bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2025–03–23
thirty-two papers selected by
Kıvanç Görgülü, Technical University of Munich



  1. Cancer Discov. 2025 Mar 19.
      Cancer cell heterogeneity is a major therapeutic challenge. Here, we identify that individual cells within cancer cell populations show significant heterogeneity in the levels of the stress-adaptive organelles, stress granules (SGs), and demonstrate that SG heterogeneity is dictated by cell-cycle state. Specifically, SG-formation is distinctively heightened in cells in G2-phase due to the interplay between a non-apoptotic function of Caspase 3 and calcium-dependent phospholipase A2 (cPLA2)-mediated production of the SG-promoting molecule, 15-deoxy-delta-prostaglandin-J2 (15d-PGJ2). We demonstrate that in G1/S phase, Caspase 3 cleaves and inactivates cPLA2, whereas in G2-phase, Caspase 3 activity is suppressed, resulting in enhanced cPLA2 activity and 15d-PGJ2 upregulation. We show that cell-cycle-dependent SG heterogeneity is a property of pancreatic ductal adenocarcinoma (PDAC) and targeting G2-SGs by inhibiting cPLA2 sensitizes PDAC to G2-arrest-inducing chemotherapeutics. Our findings highlight cell-cycle-dependent SG formation as a fundamental property of SGs, a key aspect of cancer heterogeneity, and a target for cancer treatment.
    DOI:  https://doi.org/10.1158/2159-8290.CD-24-1144
  2. Nat Commun. 2025 Mar 20. 16(1): 2756
      Biomolecular condensates play a central role in cellular processes by interacting with membranes driving wetting transitions and inducing mutual remodeling. While condensates are known to locally alter membrane properties such as lipid packing and hydration, it remains unclear how membrane composition and phase state in turn affect condensate affinity. Here, we show that it is not only the membrane phase itself, but rather the degree of lipid packing that determines the condensate affinity for membranes. Increasing lipid chain length, saturation, or cholesterol content, enhances lipid packing, thereby decreasing condensate interaction. This regulatory mechanism is consistent across various condensate-membrane systems, highlighting the critical role of the membrane interface. In addition, protein adsorption promotes extensive membrane remodeling, including the formation of tubes and double-membrane sheets. Our findings reveal a mechanism by which membrane composition fine-tunes condensate wetting, highlighting its potential impact on cellular functions and organelle interactions.
    DOI:  https://doi.org/10.1038/s41467-025-57985-2
  3. Sci Rep. 2025 Mar 19. 15(1): 9415
      Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers known to humans. However, not all patients fare equally poor survival, and a minority of patients even survives advanced disease for months or years. Thus, there is a clinical need to search corresponding prognostic biomarkers which forecast survival on an individual basis. To dig more information and identify potential biomarkers from PDAC pathological slides, we trained a deep learning (DL) model based U-net-shaped backbone. This DL model can automatically detect tumor, stroma and lymphocytes on whole slide images (WSIs) of PDAC patients. We performed an analysis of 800 PDAC scans, categorizing stroma in percentage (SIP) and lymphocytes in percentage (LIP) into two and three categories, respectively. The presented model achieved remarkable accuracy results with a total accuracy of 94.72%, a mean intersection of union rate of 78.66%, and a mean dice coefficient of 87.74%. Survival analysis revealed that SIP-mediate and LIP-high groups correlated with enhanced median overall survival (OS) across all cohorts. These findings underscore the potential of SIP and LIP as prognostic biomarkers for PDAC and highlight the utility of DL as a tool for PDAC biomarkers detecting on WSIs.
    Keywords:  Deep learning; Immune infiltration; Pancreatic cancer; Prognostic biomarker; Tumor proportion
    DOI:  https://doi.org/10.1038/s41598-025-94362-x
  4. Curr Biol. 2025 Mar 11. pii: S0960-9822(25)00265-9. [Epub ahead of print]
      All cells are subject to geometric constraints, including the surface area-to-volume (SA/V) ratio, which can limit nutrient uptake, maximum cell size, and cell shape changes. Like the SA/V ratio of a sphere, it is generally assumed that the SA/V ratio of cells decreases as cell size increases. However, the structural complexity of the plasma membrane makes studies of the surface area challenging in cells that lack a cell wall. Here, we investigate near-spherical mammalian cells using single-cell measurements of cell mass and plasma membrane proteins and lipids, which allow us to examine the cell size scaling of cell surface components as a proxy for the SA/V ratio. Surprisingly, in various proliferating cell lines, cell surface components scale proportionally with cell size, indicating a nearly constant SA/V ratio as cells grow larger. This behavior is largely independent of the cell-cycle stage and is also observed in quiescent cells, including primary human monocytes. Moreover, the constant SA/V ratio persists when cell size increases excessively during polyploidization. This is enabled by increased plasma membrane folding in larger cells, as verified by electron microscopy. We also observe that specific cell surface proteins and cholesterol can deviate from the proportional size scaling. Overall, maintaining a constant SA/V ratio ensures sufficient plasma membrane area for critical functions such as cell division, nutrient uptake, growth, and deformation across a wide range of cell sizes.
    Keywords:  area-to-volume; cell cycle; cell geometry; cell growth; cell size; membrane folding; plasma membrane; size scaling; surface area; surface proteins
    DOI:  https://doi.org/10.1016/j.cub.2025.02.051
  5. medRxiv. 2025 Mar 06. pii: 2025.03.03.25322827. [Epub ahead of print]
      Oncogenic KRAS drives initiation and maintenance of pancreatic ductal adenocarcinoma (PDAC). Here, we show that engineered exosomes with Kras G12D specific siRNA (iExoKras G12D ) reveal impressive biodistribution in pancreas with negligible toxicity in preclinical studies in mice and Rhesus macaques. Clinical testing of iExoKras G12D in the iEXPLORE (iExoKras G12D in Pancreatic Cancer) Phase I study employed a classical 3+3 dose escalation design (Phase Ia), followed by an accelerated titration design (Phase Ib) ( NCT03608631 ). Patients with advanced metastatic disease were enrolled after failure of multiple lines of therapy. iExoKras G12D therapy was well-tolerated with no reported dose-limiting toxicity with some cases of stable disease response, and maximum tolerated infusion was not reached even at the highest dose. Downregulation of KRAS G12D DNA and suppression of phopho-Erk was documented with increased intratumoral in CD8 + T cell infiltration in patient samples upon treatment. The CD8 + T cell recruitment priming by iExoKras G12D informed on potential efficacy of immune checkpoint therapy and lead to validation testing in preclinical PDAC models. Combination therapy of iExoKras G12D and anti-CTLA-4 antibodies, but not anti-PD1, revealed robust anti-tumor efficacy via FAS mediated CD8 + T cell anti-tumor activity. This first-in-human, precision medicine clinical trial offers new insights into priming of immunotherapy by oncogenic Kras inhibitor and an opportunistic combination therapy for PDAC patients.
    DOI:  https://doi.org/10.1101/2025.03.03.25322827
  6. Small. 2025 Mar 21. e2403242
      Cellular biomechanics plays a critical role in cancer metastasis and tumor progression. Existing studies on cancer cell biomechanics are mostly conducted in flat 2D conditions, where cells' behavior can differ considerably from those in 3D physiological environments. Despite great advances in developing 3D in vitro models, probing cellular elasticity in 3D conditions remains a major challenge for existing technologies. In this work, optical Brillouin microscopy is utilized to longitudinally acquire mechanical images of growing cancerous spheroids over the period of 8 days. The dense mechanical mapping from Brillouin microscopy enables us to extract spatially resolved and temporally evolving mechanical features that were previously inaccessible. Using an established machine learning algorithm, it is demonstrated that incorporating these extracted mechanical features significantly improves the classification accuracy of cancer cells, from 74% to 95%. Building on this finding, a deep learning pipeline capable of accurately differentiating cancerous spheroids from normal ones solely using Brillouin images have been developed, suggesting the mechanical features of cancer cells can potentially serve as a new biomarker in cancer classification and detection.
    Keywords:  3D microenvironment; biomechanics; breast cancer; brillouin microscopy; cellular spheroid; metastasis
    DOI:  https://doi.org/10.1002/smll.202403242
  7. Ann Transl Med. 2025 Feb 28. 13(1): 9
      
    Keywords:  Pancreatic adenocarcinoma (PDAC); gemcitabine (GEM); paclitaxel
    DOI:  https://doi.org/10.21037/atm-24-182
  8. Genes Dis. 2025 May;12(3): 101323
      Pancreatic ductal adenocarcinoma (PDAC) stands as a formidable malignancy characterized by its profound lethality. The comprehensive analysis of the transcriptional landscape holds immense significance in understanding PDAC development and exploring novel treatment strategies. However, due to the firm consistency of pancreatic cancer samples, the dissociation of single cells and subsequent sequencing can be challenging. Here, we performed single-cell RNA sequencing (scRNA-seq) on 8 PDAC patients with different lymph node metastasis status. We first identified the crucial role of MMP1 in the transition from normal pancreatic cells to cancer cells. The knockdown of MMP1 in pancreatic cancer cell lines decreased the expression of ductal markers such as SOX9 while the overexpression of MMP1 in hTERT-HPNE increased the expression of ductal markers, suggesting its function of maintaining ductal identity. Secondly, we found a S100A2 + tumor subset which fueled lymph node metastasis in PDAC. The knockdown of S100A2 significantly reduced the motility of pancreatic cancer cell lines in both wound healing and transwell migration assays. While overexpression of S100A2 led to increased migratory capability. Moreover, overexpression of S100A2 in KPC1199, a mouse pancreatic cancer cell line, caused a larger tumor burden in a hemi-spleen injection model of liver metastasis. In addition, epithelial-mesenchymal transition-related genes were decreased by S100A2 knockdown revealed by bulk RNA sequencing. We also identified several pivotal contributors to the pro-tumor microenvironment, notably OMD + fibroblast and CCL2 + macrophage. As a result, our study provides valuable insights for early detection of PDAC and promising therapeutic targets for combatting lymph node metastasis.
    Keywords:  Acinar-to-ductal metaplasia; Lymph node metastasis; Pancreatic ductal adenocarcinoma; Single-cell RNA sequencing; Tumor microenvironment
    DOI:  https://doi.org/10.1016/j.gendis.2024.101323
  9. Dis Model Mech. 2025 Mar 01. pii: dmm052113. [Epub ahead of print]18(3):
      Cancer screening relies upon a linear model of neoplastic growth and progression. Yet, historical observations suggest that malignant progression is uncoupled from growth, which may explain the paradoxical increase in early-stage breast cancer detection without a dramatic reduction in metastasis. Here, we lineage trace millions of transformed cells and thousands of tumors using a cancer rainbow mouse model of HER2 (also known as ERBB2)-positive breast cancer. Transition rates from field cell to screen-detectable tumor to symptomatic tumor were estimated from a dynamical model of tumor development. Field cells were orders of magnitude less likely to transition to a screen-detectable tumor than the subsequent transition from screen-detectable tumor to symptomatic tumor. Our model supports a critical 'occult' transition in tumor development during which a transformed cell becomes a bona fide neoplasm. Lineage tracing and test by transplantation revealed that nonlinear progression during the occult transition gives rise to nascent lethal cancers at screen detection. Simulations illustrated how occult transition rates are a critical determinant of tumor growth and malignancy. Our data provide direct experimental evidence that cancers can deviate from the predictable linear progression model that is foundational to current screening paradigms.
    Keywords:  Breast cancer; Cancer progression; Mathematical modeling; Mouse models of cancer; Quantitative biology; Systems biology
    DOI:  https://doi.org/10.1242/dmm.052113
  10. J Clin Invest. 2025 Mar 17. pii: e188127. [Epub ahead of print]135(6):
      In mammalian cells cholesterol can be synthesized endogenously or obtained exogenously through lipoprotein uptake. Plasma membrane (PM) is the primary intracellular destination for both sources of cholesterol, and maintaining appropriate membrane cholesterol levels is critical for cellular viability. The endoplasmic reticulum (ER) acts as a cellular cholesterol sensor, regulating synthesis in response to cellular needs and determining the metabolic fates of cholesterol. Upon reaching the ER, cholesterol can be esterified to facilitate its incorporation into lipoproteins and lipid droplets or converted into other molecules such as bile acids and oxysterols. In recent years, it has become clear that the intracellular redistribution of lipids, including cholesterol, is critical for the regulation of various biological processes. This Review highlights physiology and mechanisms of nonvesicular (protein-mediated) intracellular cholesterol trafficking, with a focus on the role of Aster proteins in PM to ER cholesterol transport.
    DOI:  https://doi.org/10.1172/JCI188127
  11. Annu Rev Biochem. 2025 Mar 18.
      Lipids are a major class of biological molecules, the primary components of cellular membranes, and critical signaling molecules that regulate cell biology and physiology. Due to their dynamic behavior within membranes, rapid transport between organelles, and complex and often redundant metabolic pathways, lipids have traditionally been considered among the most challenging biological molecules to study. In recent years, a plethora of tools bridging the chemistry-biology interface has emerged for studying different aspects of lipid biology. Here, we provide an overview of these approaches. We discuss methods for lipid detection, including genetically encoded biosensors, synthetic lipid analogs, and metabolic labeling probes. For targeted manipulation of lipids, we describe pharmacological agents and controllable enzymes, termed membrane editors, that harness optogenetics and chemogenetics. To conclude, we survey techniques for elucidating lipid-protein interactions, including photoaffinity labeling and proximity labeling. Collectively, these strategies are revealing new insights into the regulation, dynamics, and functions of lipids in cell biology.
    DOI:  https://doi.org/10.1146/annurev-biochem-083024-110827
  12. Autophagy. 2025 Mar 21. 1-3
      Macroautophagy/autophagy is a highly conserved cellular process, spanning from yeast to humans, and plays a vital role in maintaining cellular homeostasis. Dysregulation of autophagy has been linked to a wide range of diseases. A hallmark of autophagy is the formation of double-membrane vesicles called autophagosomes. Autophagosome biogenesis requires a large number of phospholipids, with the endoplasmic reticulum (ER) being the main lipid source. The ATG2A-WDR45/WIPI4-ATG9A complex serves as the core machinery responsible for lipid transfer and equilibration during this process. In our recent study, we resolved the cryo-electron microscopy (cryo-EM) structures of the ATG2A-WDR45/WIPI4 and ATG2A-WDR45/WIPI4-ATG9A complexes, providing critical insights into their architecture and function. Additionally, molecular dynamics simulations were employed to investigate the mechanism by which ATG2A mediates lipid extraction from donor membranes. Our findings offer structural and mechanistic insights into the spatially coupled processes of lipid transfer and re-equilibration, which are essential for phagophore membrane expansion.Abbreviation: ATG: autophagy related; ATG2A: autophagy related 2A; ATG2A[NR]: ATG2A N-terminal region; ATG9A: autophagy related 9A; cryo-EM: cryo-electron microscopy; cryo-ET: cryo-electron tomography; ER: endoplasmic reticulum; PtdIns3P: phosphatidylinositol-3-phosphate; SpAtg2[NR]: Schizosaccharomyces pombe Atg2 N-terminal region; SUVs: small unilamellar vesicles; TGN: trans-Golgi network; TMEM41B: transmembrane protein 41B; VMP1: vacuole membrane protein 1; WDR45/WIPI4: WD repeat domain 45.
    Keywords:  ATG2A-ATG9A complex; Cryo-EM; autophagosome formation; phospholipid scramblases; phospholipid transfer
    DOI:  https://doi.org/10.1080/15548627.2025.2473388
  13. Autophagy. 2025 Mar 18.
      Cancer cells depend on the reprogramming of cell metabolism to constantly adapt metabolically to the tumor microenvironment. ADSL (adenylosuccinate lyase), a rate-limiting enzyme in de novo purine synthesis, is overexpressed in various cancer cells. However, whether ADSL functions in other oncogenic signaling is largely unknown. Here, our recent study shows that ADSL interacts with BECN1 (beclin 1) to regulate macroautophagy/autophagy upon lipid deprivation. Mechanistically, ADSL is phosphorylated at S140 by EIF2AK3/PERK (eukaryotic translation initiation factor 2 alpha kinase 3) in response to lipid deprivation, which enhances the association between ADSL and BECN1. ADSL-produced fumarate reduces the BECN1-associated KDM8 activity, leading to increased BECN1 K117 dimethylation. BECN1 K117 dimethylation inhibits its interaction with BCL2 to initiate autophagy. Targeting the ADSL-BECN1 axis by knock-in mutation or a cell-penetrating peptide inhibits autophagy and blunts liver tumor growth in mice. These findings broaden the physiological significance of ADSL in autophagy and liver tumor development.
    Keywords:  ADSL; Beclin1; autophagy; fumarate
    DOI:  https://doi.org/10.1080/15548627.2025.2481125
  14. Nat Genet. 2025 Mar 18.
      Spatial omics enable the characterization of colocalized cell communities that coordinate specific functions within tissues. These communities, or niches, are shaped by interactions between neighboring cells, yet existing computational methods rarely leverage such interactions for their identification and characterization. To address this gap, here we introduce NicheCompass, a graph deep-learning method that models cellular communication to learn interpretable cell embeddings that encode signaling events, enabling the identification of niches and their underlying processes. Unlike existing methods, NicheCompass quantitatively characterizes niches based on communication pathways and consistently outperforms alternatives. We show its versatility by mapping tissue architecture during mouse embryonic development and delineating tumor niches in human cancers, including a spatial reference mapping application. Finally, we extend its capabilities to spatial multi-omics, demonstrate cross-technology integration with datasets from different sequencing platforms and construct a whole mouse brain spatial atlas comprising 8.4 million cells, highlighting NicheCompass' scalability. Overall, NicheCompass provides a scalable framework for identifying and analyzing niches through signaling events.
    DOI:  https://doi.org/10.1038/s41588-025-02120-6
  15. Proc Natl Acad Sci U S A. 2025 Mar 25. 122(12): e2427255122
      Interaction of electric fields with biological cells is indispensable for many physiological processes. Thermal electrical noise in the cellular environment has long been considered as the minimum threshold for detection of electrical signals by cells. However, there is compelling experimental evidence that the minimum electric field sensed by certain cells and organisms is many orders of magnitude weaker than the thermal electrical noise limit estimated purely under equilibrium considerations. We resolve this discrepancy by proposing a nonequilibrium statistical mechanics model for active electromechanical membranes and hypothesize the role of activity in modulating the minimum electrical field that can be detected by a biological membrane. Active membranes contain proteins that use external energy sources to carry out specific functions and drive the membrane away from equilibrium. The central idea behind our model is that active mechanisms, attributed to different sources, endow the membrane with the ability to sense and respond to electric fields that are deemed undetectable based on equilibrium statistical mechanics. Our model for active membranes is capable of reproducing different experimental data available in the literature by varying the activity. Elucidating how active matter can modulate the sensitivity of cells to electric signals can open avenues for a deeper understanding of physiological and pathological processes.
    Keywords:  Langevin equation; active matter; fluctuations; polarization
    DOI:  https://doi.org/10.1073/pnas.2427255122
  16. Nat Metab. 2025 Mar 17.
      The constant expansion of the field of metabolic research has led to more nuanced and sophisticated understanding of the complex mechanisms that underlie metabolic functions and diseases. Collaborations with scientists of various fields such as neuroscience, immunology and drug discovery have further enhanced the ability to probe the role of metabolism in physiological processes. However, many behaviours, endocrine and biochemical processes, and the expression of genes, proteins and metabolites have daily ~24-h biological rhythms and thus peak only at specific times of the day. This daily variation can lead to incorrect interpretations, lack of reproducibility across laboratories and challenges in translating preclinical studies to humans. In this Review, we discuss the biological, environmental and experimental factors affecting circadian rhythms in rodents, which can in turn alter their metabolic pathways and the outcomes of experiments. We recommend that these variables be duly considered and suggest best practices for designing, analysing and reporting metabolic experiments in a circadian context.
    DOI:  https://doi.org/10.1038/s42255-025-01237-6
  17. Cell Rep. 2025 Mar 13. pii: S2211-1247(25)00203-7. [Epub ahead of print]44(3): 115432
      Cancer-associated fibroblasts (CAFs) and immune cells make up two major components of the tumor microenvironment (TME), contributing to an ecosystem that can either support or restrain cancer progression. Metabolism is a key regulator of the TME, providing a means for cells to communicate with and influence each other, modulating tumor progression and anti-tumor immunity. Cells of the TME can metabolically interact directly through metabolite secretion and consumption or by influencing other aspects of the TME that, in turn, stimulate metabolic rewiring in target cells. Recent advances in understanding the subtypes and plasticity of cells in the TME both open up new avenues and create challenges for metabolically targeting the TME to hamper tumor growth and improve response to therapy. This perspective explores ways in which the CAF and immune components of the TME could metabolically influence each other, based on current knowledge of their metabolic states, interactions, and subpopulations.
    Keywords:  CAFs; CP: Cancer; CP: Metabolism; immune cells; metabolism; stroma immune; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.celrep.2025.115432
  18. Nat Commun. 2025 Mar 19. 16(1): 2685
      Mitochondrial dynamics are orchestrated by protein assemblies that directly remodel membrane structure, however the influence of specific lipids on these processes remains poorly understood. Here, using an inducible heterodimerization system to selectively modulate the lipid composition of the outer mitochondrial membrane (OMM), we show that local production of diacylglycerol (DAG) directly leads to transient tubulation and rapid fragmentation of the mitochondrial network, which are mediated by isoforms of endophilin B (EndoB) and dynamin-related protein 1 (Drp1), respectively. Reconstitution experiments on cardiolipin-containing membrane templates mimicking the planar and constricted OMM topologies reveal that DAG facilitates the membrane binding and remodeling activities of both EndoB and Drp1, thereby independently potentiating membrane tubulation and fission events. EndoB and Drp1 do not directly interact with each other, suggesting that DAG production activates multiple pathways for membrane remodeling in parallel. Together, our data emphasizes the importance of OMM lipid composition in regulating mitochondrial dynamics.
    DOI:  https://doi.org/10.1038/s41467-025-57439-9
  19. J Biol Chem. 2025 Mar 18. pii: S0021-9258(25)00270-4. [Epub ahead of print] 108421
      Disintegration of organelle membranes induces various cellular responses and has pathological consequences, including autoinflammatory diseases and neurodegeneration. Establishing methods to induce membrane rupture of specific organelles is essential to analyze the downstream effects of membrane rupture; however, the spatiotemporal induction of organelle membrane rupture remains challenging. Here, we develop a series of optogenetic tools to induce organelle membrane rupture by using engineered Bcl-2-associated X protein (BAX), which primarily functions to form membrane pores in the outer mitochondrial membrane (OMM) during apoptosis. When BAX is forced to target mitochondria, lysosomes, or the endoplasmic reticulum (ER) by replacing its C-terminal transmembrane domain (TMD) with organelle-targeting sequences, the BAX mutants rupture their targeted membranes. To regulate the activity of organelle-targeted BAX, the photosensitive light-oxygen-voltage-sensing 2 (LOV2) domain is fused to the N-terminus of BAX. The resulting LOV2-BAX fusion protein exhibits blue light-dependent membrane-rupture activity on various organelles, including mitochondria, the ER, and lysosomes. Thus, LOV2-BAX enables spatiotemporal induction of membrane rupture across a broad range of organelles, expanding research opportunities on the consequences of organelle membrane disruption.
    Keywords:  Bcl-2-associated X protein (BAX); Membrane rupture; light-oxygen-voltage-sensing 2 (LOV2) domain; lysosomal membrane permeabilization (LMP); mitochondrial outer membrane permeabilization (MOMP); optogenetics
    DOI:  https://doi.org/10.1016/j.jbc.2025.108421
  20. bioRxiv. 2025 Mar 04. pii: 2025.02.28.640711. [Epub ahead of print]
      Lack of sustained response to oncogenic Kras (Kras*) inhibition in preclinical models and patients with pancreatic ductal adenocarcinoma (PDAC) emphasizes the need to identify impactful synergistic combination therapies to achieve robust clinical benefit. Kras* targeting results in an influx of global T cell infiltrates including Tregs, effector CD8 + T cells and exhausted CD8 + T cells expressing several immune checkpoint molecules in PDAC. Here, we probe whether the T cell influx induced by diverse Kras* inhibitors open a therapeutic window to target the adaptive immune response in PDAC. We show a specific synergy of anti-CTLA4 immune checkpoint blockade with Kras* targeting primed by Kras G12D allele specific inhibitor, MRTX1133 and multi-selective pan-RAS inhibitor, RMC-6236, both currently in clinical testing phase. In contrast, attempted therapeutic combination following Kras* targeting with multiple checkpoint inhibitors, including anti-PD1, anti-Tim3, anti-Lag3, anti-Vista and anti-4-1BB agonist antibody failed due to compensatory mechanisms mediated by other checkpoints on exhausted CD8 + T cells. Anti-CTLA4 therapy in Kras* targeted PDAC transcriptionally reprograms effector T regs to a naïve phenotype, reverses CD8 + T cell exhaustion and is associated with recruitment of tertiary lymphoid structures (TLS) containing interferon (IFN)-stimulated/ activated B cells and germinal center B cells to enable immunotherapy efficacy and overcome resistance with long-term survival. Single cell ATAC sequencing analysis revealed that transcriptional reprogramming of Tregs is epigenetically regulated by downregulation of AP-1 family of transcription factors including Fos, Fos-b, Jun-b, Jun-d in the IL-35 promoter region. This study reveals an actionable vulnerability in the adaptive immune response in Kras* targeted PDAC with important clinical implications.
    Graphical abstract:
    DOI:  https://doi.org/10.1101/2025.02.28.640711
  21. Res Sq. 2025 Mar 03. pii: rs.3.rs-6008502. [Epub ahead of print]
      Tissue-level phase transitions are emerging as a crucial mechanism in tumour development and metastasis. This study aims to identify molecular determinants and physical conditions that control active wetting and solid-to-fluid transition of epithelial tissues. We focused on IRSp53, a protein linking plasma membranes to the cytoskeleton. Depleting IRSp53, in MCF10 DCIS.com cells, disrupts coordinated collective movement by promoting local fluctuations in cell velocity resulting in increased tissue fluidity. In dense monolayers, IRSp53 ablation allows cells to escape the physical constraint imposed by cell crowding resulting in a delayed transition toward a jammed state. In 3D spheroids, IRSp53 loss fosters active wetting of a rigid substrate, shifting spheroid behaviour to a more fluid-like state. Biophysical modelling of the spreading cells as an active polar fluid indicates that IRSp53 depletion reduces bulk viscosity and contractility in spheroids. This effect is the result of reduced supracellular tension and disrupted organization of cell-cell junctions, which lead to decreased intercellular friction and enhanced local cell rearrangements. Molecularly, IRSp53 physically and functionally interacts with the junctional protein Afadin in regulating tissue tensile state and active wetting in tumour spheroids. These findings identify IRSp53 and Afadin as key regulators of tissue viscosity in breast cancer tumoroid undergoing solid-to-fluid transition linked to tumour progression. They further provide the molecular basis to causally relate subcellular and cell scale processes to tissue-levels dynamics.
    DOI:  https://doi.org/10.21203/rs.3.rs-6008502/v1
  22. Immunity. 2025 Mar 13. pii: S1074-7613(25)00089-5. [Epub ahead of print]
      Central nervous system (CNS) malignancies include primary tumors, such as gliomas, and brain metastases (BrMs) originating from diverse extracranial cancers. The blood-brain barrier (BBB) is a key structural component of both primary and metastatic brain cancers. Here, we comprehensively analyzed the two major BBB cell types, endothelial and mural cells, across non-tumor brain tissue, isocitrate dehydrogenase (IDH) mutant (IDH mut) low-grade gliomas, IDH wild-type (IDH WT) high-grade glioblastomas (GBMs), and BrMs from various primary tumors. Bulk and single-cell RNA sequencing, integrated with spatial analyses, revealed that GBMs, but not low-grade gliomas, exhibit significant alterations in the tumor vasculature, including the emergence of diverse pathological vascular cell subtypes. However, these alterations are less pronounced in GBMs than in BrMs. Notably, the BrM vasculature shows higher permeability and more extensive interactions with distinct immune cell populations. This vascular atlas presents a resource toward understanding of tumor-specific vascular features in the brain, providing a foundation for developing vascular- and immune-targeting therapies.
    Keywords:  IDH WT glioblastoma; IDH mut glioma; RNA sequencing; brain metastasis; endothelial cells; mural cells; vasculature
    DOI:  https://doi.org/10.1016/j.immuni.2025.02.022
  23. J Clin Invest. 2025 Mar 17. pii: e185340. [Epub ahead of print]135(6):
      Adipose tissue lipolysis is the process by which triglycerides in lipid stores are hydrolyzed into free fatty acids (FFAs), serving as fuel during fasting or cold-induced thermogenesis. Although cytosolic lipases are considered the predominant mechanism of liberating FFAs, lipolysis also occurs in lysosomes via lysosomal acid lipase (LIPA), albeit with unclear roles in lipid storage and whole-body metabolism. We found that adipocyte LIPA expression increased in adipose tissue of mice when lipolysis was stimulated during fasting, cold exposure, or β-adrenergic agonism. This was functionally important, as inhibition of LIPA genetically or pharmacologically resulted in lower plasma FFAs under lipolytic conditions. Furthermore, adipocyte LIPA deficiency impaired thermogenesis and oxygen consumption and rendered mice susceptible to diet-induced obesity. Importantly, lysosomal lipolysis was independent of adipose triglyceride lipase, the rate-limiting enzyme of cytosolic lipolysis. Our data suggest a significant role for LIPA and lysosomal lipolysis in adipocyte lipid metabolism beyond classical cytosolic lipolysis.
    Keywords:  Adipose tissue; Endocrinology; Lysosomes; Metabolism; Obesity; Therapeutics
    DOI:  https://doi.org/10.1172/JCI185340
  24. Cancer Discov. 2025 Mar 18.
      Here, we observe that in human and murine melanomas, T-cell activation abates hematopoietic prostaglandin-D2 synthase (HPGDS) transcription in tumor-associated macrophages (TAMs) through TNFα signaling. Mechanistically, HPGDS installs a Prostaglandin-D2 (PGD2) autocrine loop in TAMs via DP1 and DP2 activation that sustains their pro-tumoral phenotype and promotes paracrine inhibition of CD8+ T cells via a PGD2-DP1 axis. Genetic or pharmacologic HPGDS targeting induces anti-tumoral features in TAMs and favors CD8+ T-cell recruitment, activation, and cytotoxicity, altogether sensitizing tumors to αPD1. Conversely, HPGDS overexpression in TAMs or systemic TNFα blockade sustains a pro-tumoral environment and αPD1-resistance, preventing the downregulation of HPGDS by T cells. Congruently, patients and mice resistant to αPD1 fail to suppress HPGDS in TAMs, reinforcing the evidence that circumventing HPGDS is necessary for efficient αPD1 treatment. Overall, we disclose a mechanism whereby T-cell activation controls the innate immune system, and we suggest HPGDS/PGD2 targeting to overcome immunotherapy resistance.
    DOI:  https://doi.org/10.1158/2159-8290.CD-24-0415
  25. Nat Mater. 2025 Mar 14.
      Cell competition is a tissue surveillance mechanism for eliminating unwanted cells, being indispensable in development, infection and tumourigenesis. Although studies have established the role of biochemical mechanisms in this process, due to challenges in measuring forces in these systems, how mechanical forces determine the competition outcome remains unclear. Here we report a form of cell competition that is regulated by differences in force transmission capabilities, selecting for cell types with stronger intercellular adhesion. Direct force measurements in ex vivo tissues and different cell lines reveal that there is an increased mechanical activity at the interface between two competing cell types, which can lead to large stress fluctuations resulting in upward forces and cell elimination. We show how a winning cell type endowed with a stronger intercellular adhesion exhibits higher resistance to elimination and benefiting from efficient force transmission to the neighbouring cells. This cell elimination mechanism could have broad implications for keeping the strong force transmission ability for maintaining tissue boundaries and cell invasion pathology.
    DOI:  https://doi.org/10.1038/s41563-025-02150-9
  26. Bioact Mater. 2025 Jun;48 493-509
      Cancer metabolism plays an essential role in therapeutic resistance, where significant inter- and intra-tumoral heterogeneity exists. Hypoxia is a prominent driver of metabolic rewiring behaviors and drug responses. Recapitulating the hypoxic landscape in the tumor microenvironment thus offers unique insights into heterogeneity in metabolic rewiring and therapeutic responses, to inform better treatment strategies. There remains a lack of scalable tools that can readily interface with imaging platforms and resolve the heterogeneous behaviors in hypoxia-associated metabolic rewiring. Here we present a micro-metabolic rewiring (μMeRe) assay that provides the scalability and resolution needed to characterize the metabolic rewiring behaviors of different cancer cells in the context of hypoxic solid tumors. Our assay generates hypoxia through cellular metabolism without external gas controls, enabling the characterization of cell-specific intrinsic ability to drive hypoxia and undergo metabolic rewiring. We further developed quantitative metrics that measure the metabolic plasticity through phenotypes and gene expression. As a proof-of-concept, we evaluated the efficacy of a metabolism-targeting strategy in mitigating hypoxia- and metabolic rewiring-induced chemotherapeutic resistance. Our study and the scalable platform thus lay the foundation for designing more effective cancer treatments tailored toward specific metabolic rewiring behaviors.
    Keywords:  Hypoxia; Metabolic rewiring; Metabolism-targeting therapy; Tumor heterogeneity; Tumor microenvironment
    DOI:  https://doi.org/10.1016/j.bioactmat.2025.02.030
  27. Biomaterials. 2025 Mar 14. pii: S0142-9612(25)00178-4. [Epub ahead of print]320 123259
      Despite the promise of ferroptosis in cancer therapy, selectively inducing robust ferroptosis in cancer cells remains a significant challenge. In this study, manipulation of fatty acids β-oxidation (FAO) by combination of mild photodynamic therapy (PDT) and inhibition of triglycerides (TGs) synthesis was found to induce robust and iron-independent ferroptosis in cancer cells with dysregulated lipid metabolism for the first time. To achieve that, TGs synthesis inhibitor of xanthohumol (Xan) and FAO initiator of tetrakis (4-carboxyphenyl) porphyrin (TCPP) were co-delivered by a nanoplexes composed of pH-responsive amphiphilic lipopeptide C18-pHis10 and DSPE-PEG2000. TCPP was found to rapidly increase the intracellular ROS under laser irradiation without inducing antioxidant response and apoptosis, activating the AMPK in cancer cells and accelerating mitochondrial FAO. Xan fueled the mitochondrial FAO with substrates by suppressing the conversion of fatty acids (FAs) to TGs. This also led to augmented intracellular polyunsaturated fatty acids (PUFAs) and PUFAs-phospholipids levels, increasing the intrinsic susceptibility of cancer cells to lipid peroxidization. As a result, the excessive ROS generated from the sustained mitochondrial FAO caused remarkably lipid peroxidation and ultimately ferroptosis. Collectively, our study provides a new approach to selectively induce iron-independent ferroptosis in cancer cells by taking advantage of dysregulated lipid metabolism.
    Keywords:  Cancer cell selective; Dysregulated lipid metabolism; Fatty acids β-oxidation; Iron-independent ferroptosis; Positive-feedback
    DOI:  https://doi.org/10.1016/j.biomaterials.2025.123259
  28. Nature. 2025 Mar 19.
      Tumour cells often evade immune pressure exerted by CD8+ T cells or immunotherapies through mechanisms that are largely unclear1,2. Here, using complementary in vivo and in vitro CRISPR-Cas9 genetic screens to target metabolic factors, we established voltage-dependent anion channel 2 (VDAC2) as an immune signal-dependent checkpoint that curtails interferon-γ (IFNγ)-mediated tumour destruction and inflammatory reprogramming of the tumour microenvironment. Targeting VDAC2 in tumour cells enabled IFNγ-induced cell death and cGAS-STING activation, and markedly improved anti-tumour effects and immunotherapeutic responses. Using a genome-scale genetic interaction screen, we identified BAK as the mediator of VDAC2-deficiency-induced effects. Mechanistically, IFNγ stimulation increased BIM, BID and BAK expression, with VDAC2 deficiency eliciting uncontrolled IFNγ-induced BAK activation and mitochondrial damage. Consequently, mitochondrial DNA was aberrantly released into the cytosol and triggered robust activation of cGAS-STING signalling and type I IFN response. Importantly, co-deletion of STING signalling components dampened the therapeutic effects of VDAC2 depletion in tumour cells, suggesting that targeting VDAC2 integrates CD8+ T cell- and IFNγ-mediated adaptive immunity with a tumour-intrinsic innate immune-like response. Together, our findings reveal VDAC2 as a dual-action target to overcome tumour immune evasion and establish the importance of coordinately destructing and inflaming tumours to enable efficacious cancer immunotherapy.
    DOI:  https://doi.org/10.1038/s41586-025-08732-6
  29. bioRxiv. 2025 Mar 03. pii: 2025.03.03.641220. [Epub ahead of print]
      Neomycin, an aminoglycoside antibiotic, has robust antibacterial properties, yet its clinical utility is curtailed by its nephrotoxicity and ototoxicity. The mechanism by which the polycationic neomycin enters specific eukaryotic cell types remains poorly understood. In budding yeast, NEO1 is required for neomycin resistance and encodes a phospholipid flippase that establishes membrane asymmetry. Here, we show that mutations altering Neo1 substrate recognition cause neomycin hypersensitivity by exposing phosphatidylinositol-4-phosphate (PI4P) in the plasma membrane extracellular leaflet. Human cells also expose extracellular PI4P upon knockdown of ATP9A, a Neo1 ortholog and ATP9A expression level correlates to neomycin sensitivity. In yeast, the extracellular PI4P is initially produced in the cytosolic leaflet of the plasma membrane and then delivered by Osh6-dependent nonvesicular transport to the endoplasmic reticulum (ER). Here, a portion of PI4P escapes degradation by the Sac1 phosphatase by entering the ER lumenal leaflet. COPII vesicles transport lumenal PI4P to the Golgi where Neo1 flips this substrate back to the cytosolic leaflet. Cryo-EM reveals that PI4P binds Neo1 within the substrate translocation pathway. Loss of Neo1 activity in the Golgi allows secretion of extracellular PI4P, which serves as a neomycin receptor and facilitates its endocytic uptake. These findings unveil novel mechanisms of aminoglycoside sensitivity and phosphoinositide homeostasis, with important implications for signaling by extracellular phosphoinositides.
    DOI:  https://doi.org/10.1101/2025.03.03.641220
  30. Nat Commun. 2025 Mar 16. 16(1): 2594
      Near-infrared (NIR) fluorescent reporters open interesting perspectives for multiplexed imaging with higher contrast and depth using less toxic light. Here, we propose nirFAST, a small (14 kDa) chemogenetic NIR fluorescent reporter, displaying higher cellular brightness compared to top-performing NIR fluorescent proteins. nirFAST binds and stabilizes the fluorescent state of synthetic cell permeant fluorogenic chromophores (so-called fluorogens), otherwise dark when free. nirFAST displays tunable NIR, far-red or red emission through change of fluorogen. nirFAST allows imaging and spectral multiplexing in live cultured mammalian cells, chicken embryo tissues and zebrafish larvae. Its suitability for stimulated emission depletion nanoscopy enabled protein imaging with subdiffraction resolution in live cells. nirFAST enabled the design of a two-color cell cycle indicator for monitoring the different phases of the cell cycle. Finally, bisection of nirFAST allowed the design of a chemically induced dimerization technology with NIR fluorescence readout, enabling the control and visualization of protein proximity.
    DOI:  https://doi.org/10.1038/s41467-025-58017-9
  31. Elife. 2025 Mar 18. pii: RP96892. [Epub ahead of print]13
      Mass spectrometry imaging (MSI) is a powerful technology used to define the spatial distribution and relative abundance of metabolites across tissue cryosections. While software packages exist for pixel-by-pixel individual metabolite and limited target pairs of ratio imaging, the research community lacks an easy computing and application tool that images any metabolite abundance ratio pairs. Importantly, recognition of correlated metabolite pairs may contribute to the discovery of unanticipated molecules in shared metabolic pathways. Here, we describe the development and implementation of an untargeted R package workflow for pixel-by-pixel ratio imaging of all metabolites detected in an MSI experiment. Considering untargeted MSI studies of murine brain and embryogenesis, we demonstrate that ratio imaging minimizes systematic data variation introduced by sample handling, markedly enhances spatial image contrast, and reveals previously unrecognized metabotype-distinct tissue regions. Furthermore, ratio imaging facilitates identification of novel regional biomarkers and provides anatomical information regarding spatial distribution of metabolite-linked biochemical pathways. The algorithm described herein is applicable to any MSI dataset containing spatial information for metabolites, peptides or proteins, offering a potent hypothesis generation tool to enhance knowledge obtained from current spatial metabolite profiling technologies.
    Keywords:  adipose; brain; computational biology; embryo; mouse; systems biology
    DOI:  https://doi.org/10.7554/eLife.96892