bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2025–11–02
29 papers selected by
Kıvanç Görgülü, Technical University of Munich



  1. Nat Cell Biol. 2025 Oct 29.
      Lipid droplets (LDs) are organelles that store and supply lipids, based on cellular needs. Although mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here we identify LD-localized ferroptosis suppressor protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidation in vitro. Notably, inducing polyunsaturated fatty acid-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality-control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the build-up of oxidized lipids and induction of ferroptosis.
    DOI:  https://doi.org/10.1038/s41556-025-01790-y
  2. Proc Natl Acad Sci U S A. 2025 Nov 04. 122(44): e2516822122
      The asymmetric resting distribution of the three major phospholipid classes on the mammalian plasma membrane, with phosphatidylserine and phosphatidylethanolamine mostly on the inner leaflet and phosphatidylcholine mostly on the outer leaflet, is maintained by ATP-dependent flippases and floppases that exhibit headgroup selectivity. Upon signaling cues, this asymmetry can be dissipated by various phospholipid scramblases, allowing cells to respond to stimuli and adapt to different physiological contexts. The prevailing view in the field is that phospholipid scramblases on the plasma membrane act without headgroup preference. Here, we report contrary experimental evidence based on a phospholipid scrambling assay that quantifies the fluorescence polarization (FP) of nitrobenzoxadiazole (NBD)-labeled phospholipids for kinetic monitoring of phospholipid scrambling on the plasma membrane of living cells. Our experiments reveal that the plasma membrane-residing calcium-activated phospholipid scramblase TMEM16F preferentially acts on phosphatidylserine and phosphatidylcholine over phosphatidylethanolamine.
    Keywords:  TMEM16F; coarse-grained molecular simulations; fluorescence polarization; phospholipid scrambling; plasma membrane
    DOI:  https://doi.org/10.1073/pnas.2516822122
  3. Nat Genet. 2025 Oct 30.
      Emerging evidence suggests that lineage-specifying transcription factors control the progression of pancreatic ductal adenocarcinoma (PDAC). We have discovered a transcription factor switching mechanism involving the poorly characterized orphan nuclear receptor HNF4G and the putative pioneer factor FOXA1, which drives PDAC progression. Using our unbiased protein interactome discovery approach, we identified HNF4A and HNF4G as reproducible, FOXA1-associated proteins, in both preclinical models and Whipple surgical samples. In the primary tumor context, we consistently find that the dominant transcription factor is HNF4G, where it functions as the driver. A molecular switch occurs in advanced disease, whereby HNF4G expression or activity decreases, unmasking FOXA1's transcriptional potential. Derepressed FOXA1 drives late-stage disease by orchestrating metastasis-specific enhancer-promoter loops to regulate the expression of metastatic genes. Overall survival is influenced by HNF4G and FOXA1 activity in primary tumor growth and in metastasis, respectively. We suggest that the existence of stage-dependent transcription factor activity, triggered by molecular compartmentalization, mediates the progression of PDAC.
    DOI:  https://doi.org/10.1038/s41588-025-02389-7
  4. Adv Sci (Weinh). 2025 Oct 28. e17606
      Pancreatic ductal adenocarcinoma (PDAC) is characterized by its intricate biology governed by spatiotemporal dynamics in the expression and function of specific proteins. Here, DKK3 is identified as a dynamic player with a dual role in PDAC. Using the KRASG12D-driven mouse model with homozygous (DDKC) and heterozygous (DKC) DKK3 knockout, its stage and compartment-specific functions are investigated. Knockout mice exhibited shorter lifespans with a higher incidence of high-grade, desmoplastic, and metastatic cancers. DKK3-deficient acini exhibited a marked increase in acinar-to-ductal metaplasia, with increased MAPK signaling and induction of the downstream effector Fos. During the progression of mouse and human PDAC, DKK3 expression shifted from epithelial dysplastic cells to cancer-associated fibroblasts (CAFs). At the endpoint, DKK3-expressing CAFs emerged as crucial contributors to tumor aggressiveness and fibrosis. Orthotopic transplantations confirm a stromal role, particularly in DDKC tumors, while mechanistic studies demonstrate that DKK3 activates IL6-JAK-STAT3 signaling and pro-migratory/mesenchymal programs that are reversed by pharmacologic STAT3 inhibition in DDKC cells. Concordantly, DKK3 expression correlates with IL6-JAK-STAT3 gene signatures in human PDAC datasets. Together, these findings underscore the intricate and context-sensitive role of DKK3, delaying oncogenesis during early stages while paradoxically promoting tumor progression in later stages, suggesting that therapeutic targeting strategies should be approached with caution.
    Keywords:  DKK3; PDAC; dual role; oncogene; tumor suppressor
    DOI:  https://doi.org/10.1002/advs.202417606
  5. EMBO J. 2025 Oct 30.
      Selective autophagy ensures the targeted degradation of damaged or surplus cellular components, including organelles, thereby safeguarding cellular homeostasis. This process relies on selective autophagy receptors (SARs) that link specific cargo to the autophagy machinery. These receptors exist in two distinct forms: soluble SARs that are recruited to the cargo on demand, and transmembrane SARs that are stably embedded in the membranes of organelles they target. While both receptor types converge on the same autophagy core machinery, they differ in how they recognize cargo, are regulated, and recruit this machinery to the site of degradation. In this review, we explore the unique challenges and strategies associated with transmembrane SARs, including how their activity is suppressed under basal conditions and activated in response to stress. We compare their mode of action with that of soluble SARs, highlight key differences in kinase regulation, including the roles of TBK1, ULK1, CK2, and Src, and discuss emerging models of autophagy initiation. We further highlight fundamental principles of organelle-selective autophagy and identify open questions that will guide future research.
    Keywords:  Autophagosome; ER-phagy; Mitophagy; Quality Control; Selective Autophagy
    DOI:  https://doi.org/10.1038/s44318-025-00615-w
  6. Nat Genet. 2025 Oct 27.
      Most patients with localized pancreatic ductal adenocarcinoma (PDAC) experience recurrence after resection. Analysis of 744 patients with resected PDAC revealed that patients with initial isolated liver-metastatic recurrence (n = 100) had significantly worse overall survival than those with initial isolated lung-metastatic recurrence (n = 31). Using single-nucleus RNA sequencing in a representative cohort, we found that transcriptional profiles of primary cancer cells with liver-metastatic recurrence and lung-metastatic recurrence were correlated with those of normal liver and lung parenchymal cells, respectively, suggesting adoption of organ-specific metastatic programs at the primary site. These signatures were confirmed in transcriptomes of PDAC lung and liver metastases, primary lung and liver tumors, and organotropic PDAC xenograft models. These signatures were independent of large genomic events, and analysis of large-scale tumor profiling data showed no genetic alterations predictive of recurrence patterns. Additional analyses suggested that metastatic recurrence may be determined early in tumorigenesis and influenced by tumor-infiltrating immune cells. Thus, pre-existing cellular states within primary tumors appear to guide organ-specific metastatic relapse.
    DOI:  https://doi.org/10.1038/s41588-025-02345-5
  7. Cell. 2025 Oct 30. pii: S0092-8674(25)01128-6. [Epub ahead of print]188(22): 6107-6108
      In this issue of Cell, Han et al. find that tumor cells metastasizing to the bone marrow hijack macrophages to seize iron from red blood cells. This metabolic plunder thereby fuels tumor progression while contributing to anemia.
    DOI:  https://doi.org/10.1016/j.cell.2025.09.028
  8. Trends Cancer. 2025 Oct 29. pii: S2405-8033(25)00257-2. [Epub ahead of print]
      Circulating tumor cell (CTC) clusters have emerged as key mediators of cancer spread. Among these, heterotypic CTC clusters exemplify how cooperative interactions between different cell types may enhance metastasis efficiency. Recent studies by Scholten et al. and Schuster et al. uncover additional immune cell partners, including T cells and monocytes, involved in shaping CTC biology.
    DOI:  https://doi.org/10.1016/j.trecan.2025.10.006
  9. Nat Methods. 2025 Oct 30.
      Tissue makeup depends on the local cellular microenvironment. Spatial single-cell genomics enables scalable and unbiased interrogation of these interactions. Here we introduce Nicheformer, a transformer-based foundation model trained on both human and mouse dissociated single-cell and targeted spatial transcriptomics data. Pretrained on SpatialCorpus-110M, a curated collection of over 57 million dissociated and 53 million spatially resolved cells across 73 tissues on cellular reconstruction, Nicheformer learns cell representations that capture spatial context. It excels in linear-probing and fine-tuning scenarios for a newly designed set of downstream tasks, in particular spatial composition prediction and spatial label prediction. Critically, we show that models trained only on dissociated data fail to recover the complexity of spatial microenvironments, underscoring the need for multiscale integration. Nicheformer enables the prediction of the spatial context of dissociated cells, allowing the transfer of rich spatial information to scRNA-seq datasets. Overall, Nicheformer sets the stage for the next generation of machine-learning models in spatial single-cell analysis.
    DOI:  https://doi.org/10.1038/s41592-025-02814-z
  10. Genes Dis. 2026 Jan;13(1): 101771
      Tumor cell invasion is the key driver of metastatic dissemination, resulting in the development and progression of metastatic tumors at secondary sites, and remains the major cause of cancer-related death. Recent studies suggest that, in addition to protease-mediated degradation and chemotaxis-stimulated migration, tumor invasion is significantly influenced by physical surroundings. How tumor cells decode information about their shape deformation under mechanical stress and adapt their dynamic behavior to escape the confined regions remains largely unknown. This review highlights recent findings that illustrate mechanical cues in confined tumor microenvironment contribute to tumor progression. We also systematically discuss the role of compression-induced deformation in cell membrane topology and cytoskeletal remodeling, as well as its biophysical mechanisms in regulating tumor invasion from a biomechanical perspective.
    Keywords:  Actin remodeling; Mechanical forces; Mechanical memory; Microenvironment; Tumor invasion
    DOI:  https://doi.org/10.1016/j.gendis.2025.101771
  11. Antioxidants (Basel). 2025 Sep 24. pii: 1157. [Epub ahead of print]14(10):
      Animal slaughtering causes the cessation of oxygen delivery and that of nutrients such as cystine, glucose and others to muscle cells. In muscle cells, the changes in oxygen level and pH cause mitochondria, the endoplasmic reticulum, xanthine oxidase and uncoupled NOS to increase the level of O2•-, affecting the generation of H2O2 and the release of iron ions from ferritin. The activation of enzymes that remove and dislocate fatty acids from the membrane affects the sensitivity of muscle cells to peroxidation and ferroptosis. Increasing PUFAs in membrane phospholipids, by feeding animals a diet high in w-3 fatty acids, is a driving factor that increases lipid peroxidation and possible muscle ferroptosis. The activation of lipoxygenases by ROS to Fe3+-lipoxygenase increases hydroperoxide levels in cells. The labile iron pool generated by a "redox cycle" catalyzes phospholipid hydroperoxides to generate lipid electrophiles, proximate executioners of ferroptosis. Ferroptosis in food muscle cells is protected by high concentrations of vitamin E and selenium. In fresh muscle cells, glutathione peroxidase (GSH-PX) and other endogenous antioxidant enzymes are active and prevent lipid peroxidation; however, muscle heating eliminates enzymatic activities, making cells prone to high non-enzymatic lipid peroxidation. In muscle cells, coupled myoglobin and vitamin E act as a hydroperoxidase, preventing the generation of lipid electrophiles. Free iron ion chelators or effectors such as deferoxamine, EDTA, or ceruloplasmin are strong inhibitors of muscle cell lipid peroxidation, proving that muscle ferroptosis is mostly dependent on and catalyzed by the labile iron redox cycle.
    Keywords:  ROS; ferroptosis; hydroperoxides; iron ions; lipoxygenases; muscle cells
    DOI:  https://doi.org/10.3390/antiox14101157
  12. Front Mol Biosci. 2025 ;12 1662811
      Steroid hormones, including progesterone, are known to exert genomic, non-genomic and non-specific effects. However, their influence on membrane biophysics remains unclear. In this study, we investigate the distinct membrane-modulating behaviour of progesterone compared to cholesterol, employing a multidisciplinary approach that combines fluorescence microscopy, steady-state spectroscopy, and atomistic molecular dynamics simulations. Our results demonstrate that, whereas cholesterol promotes lipid packing and stabilises phase-separated domains, progesterone disrupts phase separation, reduces line tension and increases lipid lateral diffusion, without significantly altering local membrane fluidity. Molecular simulations reveal that progesterone is more variably oriented and distributed within the bilayer than cholesterol. This results in membrane thinning and differential ordering of lipid tails. These structural effects may lead to increased membrane permeability and dynamic reorganization, which could facilitate rapid non-genomic signalling. Notably, the effects of progesterone are more pronounced in multicomponent, phase-separated membranes than in homogeneous lipid systems, suggesting context-specific roles. Our findings present progesterone as a dynamic modulator of membrane organisation, with implications for hormone signalling, drug delivery and therapeutic action in pharmacological settings.
    Keywords:  cholesterol; lipid bilayer; lipid dynamics; membrane heterogeneity; model cell membrane; non-genomic steroid signalling; progesterone; sex hormones
    DOI:  https://doi.org/10.3389/fmolb.2025.1662811
  13. Front Oncol. 2025 ;15 1580640
      Pancreatic cancer-induced cachexia drives co-morbidities that result in a poor quality of life. To expand understanding of the effects of cachexia on the brain here, for the first time, we used noninvasive oxygen enhanced (OE) multispectral optoacoustic tomography (MSOT) to evaluate the ability of the brain vasculature to respond to oxygen breathing in an established xenograft model of pancreatic cancer-induced cachexia. Studies were performed with mice bearing cachexia inducing Pa04C tumors, non-cachexia inducing Panc1 tumors and non-tumor bearing mice. OE-MSOT identified a reduced oxygen carrying capacity in the brain vasculature of mice with cachexia inducing Pa04C tumors, compared to non-tumor bearing mice, and mice with non-cachexia inducing Panc1 tumors. Brain volumes, quantified in mice with MSOT, were significantly reduced in Pa04C tumor-bearing mice compared to non-tumor bearing mice. Our data have identified the inability of brain vasculature to increase oxygenation in response to oxygen breathing in cachectic mice as a new mechanism that may contribute to cachexia-induced morbidity.
    Keywords:  brain; cachexia; optoacoustic imaging; pancreatic ductal adenocarcinoma; vascular oxygenation
    DOI:  https://doi.org/10.3389/fonc.2025.1580640
  14. Nat Methods. 2025 Oct 30.
      Imaging mass cytometry (IMC) is a powerful multiplexed imaging technology used to investigate cell phenotypes and spatial organization of tissue in health and disease. The spatial resolution of IMC is presently at 1 µm, enabling the resolution of single cells and large subcellular compartments but not submicrometer intracellular structures. Here we report a method to improve the resolution of IMC so that it approaches that of light microscopy. High-resolution IMC (HR-IMC) uses an oversampling approach coupled with point-spread function-based deconvolution to achieve a resolution below 350 nm. We demonstrate the performance of HR-IMC in resolving subcellular structures, such as nuclear foci and mitochondrial networks previously undetectable with IMC, and applied it to visualize chemotherapy-induced perturbation of patient-derived ovarian cancer cells. HR-IMC extends highly multiplex IMC analyses into the subcellular regime, enabling analysis of cell biological features and characteristics of disease.
    DOI:  https://doi.org/10.1038/s41592-025-02889-8
  15. EMBO J. 2025 Oct 29.
      Senescent cells drive age-related tissue dysfunction via the induction of a chronic senescence-associated secretory phenotype (SASP). The cyclin-dependent kinase inhibitors p21Cip1 and p16Ink4a have long served as markers of cellular senescence. However, their individual roles remain incompletely elucidated, particularly in vivo. Thus, we conducted a comprehensive examination of multiple single-cell RNA sequencing datasets spanning both murine and human tissues during aging. Our analysis revealed that p21Cip1 and p16Ink4a transcripts demonstrate significant heterogeneity across distinct cell types and tissues, frequently exhibiting a lack of co-expression. Moreover, we identified tissue-specific variations in SASP profiles linked to p21Cip1 or p16Ink4a expression. Using RNA velocity and pseudotime analyses, we discovered that p21+ and p16+ cells follow independent trajectory dynamics, with no evidence of direct transitions between these two states. Despite this heterogeneity, we identified a limited set of shared "core" SASP factors that may drive common senescence-related functions. Our study underscores the substantial diversity of cellular senescence and the SASP, emphasizing that these phenomena are inherently cell- and tissue-dependent.
    Keywords:  Aging; Cellular Senescence; Heterogeneity; Senescence-Associated Secretory Phenotype (SASP); Single-Cell Mapping
    DOI:  https://doi.org/10.1038/s44318-025-00601-2
  16. Nat Chem. 2025 Oct 30.
      Covalent inhibitors that do not rely on hijacking enzymatic activity have mainly been limited to those targeting cysteine residues. The development of such cysteine-directed covalent inhibitors has greatly profited from the use of competitive residue-specific proteomics to determine their proteome-wide selectivity. Several probes have been developed to monitor other amino acids using this technology, and many more electrophiles exist to modify proteins. Nevertheless, there has been a lack of direct, proteome-wide comparisons of the selectivity of diverse electrophiles. Here we developed an unbiased workflow to analyse electrophile selectivity proteome-wide and used it to directly compare 56 alkyne probes containing diverse reactive groups. In this way, we verified and identified probes to monitor a total of nine different amino acids, as well as the protein amino terminus, across the proteome.
    DOI:  https://doi.org/10.1038/s41557-025-01902-z
  17. Cancer Lett. 2025 Oct 28. pii: S0304-3835(25)00674-3. [Epub ahead of print]635 218102
      In the metastatic cascade, biomechanics acts as an invisible engine that drives tumor malignancy. Shaping the intrinsic mechanical microenvironment of cancer cells facilitates their distant colonization and metastasis. Mechanical cues serve as physical fingerprints that orchestrate the formation of a pre-metastatic niche (PMN), which is a critical bottleneck in metastasis. However, biomechanically oriented antitumor strategies that integrate the physicochemical interactions of tumor metastasis remain underexplored in clinical therapy. In this review, we examine the role of biomechanics in shaping the PMN and propose a two-phase model of its evolution: mechanotransductive priming and mechanical niche reconstruction. Furthermore, we clarify the role of biomechanics in tumor organotropism and the impact of anatomical differences among organs on metastasis. In conclusion, a deeper understanding of the biomechanical dimensions of the PMN may inform the development of novel biomechanical interventions to prevent and control tumor metastasis.
    Keywords:  Biomechanics; Organotropism; Pre-metastatic niche; Tumor metastasis
    DOI:  https://doi.org/10.1016/j.canlet.2025.218102
  18. Cell Rep. 2025 Oct 23. pii: S2211-1247(25)01249-5. [Epub ahead of print]44(11): 116478
      Oncogenic driver mutations are common in normal tissues, indicating that non-genetic factors are necessary for tumorigenesis. Phenotypic plasticity is a crucial gateway to malignancy, and inflammation can fuel tumorigenesis; however, little is known about the timing and mechanisms by which these hallmarks first emerge. Using single-cell transcriptomics and in vivo live imaging, we characterized the immediate cell-intrinsic and innate immune responses during the first 24 h following oncogenic Ras activation in a zebrafish model of HRASG12V-mediated skin tumor initiation. We found that in a subset of basal keratinocytes, RAS alone drives phenotypic plasticity, and these cells undergo dedifferentiation and partial epithelial-to-mesenchymal transition (EMT), resembling malignant cells in human squamous cell carcinoma. Strikingly, these cells also drive a tumor-promoting neutrophil program, which in turn enhances preneoplastic cell proliferation. Thus, oncogenic Ras effects are dictated by the cell of origin, and we revealed a link between unlocking plasticity and the onset of tumor-promoting inflammation.
    Keywords:  CP: Cancer; CP: Immunology; Ras; epithelial-mesenchymal transition; preneoplastic; tumor initiation; tumor-associated neutrophils; zebrafish
    DOI:  https://doi.org/10.1016/j.celrep.2025.116478
  19. Trends Cancer. 2025 Oct 29. pii: S2405-8033(25)00256-0. [Epub ahead of print]
      RAS genes encode molecular switches that control cell growth and survival, and their oncogenic mutations drive many cancers. Once deemed 'undruggable', RAS is now being challenged by innovative inhibitors. Recent advances, reported by Stanland and Huggins et al. and Feng et al., include EFTX-G12V, an EGFR-directed allele-specific RNAi therapeutic, and MCB-36, a dual-state pan-KRAS degrader, exemplifying precision RAS-targeted strategies.
    Keywords:  RAS allele-specific therapy; RAS selectivity; precision oncology; tumor specificity
    DOI:  https://doi.org/10.1016/j.trecan.2025.10.005
  20. Sci Adv. 2025 Oct 31. 11(44): eady0415
      Brown adipose tissue (BAT) protects against obesity, diabetes, and cardiovascular disease. During BAT activation, macroautophagy is inhibited, while chaperone-mediated autophagy (CMA) is induced, promoting thermogenic gene expression, adipokine release, oxidative activity, and lipolysis. Aging reduces BAT function and lowers levels of LAMP2A, the rate-limiting CMA component. Pharmacological CMA activation restores BAT activity in aged mice. To explore the CMA's role in BAT, we generated LAMP2A-deficient brown adipocytes and found that CMA regulates proteins essential for thermogenesis and metabolism. Blocking CMA in BAT reduced energy expenditure, raised blood triglycerides, impaired secretion, and led to an increase of thermogenesis repressors. These findings show that CMA is essential for maintaining BAT function, especially during adaptive thermogenesis. By degrading repressors of thermogenesis, CMA supports BAT activity under cold or metabolic stress. This work highlights CMA as a key regulator of BAT plasticity and a promising therapeutic target for treating age-related metabolic disorders.
    DOI:  https://doi.org/10.1126/sciadv.ady0415
  21. J Transl Med. 2025 Oct 28. 23(1): 1183
       BACKGROUND: Cancer metastasis, the process by which tumor cells spread from the primary site to other organs, is one of the leading causes of death in cancer patients. However, due to its complexity and unpredictability, the study of cancer metastasis remains a significant challenge in medicine. In recent years, with the advancement of high-throughput sequencing technologies and single-cell transcriptomics, we could gain a deeper understanding of the molecular mechanisms and cellular heterogeneity underlying cancer metastasis. There is an accumulating volume of publicly available cancer metastasis research data. Nevertheless, these resources lack proper organization, hindering systematic analysis.
    METHODS: In this study, we developed an integrated resource named Panmim ( http://www.gdwk-bioinfo.com/pan_metastasis/home ) to investigate the immune microenvironment of metastatic tumors. The database currently encompasses 90 single-cell RNA-seq datasets from metastatic cancers of diverse origins, encapsulating 14 distinct metastatic sites and 36 primary cancer types. Panmim facilitates a cellular-level comparison of similarities and differences between primary and metastatic cancers, encompassing pathway analysis, alterations in cellular metabolic pathways, cellular distribution preferences, and various aspects of intercellular communication.
    RESULTS: Panmim presents the analysis results through an intuitive interactive graphical interface, enabling users to explore and understand the complex biological phenomena during cancer metastasis more conveniently. This resource will become a valuable tool for biologists and bioinformaticians to study the mechanisms of cancer metastasis, providing important data support and scientific basis for the optimization of cancer treatment strategies.
    Keywords:  Cancer metastasis; Database; Gene expression; Immune microenvironment; ScRNA-seq
    DOI:  https://doi.org/10.1186/s12967-025-06484-5
  22. Small Methods. 2025 Oct 29. e01270
      Senescence is a durable state of cell cycle arrest that can be induced by various stressors, including DNA damage caused by chemotherapeutic agents or ionizing radiation. In the context of cancer, therapy-induced senescence (TIS) plays a dual role: while it effectively halts tumor cell proliferation, TIS also carries the risk of promoting tumor relapse through the senescence-associated secretory phenotype (SASP). Beyond its direct impact on tumor cells, cancer therapies leading to TIS often induce short- and long-term side effects that significantly affect the quality of life for patients. However, the lack of universal biomarkers for TIS hinders a comprehensive understanding of its characteristics and its role in cancer therapies. A lamin-based senescence reporter platform is developed to reliably detect and sort live senescent cancer cells. This versatile tool supports live-cell imaging, enabling real-time tracking of senescence induction and escape to investigate heterogeneity in treatment response. Additionally, it allows high-content screening and marker integration, for example incorporating IL6 as SASP marker. It is therefore a valuable tool for fundamental research addressing new questions in the field of TIS as well as for drug discovery, including the development of novel senolytics.
    Keywords:  DNA damage; lamins; live; monitoring; reporter; senescence
    DOI:  https://doi.org/10.1002/smtd.202501270
  23. iScience. 2025 Nov 21. 28(11): 113685
      During tissue development and regeneration, cells interpret and exert mechanical forces that are challenging to measure in vivo. Stress inference algorithms have thus emerged as powerful tools to estimate tissue stresses. Yet, effectively incorporating tissue dynamics into these algorithms remains elusive. Here, we introduce ForSys, a Python-based software that infers intercellular stresses and intracellular pressures from time-lapse microscopy. After validation, we applied ForSys to the migrating zebrafish lateral-line primordium, revealing increased stress during the cell rounding that precedes mitosis and accurately predicting the onset of epithelial rosettogenesis. We further used ForSys to study neuromast development and uncovered mechanical asymmetries linked to cell type-specific adhesion. The software performs both static and dynamic stress inference, supports command-line use, scripting, and a user-friendly graphical interface within Fiji, and accepts segmentation inputs from EPySeg and Cellpose. This versatility of ForSys enables the analysis of spatiotemporal patterns of mechanical forces during tissue morphogenesis in vivo.
    Keywords:  Optical imaging
    DOI:  https://doi.org/10.1016/j.isci.2025.113685
  24. Cell Death Discov. 2025 Oct 31. 11(1): 495
      Diffuse large B-cell lymphoma (DLBCL) exhibits marked clinical heterogeneity and frequent treatment resistance, particularly in molecularly defined high-risk subtypes such as ABC-DLBCL. While current therapies largely rely on apoptosis induction, non-apoptotic cell death pathways remain underexplored in hematologic malignancies. Here, we identify ferroptosis, an iron-dependent, lipid peroxidation-driven form of regulated necrosis, as an effective baseline in additive therapy with ibrutinib for the treatment of DLBCL. Transcriptomic and lipidomic analyses revealed that DLBCL cells, despite lacking overt enrichment of polyunsaturated fatty acids (PUFAs), display elevated expression of the core ferroptosis protective machinery. Inhibition of GPX4 induced rapid and selective lipid ROS accumulation and cell death across a panel of human and murine DLBCL cellular models irrespective of subtype. Notably, the BTK inhibitor and clinical compound ibrutinib showed additive effects with GPX4 inhibition, even at concentrations below its cytotoxic threshold, expanding its therapeutic relevance beyond BTK inhibition. Mechanistically, we uncover two activities of ibrutinib to enhance ferroptosis sensitivity: First, chemical scavenging of glutathione and second the inhibition of GPX4 protein expression via translational repression. Thereby, our findings define ferroptosis as a basis for additive therapy in combination with ibrutinib in DLBCL and reveal a previously unrecognized role for ibrutinib in directly modulating anti-oxidant defense.
    DOI:  https://doi.org/10.1038/s41420-025-02826-w
  25. STAR Protoc. 2025 Oct 27. pii: S2666-1667(25)00569-6. [Epub ahead of print]6(4): 104163
      Tumor hypoxia plays a critical role in cancer progression and therapeutic resistance. Here, we present a protocol for the self-generation of hypoxia by metastatic cancer cells using phosphorescence-based O2 sensing. We describe steps for phosphorescent film calibration, system assembly, and real-time imaging of hypoxia development. We then detail approaches to spatially map resulting O2 gradients. This protocol supports applications for studying key behaviors linked to metastatic progression, including motility and aerotaxis, under physiologically relevant hypoxic conditions. For complete details on the use and execution of this protocol, please refer to Hosny et al.1.
    Keywords:  Biotechnology and bioengineering; Cancer; Cell Biology
    DOI:  https://doi.org/10.1016/j.xpro.2025.104163
  26. Nucleic Acids Res. 2025 Oct 31. pii: gkaf1119. [Epub ahead of print]
      Regulated cell death (RCD) is essential to both physiological homeostasis and numerous diseases. FerrDb is a curated database for ferroptosis regulators and ferroptosis-disease associations. Though widely used, FerrDb is limited by its singular focus on ferroptosis. The field of cell death is rapidly expanding, marked by continuous discovery of novel RCD modalities. The need for a high-quality database that encompasses the entire spectrum of RCD is urgent, but none exists. Here, we introduce FerrDb V3, an upgraded version featuring extensive enhancements in content and functionality. Remarkably, it expands from the focus on ferroptosis to 22 RCD modalities. RCD regulators and RCD-disease associations were manually curated from >20 000 articles. Database content was additionally enriched by public resources. A conversational intelligent assistant that enables users to explore the database through natural language queries was created. A suite of web-based analytical utilities tailored for RCD research was developed. The web interface was updated accordingly to offer a seamless user experience. In conclusion, FerrDb V3 has evolved into a comprehensive resource and a valuable research tool for the RCD research community. FerrDb V3 is freely accessible at https://www.zhounan.org/ferrdb/.
    DOI:  https://doi.org/10.1093/nar/gkaf1119
  27. Cancer Res. 2025 Oct 30.
      Small molecule KRASG12C(OFF) inhibitors that bind to the inactive GDP-bound state of KRAS have demonstrated efficacy in patients with KRASG12C mutant tumors, yet responses tend to be transient due to emergence of on-treatment resistance. Recently, RAS(ON) G12C-selective inhibitors, which bind to the active GTP-bound state of RAS, were described, and elironrasib is undergoing evaluation in multiple clinical trials. Here, we generated resistant cell lines and patient-derived xenograft models to KRASG12C(OFF) and RAS(ON) G12C-selective inhibitors and interrogated resistance mechanisms using a multi-omics strategy consisting of phosphoproteomics, whole exome sequencing, and RNA-sequencing combined with functional testing using small molecule and CRISPR screens and RAS(ON) inhibitors being evaluated in clinical trials. Two models reactivated RAS signaling, either via KRASG12C gene amplification or NRASG13R mutation, and were vulnerable to dual inhibition by RAS(ON) G12C-selective and RAS(ON) multi-selective inhibitors, RMC-4998 and RMC-7977. Two models, which lacked any discernable genomic alteration, acquired resistance associated with increased receptor tyrosine kinase activity and downstream persistent RAS activity and were sensitive to RAS-GTP inhibition by RMC-7977. Finally, one model displayed epithelial-mesenchymal transition, loss of RAS dependance, and acquired reliance on cell cycle kinases and proteins associated with DNA damage response. This work highlights KRASG12C-selective inhibitor resistant states that parallel and complement clinical findings and demonstrate that a large subset could be overcome with a RAS(ON) multi-selective inhibitor as a standalone agent or in combination with other therapies.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-0600
  28. Dis Model Mech. 2025 Oct 30. pii: dmm.052543. [Epub ahead of print]
      Drosophila has long been a powerful model for cancer research, yet the development of robust metastatic tumor models remains a challenge. While allograft transplantation offers a promising approach, its use has been limited by technical constraints. Here, we establish a reproducible serial transplantation protocol using lgl mutant brain tumors, enabling exponential expansion of tumor material and precise tracking of temporal tumor progression. Extending this approach to other Neural Stem Cell (NSC)-derived tumors, we identify shared metastatic characteristics between lgl and pins mutants. Additionally, we compare tumors of different tissue origins, demonstrating that epithelial tumors, like NSC tumors, can also be serially propagated. Using these models, we show that tumors metastasize to host organs, establish tumor colonies in the ovaries, distort the GI tract, and invade the cellular cortex of the adult brain. Overall, our study provides a systematic framework for generating metastatic tumors in adult flies from two distinct tissue origins, establishing organ-specific metastatic patterns and offering a platform for studying tumor-host interactions at secondary organ sites.
    Keywords:  Allograph transplantation; Cancer; Drosophila; Metastasis; Tumor
    DOI:  https://doi.org/10.1242/dmm.052543
  29. Database (Oxford). 2025 Jan 18. pii: baaf068. [Epub ahead of print]2025
      Here, we introduce SEND (Share Easily bioiNformatics Data), a suite of tools that allow users to share heterogeneous and linked biological data, in an easy and highly customizable way. The code for SEND is freely available on GitHub (https://github.com/targetmine). Also, docker images of all different components of the system are directly available for download from DockerHub (https://hub.docker.com/search?q=rallendes; contact: Rodolfo S. Allendes Osorio, rodolfo.allendes.prime@osaka-u.ac.jp; Kenji Mizuguchi, kenji@protein.osaka-u.ac.jp). Links to additional figures/data available on a web site, or references to online-only supplementary data available at the journal's web site.
    DOI:  https://doi.org/10.1093/database/baaf068