulation of autophagy has therefore been considered in the treatment and chemosensitization of hepatocellular carcinoma (HCC), a heterogeneous malignancy that remains difficult to treat (limited impact of genomic discoveries for the implementation of personalized precision medicine). We analyzed the autophagy marker proteins p62 and LC3 in paired tumor and adjacent cirrhotic non-tumor tissues of human HCC. We show strong variability in p62 and LC3-II levels between tumor parts of different HCC patients and between tumor and non-tumor HCC in the same patient, suggesting heterogeneity in autophagy flux. This diversity in flux led us to consider a non-personalized method of autophagy targeting, combining simultaneous activation and blockade of autophagy, which could, in theory, benefit a substantial number of HCC patients, irrespective of tumor autophagic flux. We show that the combination of sodium butyrate (NaB, autophagy inducer) and chloroquine (CQ, autophagy blocker) has a marked and synergistic cytotoxic effect in vitro on all human liver cancer cell lines studied, compared with the cellular effect of each product separately, and with no deleterious effect on normal hepatocytes in culture. Cancer cell death was associated with accumulation of autophagosomes, induction of lysosome membrane permeabilization and increased oxidative stress. Our results suggest that simultaneous activation and blockade of autophagy may be a valuable approach against HCC, and that microbiota-derived products improve the sensitivity of HCC cells to antitumor agents. Abbreviations AV: annexin V; CI: combination index; CTSB: Cathepsin B; CTSD: Cathepsin D; CTSF: Cathepsin F; CQ: chloroquine; DEN: N-diethylnitrosamine; DMEM: Dulbecco's modified eagle medium; FBS: fetal bovine serum; FSC: forward scatter; GNS: N-acetylglucosamine-6-sulfatase; HCC: hepatocellular carcinoma; HDACi: histone deacetylase inhibitor; HCQ: hydroxychloroquine; LMP: lysosomal membrane permeabilization; LAMP1: lysosome-associated membrane protein; LIPA: Lysosomal acid lipase; LSR: Lysosomal staining cells; MAP1LC3A: microtubule associated protein 1 light chain 3 alpha; NaB: sodium butyrate; NASH: non-alcoholic steatohepatitis; NRF2: nuclear factor erythroid 2-related factor 2; PI: propidium iodide; PMSF: phenylmethanesulfonyl fluoride; ROS: reactive oxygen species; SCARB2: Scavenger receptor class B member 2; SQSTM1/p62: sequestosome 1; SMPD1: Sphingomyelin phosphodiesterase 1; SSC: side scatter; TFEB: transcription factor EB.
    Keywords:  Liver cancer; butyrate; cell death; chloroquine; cholangiocarcinoma; microbial metabolite; oxidative stress; therapy
    DOI:  https://doi.org/10.1080/27694127.2024.2326241
  19. Neuron. 2025 May 14. pii: S0896-6273(25)00303-4. [Epub ahead of print]
      Cellular senescence is characterized by irreversible cell-cycle exit, a pro-inflammatory secretory phenotype, macromolecular damage, and deregulated metabolism. Senescent cells are highly associated with age-related diseases. We previously demonstrated that targeted elimination of senescent cells prevents neurodegenerative disease in tau (MAPTP301S;PS19) mutant mice. Here, we show that genetic ablation of the senescence mediator p16Ink4a is sufficient to attenuate senescence signatures in PS19 mice. Disease phenotypes-including neuroinflammation, phosphorylated tau, neurodegeneration, and cognitive impairment-were blunted in the absence of p16Ink4a. Additionally, we found that PS19 mouse brains display p16Ink4-dependent neurovascular alterations such as vessel dilation, increased vessel density, deregulated endothelial cell extracellular matrix, and astrocytic endfoot depolarization. Finally, we show that p16Ink4a deletion in endothelial cells and microglia alone attenuates many of the same phenotypes. Altogether, these results indicate that neurodegenerative disease in PS19 mice is driven, at least in part, by p16Ink4a-expressing endothelial cells and microglia.
    Keywords:  cellular senescence; endothelial cells; microglia; mouse model; neurodegeneration; p16(Ink4a); tauopathy
    DOI:  https://doi.org/10.1016/j.neuron.2025.04.020
  20. J Nanobiotechnology. 2025 May 20. 23(1): 363
      Metal drugs, such as platinum drugs, are widely used in tumor treatment. However, most traditional tumor treatments face the risk of failure due to the ineffective control over drug resistance and tumor metastasis. Targeting the cell membrane and disrupting its function to combat drug resistance and metastasis is a promising strategy. Nevertheless, membranolytic drugs always cause significant cytotoxicity. In this study, we developed a zinc-containing molecule to selectively kill tumor cells by targeting phosphatidylserine in the tumor cell membrane, which is commonly distributed in the outer cell membrane of tumor cells. Herein, a structurally optimized amphiphilic zinc-containing molecule, 2aZn, was developed by screening the appropriate hydrophobic tail and linker. This functional molecule can disrupt the tumor cell membrane to kill various types of tumor cells with minimal damage to normal tissue. After repeated stimulation, no obvious drug resistance was observed. Importantly, 2aZn could successfully combat tumor metastasis by destroying the cell membrane and reducing the capacity of cells to invade. As a result, zinc-containing molecules have the potential to overcome drug resistance and tumor metastasis in the treatment of tumors, providing a new perspective for the design of effective antitumour medications.
    Keywords:  Antitumour drug; Cell membrane disruption; Overcoming drug resistance; Phosphatidylserine; Tumor metastasis inhibition; Tumor targeting
    DOI:  https://doi.org/10.1186/s12951-025-03418-7
  21. Trends Cell Biol. 2025 May 15. pii: S0962-8924(25)00110-2. [Epub ahead of print]
      Compartmentalization by phase separation is an emerging principle for regulating transcription. While the compartmentalization mechanisms by which cells regulate genetic activities in response to specific environmental signals remain largely unclear, a recent study by Gao et al. suggests that hypoxia induces the formation of phase-separated condensates, which impacts metastasis-related transcription through chromatin organization.
    Keywords:  CTCF; ZHX2; enhancer; hypoxia; phase separation; transcriptional condensates
    DOI:  https://doi.org/10.1016/j.tcb.2025.04.008
  22. Nature. 2025 May 21.
      Around 40% of the US population and 1 in 6 individuals worldwide have obesity, with the incidence surging globally1,2. Various dietary interventions, including carbohydrate, fat and, more recently, amino acid restriction, have been explored to combat this epidemic3-6. Here we investigated the impact of removing individual amino acids on the weight profiles of mice. We show that conditional cysteine restriction resulted in the most substantial weight loss when compared to essential amino acid restriction, amounting to 30% within 1 week, which was readily reversed. We found that cysteine deficiency activated the integrated stress response and oxidative stress response, which amplify each other, leading to the induction of GDF15 and FGF21, partly explaining the phenotype7-9. Notably, we observed lower levels of tissue coenzyme A (CoA), which has been considered to be extremely stable10, resulting in reduced mitochondrial functionality and metabolic rewiring. This results in energetically inefficient anaerobic glycolysis and defective tricarboxylic acid cycle, with sustained urinary excretion of pyruvate, orotate, citrate, α-ketoglutarate, nitrogen-rich compounds and amino acids. In summary, our investigation reveals that cysteine restriction, by depleting GSH and CoA, exerts a maximal impact on weight loss, metabolism and stress signalling compared with other amino acid restrictions. These findings suggest strategies for addressing a range of metabolic diseases and the growing obesity crisis.
    DOI:  https://doi.org/10.1038/s41586-025-08996-y
  23. Trends Cancer. 2025 May 16. pii: S2405-8033(25)00112-8. [Epub ahead of print]
      Most colorectal cancers (CRCs) are characterized by a low mutational burden and an immune-cold microenvironment, limiting the efficacy of immune checkpoint blockade (ICB) therapies. While advanced tumors exhibit diverse immune evasion mechanisms, emerging evidence suggests that aspects of immune escape arise much earlier, within precancerous lesions. In this review, we discuss how early driver mutations and epigenetic alterations contribute to the establishment of an immunosuppressive microenvironment in CRC. We also highlight the dynamic crosstalk between cancer cells, stromal niche cells, and immune cells driving immune evasion and liver metastasis. A deeper understanding of these early events may guide the development of more effective preventive and therapeutic strategies for CRC.
    Keywords:  colorectal cancer; immune evasion; niche cell; stem cell
    DOI:  https://doi.org/10.1016/j.trecan.2025.04.016
  24. Aging Cell. 2025 May 22. e70118
      Stiffening of the aorta is a key antecedent to cardiovascular diseases (CVD) with aging. Age-related aortic stiffening is driven, in part, by cellular senescence-a hallmark of aging defined primarily by irreversible cell cycle arrest. In this study, we assessed the efficacy of 25-hydroxycholesterol (25HC), an endogenous cholesterol metabolite, as a naturally occurring senolytic to reverse vascular cell senescence and reduce aortic stiffness in old mice. Old (22-26 months) p16-3MR mice, a transgenic model allowing for genetic clearance of p16-positive senescent cells with ganciclovir (GCV), were administered vehicle, 25HC, or GCV to compare the efficacy of the experimental 25HC senolytic versus genetic clearance of senescent cells. We found that short-term (5d) treatment with 25HC reduced aortic stiffness in vivo, assessed via aortic pulse wave velocity (p = 0.002) to a similar extent as GCV. Ex vivo 25HC exposure of aorta rings from the old p16-3MR GCV-treated mice did not further reduce elastic modulus (measure of intrinsic mechanical stiffness), demonstrating that 25HC elicited its beneficial effects on aortic stiffness, in part, through the suppression of excess senescent cells. Improvements in aortic stiffness with 25HC were accompanied by favorable remodeling of structural components of the vascular wall (e.g., lower collagen-1 abundance and higher α-elastin content) to a similar extent as GCV. Moreover, 25HC suppressed its putative molecular target CRYAB, modulated CRYAB-regulated senescent cell anti-apoptotic pathways, and reduced markers of cellular senescence. The findings from this study identify 25HC as a potential therapy to target vascular cell senescence and reduce age-related aortic stiffness.
    Keywords:  aging; cellular senescence; elasticity; p16; replicative senescence
    DOI:  https://doi.org/10.1111/acel.70118
  25. J Phys Chem B. 2025 May 21.
      Large-scale simulations of realistic crowded cell membranes can bridge the gap between the simulations and experiments. However, the compositional complexity and structural asymmetry of cell membranes continue to pose significant challenges in computational biology. Recent advances in understanding native membranes, including their composition and protein structures, enable us to construct a highly realistic model of the mammalian plasma membrane. Using this model, we explore the organization and dynamics of biological cell membranes at the molecular level. We found that the interaction preferences of protein-lipid mediate the formation of dynamic clusters of nonrandomly distributed proteins, accompanied by heterogeneous structural properties and anomalous diffusion. These evolving dynamic clusters intertwine to form a highly complex and continuously changing protein network. Our study provides significant insights into the intricate lateral dynamic organization of cell membranes.
    DOI:  https://doi.org/10.1021/acs.jpcb.5c00909
  26. Curr Opin Cell Biol. 2025 May 21. pii: S0955-0674(25)00071-7. [Epub ahead of print]95 102533
      Intracellular organelles are essential for cellular architecture and function, and their size regulation is critical for maintaining cellular homeostasis. Organelle size often scales with cell size, governed by mechanisms that integrate resource allocation, stochastic dynamics, and feedback controls. Here we review these underlying biophysical principles of organelle size control, including the limiting pool hypothesis, stochastic assembly processes, and feedback-driven growth dynamics. We discuss how negative feedback motifs stabilize size, while positive feedback can amplify growth and maintain size under specific conditions. Additionally, we discuss recent advances in modeling size control for organelles with nucleation and fission-fusion dynamics. By integrating experimental observations with theoretical insights, this review provides a conceptual understanding of the design principles governing organelle size regulation in dynamic cellular environments.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102533
  27. Autophagy Rep. 2024 ;3(1): 2396696
      Beiging of adipocytes is characteristic of a higher number of mitochondria, the central hub of metabolism in the cell. However, studies show that beiging can improve metabolic health or cause metabolic disorders. Here we discuss a liver-fat crosstalk for iron flux associated with healthy beiging of adipocytes. Deletion of the transcription factor FoxO1 in adipocytes (adO1KO mice) induces a higher iron flux from the liver to white adipose tissue, concurrent with augmented mitochondrial biogenesis that increases iron demands. In addition, adO1KO mice adopt an alternate mechanism to sustain mitophagy, which enhances mitochondrial quality control, thereby improving mitochondrial respiratory capacity and metabolic health. However, the liver-fat crosstalk is not detectable in adipose Atg7 knockout (ad7KO) mice, which undergo beiging of adipocytes but have metabolic dysregulation. Autophagic clearance of mitochondria is blocked in ad7KO mice, which accumulates dysfunctional mitochondria and elevates mitochondrial content but lowers mitochondrial respiratory capacity. Mitochondrial biogenesis is comparable in the control and ad7KO mice, and the iron influx into adipocytes and iron efflux from the liver remain unchanged. Therefore, activation of the liver-fat crosstalk is critical for mitochondrial quality control that underlies healthy beiging of adipocytes.
    Keywords:  Adipose beiging; Atg7; FoxO1; iron flux; liver-fat crosstalk
    DOI:  https://doi.org/10.1080/27694127.2024.2396696
  28. Cell Rep. 2025 May 22. pii: S2211-1247(25)00505-4. [Epub ahead of print]44(6): 115734
      Doublecortin-like kinase 1 (Dclk1) expression identifies cells that are rare in normal pancreas but occur with an increased frequency in pancreatic neoplasia. The identity of these cells has been a matter of debate. We employed Dclk1 reporter mouse models and single-cell RNA sequencing (scRNA-seq) to define Dclk1-expressing cells. In normal pancreas, Dclk1 identifies subsets of ductal, islet, and acinar cells. In pancreatic neoplasia, Dclk1 identifies several cell populations, among which acinar-to-ductal metaplasia (ADM)-like cells and tuft-like cells are predominant. These two populations play opposing roles, with Dclk1+ ADM-like cells sustaining and Dclk1+ tuft-like cells restraining tumor progression. The generation of Dclk1+ tuft-like cells requires the transcription factor SPIB and is sustained by a paracrine loop involving type 2 innate lymphoid cells (ILC2s) and cancer-associated fibroblasts (CAFs) that provide interleukin (IL)-13 and IL-33, respectively. Dclk1+ tuft-like cells release angiotensinogen to restrain tumor progression. Overall, our study defines pancreatic Dclk1+ cells and unveils a protective tuft cell-ILC2 axis against pancreatic neoplasia.
    Keywords:  CP: Cancer; Dclk1; ILC2; pancreatic neoplasia; tuft cell
    DOI:  https://doi.org/10.1016/j.celrep.2025.115734
  29. Methods Mol Biol. 2025 ;2930 103-126
      Studying metabolism in the different cellular compartments of the tumor microenvironment (TME) is crucial to identify the specific metabolic signatures that contribute to tumor progression. Additionally, TME-driven metabolic changes can disrupt the essential metabolic processes involved in immune cell function, hindering immunotherapy success. Extracellular flux analysis (Seahorse) is a well-established approach used to characterize cellular metabolism. When combined with flow cytometry-based measurements, it offers a comprehensive view of the metabolic signatures within the different cellular compartments of the TME. Here we provide a detailed description on the procedures of Seahorse analysis and complementary flow cytometry-based metabolic readouts on tumor cells and T cells in the context of cancer, which can also be applied to other physiological and pathological situations.
    Keywords:  Extracellular flux analysis; Flow cytometry; Immunotherapy; Metabolism; Mitochondria; Tumor microenvironment
    DOI:  https://doi.org/10.1007/978-1-0716-4558-1_9
  30. Autophagy Rep. 2025 ;4(1): 2438563
      LC3-interacting region (LIR) motifs are essential for recruiting proteins onto autophagosomes, the hallmark of autophagy. We recently explored the relevance of the specific position of the LIRs in RavZ and ATG4B (autophagy-related 4B). RavZ's N-terminal LIRs drive substrate recognition and enzymatic activity, while its C-terminal LIR aids membrane localization. In contrast, ATG4B's C-terminal LIR is indispensable for LC3B (microtubule-associated protein 1 light chain 3B)-phosphatidylethanolamine (PE) delipidation on autophagosomes but not required for cytosolic LC3B priming, which is mediated solely by its catalytic domain (CAD). These findings underscore the structural adaptation of LIRs for context-specific functions. This novel nuanced understanding provides a framework for developing therapeutic tools to modulate autophagy by precisely targeting LIRs or their associated processes, offering potential treatment for diseases like neurodegenerative disorders and infections characterized by autophagy dysregulation.
    Keywords:  ATG4B; Autophagy; LC3/GABARAP; LIR; RavZ; delipidation
    DOI:  https://doi.org/10.1080/27694127.2024.2438563
  31. Proc Natl Acad Sci U S A. 2025 May 27. 122(21): e2416440122
      Motile cells migrate directionally in the electric field (EF) in a process known as galvanotaxis, an important phenomenon in wound healing and development. We previously reported that individual fish keratocyte cells migrate to the cathode in EFs, that inhibition of PI3 kinase (PI3K) reverses single cells to the anode, and that large cohesive groups of either unperturbed or PI3K-inhibited cells migrate to the cathode. Here, we report that small uninhibited cell groups move to the cathode, while small groups of PI3K-inhibited cells move to the anode. Small groups move faster than large groups, and groups of unperturbed cells move faster than PI3K-inhibited cell groups of comparable sizes. The shapes and sizes of large groups change little when they start migrating, while size and shapes of small groups change significantly, and lamellipodia disappear from the rear edges of these groups. The computational model, according to which cells inside and at the edge of the group interpret directional signals differently, explains the observations. Namely, cells in the group interior are directed to the cathode independently whether they are PI3K-inhibited or not. Meanwhile, the edge cells behave like individual cells: They are directed to the cathode in uninhibited groups and to the anode in PI3K-inhibited groups. As a result, all cells drive uninhibited groups to the cathode, while larger PI3K-inhibited groups are directed by cell majority in the group interior to the cathode, while majority of the edge cells in small groups win the tug-of-war driving these groups to the anode.
    Keywords:  PI3 Kinase; collective cell migration; galvanotaxis
    DOI:  https://doi.org/10.1073/pnas.2416440122
  32. Soft Matter. 2025 May 21.
      Cancer mechano-adaptation remains poorly understood due to the lack of imaging technologies capable of quantifying both mechanical and biochemical properties of cells and their microenvironment in 3D culture and in vivo. This challenge arises primarily due to the invasiveness of existing mechanical measurement techniques and their inability to assess mechanical properties in highly heterogeneous structures such as living tissues. Brillouin microscopy is an emerging, label-free technique that enables measurements of local mechanical properties with microscopic spatial resolution. In this study, we non-invasively imaged the elastic properties of monolayer 4T1 murine fibroblast cells using Brillouin microscopy and analyzed their response to variations in the mechanical properties of the external environment. Our findings demonstrate a significant correlation between the mechanical properties of the extracellular matrix and cancer cells, as assessed through Brillouin microspectroscopy in a non-invasive and safe manner. These results highlight the potential of Brillouin spectroscopy as a robust and effective technique for the characterization of biomechanical properties in cancer cells, offering valuable insights into their mechanical behavior.
    DOI:  https://doi.org/10.1039/d5sm00315f
  33. Chem Sci. 2025 May 14.
      Ferroptosis, a form of iron-dependent programmed cell death, is linked to various diseases and physiological processes. Despite the availability of various types of ferroptosis inducers, its inhibitors are limited to iron chelators or radical scavengers. This study demonstrates that Fe(ii)-selective fluorescent probes developed in our lab could serve as ferroptosis inhibitors via selective oxidation of Fe(ii), which is required for lipid peroxidation. This finding opens the door to a new class of ferroptosis inhibitors with potential therapeutic applications.
    DOI:  https://doi.org/10.1039/d4sc07972h
  34. Prog Biophys Mol Biol. 2025 May 15. pii: S0079-6107(25)00023-9. [Epub ahead of print]197 11-20
      Lipid droplets (LDs) store lipids in cells, provide phospholipids for membrane synthesis, and maintain the intracellular balance of energy and lipid metabolism. Undoubtedly, the crosstalk between LDs and other organelles is the foundation for performing functions. Many studies indicate that LDs promote tumor progression. LD accumulation has been observed in a variety of cancers, and high LD content is associated with malignant phenotype and poor prognosis of cancers. In this paper, we summarized the intimate crosstalk between LDs and intracellular organelles, including endoplasmic reticulum (ER), mitochondria, lysosomes and peroxisomes, and addressed the effects of LD-organelle crosstalk on cancer initiation and progression. We also integrated the changes of LD-organelle interactions in cancers to provide an insightful knowledge for cancer therapeutics.
    Keywords:  Cancer therapy; Lipid droplet; Organelles crosstalk
    DOI:  https://doi.org/10.1016/j.pbiomolbio.2025.05.002
  35. Faraday Discuss. 2025 May 19.
      The fusion of lipid membranes progresses through a series of intermediate steps with two significant energy barriers: hemifusion-stalk formation and fusion-pore expansion. The cell's ability to tune these energy barriers is crucial as they determine the rate of many biological processes involving membrane fusion. However, a mechanism that allows the cell to manipulate both barriers in the same direction remains elusive, since membrane properties that the cell could dynamically tune during its life cycle, such as the lipids' spontaneous curvatures and membrane tension, have an opposite effect on the two barriers: tension inhibits stalk formation while promoting fusion-pore expansion. In contrast, increasing the total membrane concentration of lipids with negative intrinsic curvatures, such as cholesterol, promotes hemifusion-stalk formation while inhibiting pore expansion, and vice versa for lipids with positive intrinsic curvatures. Therefore, changes in these membrane properties increase one energy barrier at the expense of the other, resulting in a mixed effect on the fusion reaction. A possible mechanism to change both barriers in the same direction is by inducing lipid composition asymmetry, which results in tension and spontaneous curvature differences between the monolayers. To test the feasibility of this mechanism, a continuum elastic model was used to simulate the fusion intermediates and calculate the changes in the energy barriers. The calculations showed that a reasonable lipid composition asymmetry could lead to a 10-20kBT difference in both energy barriers, depending on the direction from which fusion occurs. We further provide experimental support to the model predictions, demonstrating changes in the time to hemifusion upon asymmetry introduction. These results indicate that biological membranes, which are asymmetric, have a preferred direction for fusion.
    DOI:  https://doi.org/10.1039/d4fd00189c
  36. Sci Signal. 2025 May 20. 18(887): eadw1245
    Nils Helge Schebb, Nadja Kampschulte, Gerhard Hagn, Kathrin Plitzko, Sven W Meckelmann, Soumita Ghosh, Robin Joshi, Julia Kuligowski, Dajana Vuckovic, Marina T Botana, Ángel Sánchez-Illana, Fereshteh Zandkarimi, Aditi Das, Jun Yang, Louis Schmidt, Antonio Checa, Helen M Roche, Aaron M Armando, Matthew L Edin, Fred B Lih, Juan J Aristizabal-Henao, Sayuri Miyamoto, Francesca Giuffrida, Arieh Moussaieff, Rosário Domingues, Michael Rothe, Christine Hinz, Ujjalkumar Subhash Das, Katharina M Rund, Ameer Y Taha, Robert K Hofstetter, Markus Werner, Oliver Werz, Astrid S Kahnt, Justine Bertrand-Michel, Pauline Le Faouder, Robert Gurke, Dominique Thomas, Federico Torta, Ivana Milic, Irundika H K Dias, Corinne M Spickett, Denise Biagini, Tommaso Lomonaco, Helena Idborg, Jun-Yan Liu, Maria Fedorova, David A Ford, Anne Barden, Trevor A Mori, Paul D Kennedy, Kirk Maxey, Julijana Ivanisevic, Hector Gallart-Ayala, Cécile Gladine, Markus Wenk, Jean-Marie Galano, Thierry Durand, Ken D Stark, Coral Barbas, Ulrike Garscha, Stacy L Gelhaus, Uta Ceglarek, Nicolas Flamand, Julian L Griffin, Robert Ahrends, Makoto Arita, Darryl C Zeldin, Francisco J Schopfer, Oswald Quehenberger, Randall Julian, Anna Nicolaou, Ian A Blair, Michael P Murphy, Bruce D Hammock, Bruce Freeman, Gerhard Liebisch, Charles N Serhan, Harald C Köfeler, Per-Johan Jakobsson, Dieter Steinhilber, Michael H Gelb, Michal Holčapek, Ruth Andrew, Martin Giera, Garret A FitzGerald, Robert C Murphy, John W Newman, Edward A Dennis, Kim Ekroos, Ginger L Milne, Miguel A Gijón, Hubert W Vesper, Craig E Wheelock, Valerie B O'Donnell.
      Several oxylipins are potent lipid mediators that regulate diverse aspects of health and disease and whose quantitative analysis by liquid chromatography-mass spectrometry (LC-MS) presents substantial technical challenges. As members of the lipidomics community, we developed technical recommendations to ensure best practices when quantifying oxylipins by LC-MS.
    DOI:  https://doi.org/10.1126/scisignal.adw1245
  37. ACS Chem Biol. 2025 May 20.
      The nucleolus, a membraneless organelle crucial for ribosome production, has a unique nanoscale structure whose organization is responsive to cell signals and disease progression. Here, we highlight the potential of Expansion Microscopy (ExM) for capturing intricate spatial and functional information about membraneless organelles such as the nucleolus and nuclear foci. We apply dual protein Expansion Microscopy (dual-proExM) in combination with click Expansion Microscopy (click-ExM) to capture images at the highest resolution reported for the nucleolus of ∼45 ± 2 nm. Inhibition of nucleolar processes triggers a nucleolar stress response, causing distinct structural rearrangements whose molecular basis is an area of active investigation. We investigate time-dependent changes in nucleolar structure and function under nucleolar stress induced by oxaliplatin, actinomycin D, and other platinum-based compounds. Our findings reveal new stages that occur prior to the complete sequestration of RNA Pol I into nucleolar caps, shedding light on the early mechanisms of the nucleolar stress response. RNA transcription is linked to nanoscale protein rearrangements using a combination of click-ExM and pro-ExM, revealing locations of active transcripts during the early stages of nucleolar stress reorganization. With prolonged stress, fibrillarin and NPM1 segregate from the nucleolus into nucleoplasmic foci that are for the first time imaged at nanometer resolution. In addition to revealing new morphological information about the nucleolus, this study demonstrates the potential of ExM for imaging membraneless organelles with nanometer-scale precision.
    DOI:  https://doi.org/10.1021/acschembio.5c00104
  38. ArXiv. 2025 May 08. pii: arXiv:2505.05612v1. [Epub ahead of print]
      Drug resistance remains a significant barrier to improving the effectiveness of cancer therapies. To better understand the biological mechanisms driving resistance, single-cell profiling has emerged as a powerful tool for characterizing cellular heterogeneity. Recent advancements in large-scale foundation models have demonstrated potential in enhancing single-cell analysis, yet their performance in drug response prediction remains underexplored. In this study, we developed scDrugMap, an integrated framework for drug response prediction that features both a Python command-line tool and an interactive web server. scDrugMap supports the evaluation of a wide range of foundation models, including eight single-cell foundation models and two large language models (LLMs), using large-scale single-cell datasets across diverse tissue types, cancer types, and treatment regimens. The framework incorporates a curated data resource consisting of a primary collection of 326,751 cells from 36 datasets across 23 studies, and a validation collection of 18,856 cells from 17 datasets across 6 studies. Using scDrugMap, we conducted comprehensive benchmarking under two evaluation scenarios: pooled-data evaluation and cross-data evaluation. In both settings, we implemented two model training strategies-layer freezing and fine-tuning using Low-Rank Adaptation (LoRA) of foundation models. In the pooled-data evaluation, scFoundation outperformed all others, while most models achieved competitive performance. Specifically, scFoundation achieved the highest mean F1 scores of 0.971 and 0.947 using layer-freezing and fine-tuning, outperforming the lowest-performing model by 54% and 57%, respectively. In the cross-data evaluation, UCE achieved the highest performance (mean F1 score: 0.774) after fine-tuning on tumor tissue, while scGPT demonstrated superior performance (mean F1 score: 0.858) in a zero-shot learning setting. Together, this study presents the first comprehensive benchmarking of large-scale foundation models for drug response prediction in single-cell data and introduces a user-friendly, flexible platform to support drug discovery and translational research.
    Keywords:  Computational Drug Discovery; Drug Resistance; Drug Response Prediction; Foundation Models; Low-Rank Adaptation; Single-cell Profiling; Zero-shot Learning; scDrugMap
  39. Genes Dev. 2025 May 20.
      The adipose-derived hormone leptin signals the adequacy of body triglyceride stores to specialized leptin receptor (LepRb)-containing cells, which modulate physiology and behavior appropriately for the status of energy reserves. Decreased leptin action initiates a program that restrains a host of energy-intensive processes, promotes food seeking and consumption, and supports the continued availability of glucose and other metabolic fuels in the face of diminished fat stores. In addition to activating the STAT3-dependent transcriptional regulation that mediates most leptin action in vivo, LepRb mediates some leptin effects via a poorly understood second intracellular signaling pathway. Leptin also activates feedback pathways that restrain LepRb signaling in the face of high leptin, as in obesity. Leptin mediates most of its metabolic effects via multiple populations of Lepr-expressing hypothalamic neurons, each of which controls different aspects of leptin action. Although most of these neuron populations contribute only modestly to the control of food intake and body weight by leptin, Glp1r-expressing Lepr neurons inhibit Agrp neurons and strongly suppress feeding and body weight. Going forward, it will be important to define the potentially distinct intracellular responses to leptin for individual Lepr neuron populations, along with the cell type-specific roles for these responses in the physiologic effects of leptin.
    Keywords:  JAK2; STAT3; hypothalamus; leptin receptor; obesity
    DOI:  https://doi.org/10.1101/gad.352550.124
  40. Biochim Biophys Acta Mol Cell Biol Lipids. 2025 May 20. pii: S1388-1981(25)00045-9. [Epub ahead of print] 159637
      The myelin sheath is a lipid-rich membrane that ensheathes axons and is required for healthy and efficient signal transduction. Myelin is damaged in neurological diseases like multiple sclerosis, but remyelination can occur through the action of oligodendrocyte precursor cells (OPCs), which differentiate into mature oligodendrocytes that wrap axons to form repaired myelin. In this study, a genetic-based mouse model of demyelination was used, which features near-complete demyelination followed by robust remyelination in the brain. Lipid mass spectrometry on isolated myelin from the remyelinated brain revealed a decrease in the percent mole fraction of cholesterol when compared to healthy myelin. Biophysical studies on monomolecular lipid films formed using myelin lipid extracts from repaired myelin showed changes in the surface behavior of the lipid films, compared to the healthy myelin. Films formed using the remyelinated lipid extracts resulted in lower surface pressures and lower compressional moduli when compared to healthy controls, suggesting that repaired myelin membranes have lower lateral molecular packing within the lipid film. Synthetically prepared model membranes, based on the major lipid compositions of the healthy and diseased extracts, revealed that changes in cholesterol levels were the primary contributor to the changes in biophysical properties. Supplementation of the diseased lipid extracts with cholesterol led to a robust improvement in membrane surface pressures and compressibility. Together, these results suggest that high cholesterol levels are required for myelin membrane stability and that reduced cholesterol in repaired myelin may have a profound impact on the biophysical properties of the myelin membrane.
    Keywords:  Cholesterol; Lipid monolayers; Lipidomics; Myelin; Surface pressure
    DOI:  https://doi.org/10.1016/j.bbalip.2025.159637
  41. Nat Metab. 2025 May 19.
    CRUK Rosetta Grand Challenge Consortium
      Transcriptomic studies have attempted to classify glioblastoma (GB) into subtypes that predict survival and have different therapeutic vulnerabilities1-3. Here we identified three metabolic subtypes: glycolytic, oxidative and a mix of glycolytic and oxidative, using mass spectrometry imaging of rapidly excised tumour sections from two patients with GB who were infused with [U-13C]glucose and from spatial transcriptomic analysis of contiguous sections. The phenotypes are not correlated with microenvironmental features, including proliferation rate, immune cell infiltration and vascularization, are retained when patient-derived cells are grown in vitro or as orthotopically implanted xenografts and are robust to changes in oxygen concentration, demonstrating their cell-intrinsic nature. The spatial extent of the regions occupied by cells displaying these distinct metabolic phenotypes is large enough to be detected using clinically applicable metabolic imaging techniques. A limitation of the study is that it is based on only two patient tumours, albeit on multiple sections, and therefore represents a proof-of-concept study.
    DOI:  https://doi.org/10.1038/s42255-025-01293-y
  42. Cancer Cell. 2025 May 12. pii: S1535-6108(25)00172-2. [Epub ahead of print]
      MYC-driven group-3 medulloblastomas (MBs) are malignant pediatric brain cancers without cures. To define actionable metabolic dependencies, we identify upregulation of dihydrolipoyl transacetylase (DLAT), the E2-subunit of pyruvate dehydrogenase complex (PDC) in a subset of group-3 MB with poor prognosis. DLAT is induced by c-MYC and targeting DLAT lowers TCA cycle metabolism and glutathione synthesis. We also note upregulation of isocitrate dehydrogenase 1 (IDH1) gene expression in group-3 MB patient tumors and suppression of IDH1 epigenetically reduces c-MYC and downstream DLAT levels in multiple c-MYC amplified cancers. DLAT is a central regulator of cuproptosis (copper-dependent cell death) induced by the copper ionophore elesclomol. DLAT expression in group-3 MB cells correlates with increased sensitivity to cuproptosis. Elesclomol is brain-penetrant and suppresses tumor growth in vivo in multiple group-3 MB animal models. Our data uncover an IDH1/c-MYC dependent vulnerability that regulates DLAT levels and can be targeted to kill group-3 MB by cuproptosis.
    Keywords:  cancer metabolism; cell death; copper; cuproptosis; elesclomol; epigenetics; pediatric brain tumor; protein lipoylation
    DOI:  https://doi.org/10.1016/j.ccell.2025.04.013
  43. bioRxiv. 2025 May 13. pii: 2025.05.12.653341. [Epub ahead of print]
      The tumor suppressor p53 is a transcription factor that controls the expression of hundreds of genes. Emerging evidence suggests that the p53-induced RNA-binding protein ZMAT3 is a key splicing regulator that functions in p53-dependent tumor suppression in vitro and in vivo . However, the mechanism by which ZMAT3 functions in the p53 pathway is largely unclear. Here, we discovered a function of ZMAT3 in inhibiting transcription of HKDC1 , a hexokinase that regulates glucose metabolism and mitochondrial respiration. Using quantitative proteomics, we identified HKDC1 as the most significantly upregulated protein in ZMAT3 -depleted colorectal cancer cells. ZMAT3 depletion results in increased mitochondrial respiration that was rescued upon depletion of HKDC1 , suggesting that HKDC1 is a critical downstream effector of ZMAT3 . Unexpectedly, ZMAT3 did not bind to the HKDC1 RNA or DNA but the identification of the ZMAT3-interactome uncovered its interaction with the oncogenic transcription factor JUN. ZMAT3 depletion resulted in increased JUN binding at the HKDC1 promoter and increased HKDC1 transcription that was rescued upon JUN depletion, suggesting that JUN activates HKDC1 transcription in ZMAT3-depleted cells. Collectively, these data reveal a mechanism by which ZMAT3 regulates transcription and demonstrates that HKDC1 is a key component of the ZMAT3-regulated transcriptome in the context of mitochondrial respiration regulation.
    DOI:  https://doi.org/10.1101/2025.05.12.653341
  44. Pancreatology. 2025 Apr 16. pii: S1424-3903(25)00075-4. [Epub ahead of print]
       BACKGROUND & AIMS: Pancreatic ductal adenocarcinoma (PDAC) is often associated with debilitating abdominal pain that is poorly understood. The aim of this study is to evaluate pain processing in patients with PDAC using Pancreatic Quantitative Sensory Testing (P-QST).
    METHODS: We conducted a cross-sectional study enrolling histologically confirmed PDAC patients from referral centers in the United States and Germany, and healthy controls from the United States, Germany, and Denmark. P-QST assesses central pain processing by measuring pressure pain thresholds at dermatomal sites (C5, T10 back, T10 abdomen, L1, L4), evaluating temporal summation with pinprick stimulation, and using a cold pressor test with a conditioned pain modulation (CPM) paradigm. Using an established algorithm, it differentiates normal pain processing from segmental (pancreatic dermatome-related) hyperalgesia and widespread hyperalgesia.
    RESULTS: A total of 104 patients with painful, treatment-naive PDAC (56.7% men, mean age 65.9 ± 10.6 years) and 122 healthy controls (50% men, mean age 48.9 ± 12.1 years) were enrolled. PDAC patients were 29% early tumor stage (I/II) and 71% advanced tumor stage (III/IV). Overall, PDAC patients had lower pressure pain thresholds, higher temporal summation and shorter cold pressor endurance time compared to controls. Abnormal central pain processing, i.e., segmental hyperalgesia (19% vs. 12%) and widespread hyperalgesia (19% vs. 4%), was significantly more common in PDAC patients (p < 0.001). Advanced tumor stage and metastases were associated with lower CPM and more widespread hyperalgesia, Advanced tumor stage and metastases were associated with lower CPM and more widespread hyperalgesia, though not remain significant after false discovery rate correction.
    CONCLUSIONS: P-QST revealed abnormal central pain processing in PDAC patients compared to healthy controls, which may have implications for pain management.
    Keywords:  Cancer pain; Pain management; Pancreatic cancer; Sensory testing
    DOI:  https://doi.org/10.1016/j.pan.2025.04.010
  45. Chembiochem. 2025 May 21. e202500327
      Upon cell stimulation, mammalian cells activate various signaling proteins and lipids by recruiting their upstream regulators to the inner leaflet of the plasma membrane (PM), which in turn determines their cellular response. Therefore, artificially inducing protein translocation to the PM is an effective strategy for dissecting cell signaling networks and engineering cellular functions. Self-localizing ligand-induced protein translocation (SLIPT) is an emerging technique that we developed to control protein localization in living cells using synthetic self-localizing ligands (SLs). Building on this strategy, we recently introduced a versatile chemogenetic SLIPT platform that rapidly recruits proteins of interest fused to an engineered Escherichia coli dihydrofolate reductase tag from the cytoplasm to the PM using a trimethoprim-based SL. The PM-specific SLIPT (SLIPT-PM) system is easy to use and enables researchers to manipulate diverse intracellular signaling molecules and pathways with controlled reversibility and repeatability. Owing to its modular design, related SLIPT-PM tools have also been developed to support more sophisticated experiments, such as light-induced spatially regulated protein recruitment and multiplexed signal manipulation. In this Concept article, we review the development, principal features, current applications, and future challenges of SLIPT-PM as a unique tool in chemical biology and synthetic biology.
    Keywords:  Cell Signaling; Chemogenetics; Protein Localization; Protein Translocation; Self-localizing Ligands
    DOI:  https://doi.org/10.1002/cbic.202500327
  46. Cancer Metab. 2025 May 19. 13(1): 23
      Metabolite nutrients within the tumor microenvironment shape both tumor progression and immune cell functionality. It remains elusive how the metabolic interaction between T cells and tumor cells results in different anti-cancer immunotherapeutic responses. Here, we use untargeted metabolomics to investigate the metabolic heterogeneity in patients with colorectal cancer (CRC). Our analysis reveals enhanced S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) metabolism in microsatellite stable (MSS) CRC, a subtype known for its resistance to immunotherapy. Functional studies reveal that SAM and SAH enhance the initial activation and effector functions of CD8+ T cells. Instead, cancer cells outcompete CD8+ T cells for SAM and SAH availability to impair T cell survival. In vivo, SAM supplementation promotes T cell proliferation and reduces exhaustion of the tumor-infiltrating CD8+ T cells, thus suppressing tumor growth in tumor-bearing mice. This study uncovers the metabolic crosstalk between T cells and tumor cells, which drives the development of tumors resistant to immunotherapy.
    Keywords:  CD8+ T cell function; Metabolite nutrients; Metabolomics; Microsatellite stable colorectal cancer; S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) metabolism
    DOI:  https://doi.org/10.1186/s40170-025-00394-2
  47. Nat Phys. 2025 ;21(5): 799-807
      Living cells can adapt their shape in response to their environment, a process driven by the interaction between their flexible membrane and the activity of the underlying cytoskeleton. However, the precise physical mechanisms of this coupling remain unclear. Here we show how cytoskeletal forces acting on a biomimetic membrane affect its deformations. Using a minimal cell model that consists of an active network of microtubules and molecular motors encapsulated inside lipid vesicles, we observe large shape fluctuations and travelling membrane deformations. Quantitative analysis of membrane and microtubule dynamics demonstrates how active forces set the temporal scale of vesicle fluctuations, giving rise to fluctuation spectra that differ in both their spatial and temporal decays from their counterparts in thermal equilibrium. Using simulations, we extend the classical framework of membrane fluctuations to active cytoskeleton-driven vesicles, demonstrating how correlated activity governs membrane dynamics and the roles of confinement, membrane material properties and cytoskeletal forces. Our findings provide a quantitative foundation for understanding the shape-morphing abilities of living cells.
    Keywords:  Biological physics; Membrane biophysics
    DOI:  https://doi.org/10.1038/s41567-025-02839-3
  48. Curr Opin Cell Biol. 2025 May 16. pii: S0955-0674(25)00067-5. [Epub ahead of print]95 102529
      Cells respond to the physical and geometrical tissue properties by multiple mechanotransduction mechanisms that can profoundly influence cells' decision-making, extending to cell metabolism. This review incorporates the most recent findings on this topic, organized along the idea that the mechano-metabolic connection serves three main functions, namely to inform systemic metabolism on the general functioning of a tissue/organ, to tune cells' energy production with the mechanical requirements imposed by their surroundings, and to coordinate cell metabolism with cell fate choices induced in response to mechanical cues. This connection highlights the pervasive influence of mechanical cues on cell activity, opens interesting questions on its physiological and pathological roles, and lays the foundations for exploiting the mechano-metabolism axis to design new therapeutic approaches.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102529