bims-cagime 2025-12-07 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–12–07
34 papers selected by
Kıvanç Görgülü, Technical University of Munich

C-COMPASS: a user-friendly neural network tool profiles cell compartments at protein and lipid levels.
A fin-loop-like structure in GPX4 underlies neuroprotection from ferroptosis.
Mechanistic insights into the dynamics of plasma membrane repair in cancer.
Apical and basolateral plasma membranes in epithelial cells have distinct lipidomes and biophysical properties.
A guide to transcriptomic deconvolution in cancer.
Age-related decline of chaperone-mediated autophagy in skeletal muscle leads to progressive myopathy.
Reprogramming of cholesterol sensing in epithelial cells supports pancreatic inflammation.
Macrophages rescue cells from ferroptotic death.
GFER Represents a Target for Dual Disruption of Redox Homeostasis and Reactivation of the Immune Response in Pancreatic Adenocarcinoma.
Integrin is required for basement membrane crossing and branching of an invading intracellular tube.
Drink Responsibly: Cancer Cells also Like Sugary Drinks.
Live-cell Imaging of Lysosomal Membrane Permeabilization During Necroptosis.
Precancer exercise capacity and metabolism during tumor development coordinate the skeletal muscle-tumor metabolic competition.
Chaperone-mediated autophagy sustains muscle stem cell regenerative functions but declines with age.
Recurrent Breast Cancer Cells Depend on De novo Pyrimidine Biosynthesis to Suppress Ferroptosis.
Neural hijacking in cancer metabolism: from nutrients to organelles.
Dietary Polyunsaturated Fatty Acids Regulate Dendritic Cell Function via Nrf2-dependent Control of Ferroptosis.
RASH3D19 mediates RAS activation through a positive feedback loop in KRAS-mutant cancer.
A low-protein diet drives short- and long-term improvements in metabolic health in a mouse model of sleeve gastrectomy.
NQO1 as a predictor of response to adjuvant GemCap treatment for pancreatic cancer.
Differential regulation of p62-ubiquitin conjugates in neurons versus astrocytes during cellular stress.
Membrane potential mediates the cellular response to mechanical pressure.
A targeted combination therapy achieves effective pancreatic cancer regression and prevents tumor resistance.
A Versatile GPMV-Imaging Platform for Quantitative Analysis of Receptor Binding and Membrane Fusion.
Involvement of ACSL3 in the formation of autophagosomes and lipid droplets during starvation conditions.
Polarized Distribution of Lipid Droplets with Long Acyl Chains and Unsaturation are Hallmarks of Human Intestinal Enteroid Differentiation.
Tumor acidosis: Fusing mitochondrial dynamics and lipid metabolism.
Oxidative pentose phosphate pathway is required for T cell activation and antitumor immunity.
A phase III randomized clinical trial of Gemcitabine and Nab-Paclitaxel as switch maintenance versus continuation of modified FOLFIRINOX as first-line chemotherapy in patients with advanced pancreatic cancer: The PANThEON Study.
Lymphotoxin-driven cancer cell eradication by tumoricidal CD8 + TIL.
Bioengineering mini-colons for ex vivo colorectal cancer research.
Efficacy and safety of garsorasib in patients with KRAS G12C-mutated advanced pancreatic cancer.
Deciphering precursor cell dynamics in esophageal preneoplasia via genetic barcoding and single-cell transcriptomics.
KRAS-targeted therapies in cancer: novel approaches and overcoming resistance.

Nat Methods. 2025 Dec 04.

C-COMPASS: a user-friendly neural network tool profiles cell compartments at protein and lipid levels.

Daniel T Haas, Daniel Weindl, Pamela Kakimoto, Eva-Maria Trautmann, Julia P Schessner, Xia Mao, Mathias J Gerl, Maximilian Gerwien, Timo D Müller, Christian Klose, Xiping Cheng, Jan Hasenauer, Natalie Krahmer.

Systematic proteomic organelle profiling methods including protein correlation profiling and LOPIT have advanced our understanding of cellular compartmentalization. To manage the complexity of organelle profiling data, we introduce C-COMPASS, a user-friendly open-source software that employs a neural network-based regression model to predict the spatial cellular distribution of proteins. C-COMPASS handles complex multilocalization patterns and integrates protein abundance to model organelle composition changes across conditions. We apply C-COMPASS to mice with humanized livers to elucidate organelle remodeling during metabolic perturbations. Additionally, by training neural networks with co-generated marker protein profiles, C-COMPASS extends spatial profiling to lipids, overcoming the lack of organelle-specific lipid markers, allowing for determination of localization and tracking of lipid species across different compartments. This provides integrated snapshots of organelle lipid and protein compositions. Overall, C-COMPASS offers an accessible tool for multiomic studies of organelle dynamics without needing advanced computational skills, empowering researchers to explore new questions in lipidomics, proteomics and organelle biology.

DOI: https://doi.org/10.1038/s41592-025-02880-3
Cell. 2025 Dec 04. pii: S0092-8674(25)01310-8. [Epub ahead of print]

A fin-loop-like structure in GPX4 underlies neuroprotection from ferroptosis.

Svenja M Lorenz, Adam Wahida, Mark J Bostock, Tobias Seibt, André Santos Dias Mourão, Anastasia Levkina, Dietrich Trümbach, Mohamed Soudy, David Emler, Nicola Rothammer, Marcel S Woo, Jana K Sonner, Mariia Novikova, Bernhard Henkelmann, Maceler Aldrovandi, Daniel F Kaemena, Eikan Mishima, Perrine Vermonden, Zhi Zong, Deng Cheng, Toshitaka Nakamura, Junya Ito, Sebastian Doll, Bettina Proneth, Erika Bürkle, Francesca Rizzollo, Abril Escamilla Ayala, Valeria Napolitano, Marta Kolonko-Adamska, Stefan Gaussmann, Juliane Merl-Pham, Stefanie Hauck, Anna Pertek, Tanja Orschmann, Emily van San, Tom Vanden Berghe, Daniela Hass, Adriano Maida, Joris M Frenz, Lohans Pedrera, Amalia Dolga, Markus Kraiger, Martin Hrabé de Angelis, Helmut Fuchs, Gregor Ebert, Jerica Lenberg, Jennifer Friedman, Carolin Scale, Patrizia Agostinis, Annemarie Zimprich, Daniela Vogt-Weisenhorn, Lillian Garrett, Sabine M Hölter, Wolfgang Wurst, Enrico Glaab, Jan Lewerenz, Bastian Popper, Christian Sieben, Petra Steinacker, Hans Zischka, Ana J Garcia-Saez, Anna Tietze, Sanath Kumar Ramesh, Scott Ayton, Michelle Vincendeau, Manuel A Friese, Kristen Wigby, Michael Sattler, Matthias Mann, Irina Ingold, Ashok Kumar Jayavelu, Grzegorz M Popowicz, Marcus Conrad.

  Ferroptosis, driven by uncontrolled peroxidation of membrane phospholipids, is distinct from other cell death modalities because it lacks an initiating signal and is surveilled by endogenous antioxidant defenses. Glutathione peroxidase 4 (GPX4) is the guardian of ferroptosis, although its membrane-protective function remains poorly understood. Here, structural and functional analyses of a missense mutation in GPX4 (p.R152H), which causes early-onset neurodegeneration, revealed that this variant disrupts membrane anchoring without considerably impairing its catalytic activity. Spatiotemporal Gpx4 deletion or neuron-specific GPX4R152H expression in mice induced degeneration of cortical and cerebellar neurons, accompanied by progressive neuroinflammation. Patient induced pluripotent stem cell (iPSC)-derived cortical neurons and forebrain organoids displayed increased ferroptotic vulnerability, mirroring key pathological features, and were sensitive to ferroptosis inhibition. Neuroproteomics revealed Alzheimer's-like signatures in affected brains. These findings highlight the necessity of proper GPX4 membrane anchoring, establish ferroptosis as a key driver of neurodegeneration, and provide the rationale for targeting ferroptosis as a therapeutic strategy in neurodegenerative disease.

Keywords:  Alzheimer’s disease; GPX4; SSMD; Sedaghatian type; cell death; ferroptosis; neurodegeneration; neuroinflammation; spondylometaphyseal dysplasia

DOI:  https://doi.org/10.1016/j.cell.2025.11.014
Mol Biol Rep. 2025 Dec 05. 53(1): 163

Mechanistic insights into the dynamics of plasma membrane repair in cancer.

Yufeng Huang, Asad Ullah, Muhammad Muddassir Ali.

  Cancer cells are well equipped with plasma membrane repair to survive mechanical tension, chemical stress, immune assaults and therapeutic interventions. Maintaining plasma membrane integrity is quintessential for tumor cells as it plays a pivotal role in communication between the internal environment of the tumor cell and the extracellular surroundings. Therefore, tumor cells achieve plasma membrane repair by several dynamic repair pathways such as calcium (Ca2+) guided lysosomal exocytosis, annexins (ANXs) mediated membrane repair and shedding, damaged oriented membrane repair via endocytosis, ESCRT (Endosomal Sorting Complex Required for Transport) mediated plasma Membrane repair and LC-3 Associated Macropinocytosis (LAM) to survive persistent membrane damage inflicted by immune attack, mechanical stress especially during metastasis and chemotherapy induction. These processes rapidly restore membrane integrity, maintaining cellular homeostasis and conferring survival advantages during metastasis and immune evasion. Notably, key repair proteins such as ANXs, synaptotagmin VII (Syt VII), ESCRT components, and autophagy-related factors (ATGs, rubicon and LC-3) are often upregulated in various cancers including breast, pancreatic, bladder, liver, and aggressive solid tumors, highlighting their clinical relevance and potential as therapeutic targets. Moreover, an understanding of the mechanistic interplay among different pathways unveils a new therapeutic window to selectively disrupt these repair pathways, sensitizing cancer cells to persistent damage while sparing normal tissues. This review elucidates the mechanisms of plasma membrane repair in cancer, highlights the differential regulation of their key mediators across multiple tumor types, and briefly explores their therapeutic potential.

Keywords:  Cancer; Membrane repair mechanisms; Molecular oncology and cell biology; Plasma membrane repair

DOI:  https://doi.org/10.1007/s11033-025-11329-x
bioRxiv. 2025 Nov 21. pii: 2025.11.20.689573. [Epub ahead of print]

Apical and basolateral plasma membranes in epithelial cells have distinct lipidomes and biophysical properties.

Carolyn R Shurer, Kandice R Levental, Ilya Levental.

Epithelial cell polarization is essential for many physiological processes, including tissue morphogenesis, nutrient absorption, barrier integrity, and directional secretion. A defining feature of such polarization is the separation of plasma membrane lipids and proteins into distinct apical and basolateral compartments. It has long been suggested that the apical compartment is rich in glycolipids and cholesterol and that this composition arises through trafficking of self-assembled membrane domains (termed lipid rafts). However, neither the detailed composition nor the mechanisms of protein and lipid sorting between plasma membrane compartments in epithelial cells have been fully resolved. Particularly, the lipid profile of the basolateral membrane, and consequently the lipid disparity between the apical and basolateral membrane, remain undefined. The general determinants of protein sorting are also poorly understood. We developed a novel method to separately isolate the apical and basolateral plasma membranes and used lipidomics and biophysical profiling to characterize the changes in membrane composition and properties between these compartments in polarized Madin-Darby canine kidney cells. We find that the apical membrane is enriched in cholesterol, saturated lipids, and glycolipids relative to the basolateral membrane, and that its biophysical properties reflect a more ordered environment. Further, we evaluate the longstanding hypothesis that lipid rafts contribute to apical protein trafficking by assessing the relationship between transmembrane domain raft affinity and apical localization. We observed that lipid raft affinity only modestly influences apical versus basolateral sorting. These findings define the distinct compositional and biophysical features of apical and basolateral compartments of epithelial cells and provide mechanistic evidence for their biogenesis.

DOI: https://doi.org/10.1101/2025.11.20.689573
Nat Rev Cancer. 2025 Dec 02.

A guide to transcriptomic deconvolution in cancer.

Yaoyi Dai, Shuai Guo, Yidan Pan, Carla Castignani, Matthew D Montierth, Peter Van Loo, Wenyi Wang.

Cancer tissues are heterogeneous mixtures of tumour, stromal and immune cells, where each component comprises multiple distinct cell types and/or states. Mapping this heterogeneity and understanding the unique contributions of each cell type to the tumour transcriptome is crucial for advancing cancer biology, yet high-throughput expression profiles from tumour tissues only represent combined signals from all cellular sources. Computational deconvolution of these mixed signals has emerged as a powerful approach to dissect both cellular composition and cell-type-specific expression patterns. Here, we provide a comprehensive guide to transcriptomic deconvolution, specifically tailored for cancer researchers, presenting a systematic framework for selecting and applying deconvolution methods, considering the unique complexities of tumour tissues, data availability and method assumptions. We detail 43 deconvolution methods and outline how different approaches serve distinctive applications in cancer research: from understanding tumour-immune surveillance to identifying cancer subtypes, discovering prognostic biomarkers and characterizing spatial tumour architecture. By examining the capabilities and limitations of these methods, we highlight emerging trends and future directions, particularly in addressing tumour cell plasticity and dynamic cell states.

DOI: https://doi.org/10.1038/s41568-025-00886-9
Nat Metab. 2025 Dec 03.

Age-related decline of chaperone-mediated autophagy in skeletal muscle leads to progressive myopathy.

Olaya Santiago-Fernández, Luisa Coletto, Inmaculada Tasset, Susmita Kaushik, Axel R Concepcion, Rizwan Qaisar, Adrián Macho-González, Kristen Lindenau, Antonio Diaz, Rabia R Khawaja, Stefano Donega, Nirad Banskota, Ceereena Ubaida-Mohien, Gavin Pharaoh, Bumsoo Ahn, Lisa M Hartnell, Ignacio Ramírez-Pardo, Bhakti Chavda, Aiara Gazteluiturri, Michael Kinter, Luigi Ferrucci, Julie A Reisz, Angelo D'Alessandro, Holly Van Remmen, Pura Muñoz-Cánoves, Stefan Feske, Ana Maria Cuervo.

Chaperone-mediated autophagy (CMA) contributes to proteostasis maintenance by selectively degrading a subset of proteins in lysosomes. CMA declines with age in most tissues, including skeletal muscle. However, the role of CMA in skeletal muscle and the consequences of its decline remain poorly understood. Here we demonstrate that CMA regulates skeletal muscle function. We show that CMA is upregulated in skeletal muscle in response to starvation, exercise and tissue repair, but declines in ageing and obesity. Using a muscle-specific CMA-deficient mouse model, we show that CMA loss leads to progressive myopathy, including reduced muscle force and degenerative myofibre features. Comparative proteomic analyses reveal CMA-dependent changes in the mitochondrial proteome and identify the sarcoplasmic-endoplasmic reticulum Ca2+-ATPase (SERCA) as a CMA substrate. Impaired SERCA turnover in CMA-deficient skeletal muscle is associated with defective calcium (Ca2+) storage and dysregulated Ca2+ dynamics. We confirm that CMA is also downregulated with age in human skeletal muscle. Remarkably, genetic upregulation of CMA activity in old mice partially ameliorates skeletal muscle ageing phenotypes. Together, our work highlights the contribution of CMA to skeletal muscle homoeostasis and myofibre integrity.

DOI: https://doi.org/10.1038/s42255-025-01412-9
Mol Metab. 2025 Dec 02. pii: S2212-8778(25)00199-1. [Epub ahead of print] 102292

Reprogramming of cholesterol sensing in epithelial cells supports pancreatic inflammation.

Giulia Milan, Olga A Mareninova, Marco Fantuz, Martina Spacci, Carlotta Paoli, Jerik A Pineda, Roberta Noè, Beatrice Calciolari, Roberto Zoncu, Anna S Gukovskaya, Alessandro Carrer.

  Pancreatitis is a common cause of hospitalization that necessitates attentive clinical management. Affected individuals are at risk for pancreatic cancer due to aberrant signaling and empowered cell plasticity. Yet, molecular and cellular dynamics that govern epithelial cell behavior in response to inflammation remain largely elusive. Here we found that inflammation induces Endoplasmic Reticulum-Associated Degradation protein (ERAD)-mediated downregulation of Niemann-Pick type C protein 1 (NPC1), which leads to the sequestration of free cholesterol within acinar cells' lysosomes. Reducing intra-pancreatic cholesterol levels through genetic ablation of Acly ameliorates cerulein-induced pancreatitis, while pharmacological targeting of NPC1 exacerbates tissue damage. Mechanistically, the accumulation of lysosomal cholesterol is sensed by the mechanistic Target of Rapamycin Complex 1 (mTORC1) that promotes metaplasia of pancreatic acinar cells, an event commonly associated to pancreatitis and tissue regeneration. Indeed, cholesterol supplementation or NPC1 inhibition facilitate acinar-to-ductal metaplasia (ADM) both ex vivo and in vivo, in an mTORC1-dependent manner. These results identify a metabolic/signaling axis driving the reprogramming of pancreatic epithelial cells in response to inflammation. This hinges on a nutrient sensing paradigm, previously documented exclusively in pathological conditions.

Keywords:  acinar-to-ductal metaplasia (ADM); cholesterol; lysosome; mTORC1; pancreatitis

DOI:  https://doi.org/10.1016/j.molmet.2025.102292
Cell Death Dis. 2025 Dec 01.

Macrophages rescue cells from ferroptotic death.

Ruth Hefetz, Sapir Harush, Lucy Ghantous, Yael Volman, Yoel Sadovsky, Ofer Beharier, Jacob Rachmilewitz.

Ferroptosis, a non-apoptotic form of cell death marked by iron-dependent lipid peroxidation, has a key role in organ injury, degenerative disease, and vulnerability of therapy-resistant cancers. Although substantial progress has been made in understanding the molecular processes relevant to ferroptosis, additional cell-extrinsic processes that determine cell sensitivity toward ferroptosis remain unknown. Here we demonstrate that macrophages co-cultured with ferroptotic cancer cells from various types effectively mitigate cell death induced by GPX4 inhibitors (RSL3 and ML162), GPX4 silencing via shRNA, or the Xc- system inhibitor IKE. Furthermore, macrophages effectively reduced lipid peroxidation in ferroptotic cells. Importantly, macrophage function relies on direct cell-to-cell contact and is affected by their differentiation. Specifically, polarization into M1 macrophages, but not M2, greatly hinders their protective capabilities. Interestingly, unlike apoptotic cells, ferroptotic cells retain elevated levels of the 'don't eat me' signal, CD47, and conversely, fail to present the "eat me" signal phosphatidylserine (PS) on the outer layer of the plasma membrane, providing an opportunity for their rescue. Furthermore, in placental villi explants, macrophages protect trophoblasts from ferroptotic death. These results underscore the intricate interplay between ferroptotic cells and their microenvironment and provide compelling evidence of a yet-unrecognized anti-ferroptotic activity of macrophages as a cell-extrinsic mechanism that could be exploited by cancer cells to escape ferroptosis.

DOI: https://doi.org/10.1038/s41419-025-08277-6
Cancer Res. 2025 Dec 02.

GFER Represents a Target for Dual Disruption of Redox Homeostasis and Reactivation of the Immune Response in Pancreatic Adenocarcinoma.

Ziheng Chen, I-Lin Ho, Jintan Liu, Melinda Soeung, Er-Yen Yen, Sara Sainani, Charles A Dyke, Rutvi Shah, Hyuk Jean Kwon, Guangchun Han, Xinmiao Yan, Shaojun Zhang, Sanjana Srinivasan, Johnathon L Rose, Francesca Citron, Shan Jiang, Qing Chang, Ningping Feng, Giannicola Genovese, Sisi Gao, Wantong Yao, Linghua Wang, Huamin Wang, Haoqiang Ying, Andrea Viale, Giulio F Draetta.

Both metabolic dysregulation and the immunosuppressive tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC) contribute to the recalcitrance of this lethal disease to treatment. Accordingly, we aimed to identify and characterize a target that elicits an anti-cancer response through both disrupting cancer cell redox homeostasis and increasing the immunogenicity of PDAC. First, mitochondrial metabolic dependencies in PDAC were identified by using a CRISPR-Cas9 screening system with a custom sgRNA library. Functional validation analyses revealed GFER, a mitochondrial FAD-dependent sulfhydryl oxidase, as an essential regulator of tumor growth. In vitro and in vivo methodologies demonstrated that GFER depletion perturbed redox homeostasis and stimulated tumor immunogenicity, including sensitization to immune checkpoint blockade. In patient-derived xenograft models of PDAC, the growth-inhibitory response induced by GFER depletion was mediated by an altered oxidative balance that released damaged mitochondrial DNA into the cytoplasm of tumor cells, leading to the activation of the cGAS-STING pathway and expression of type I interferons. This effect was recapitulated in a mouse immunocompetent syngeneic PDAC model, where GFER depletion suppressed tumor growth and promoted T cell infiltration to enhance tumor-killing effects. Consequently, GFER depletion significantly increased the anti-tumor efficacy of immune checkpoint blockade. Overall, these findings identify GFER as a critical node for both mitochondrial redox homeostasis and immunomodulation in PDAC and reveal a therapeutic opportunity for sensitizing PDAC to immune checkpoint blockade.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-4211
Development. 2025 Dec 01. pii: dev.204893. [Epub ahead of print]

Integrin is required for basement membrane crossing and branching of an invading intracellular tube.

Lauren N Meyer, Michael Hertel, Jeremy Nance.

  The narrowest biological tubes are comprised of cells that hollow to form an intracellular lumen. Here, we examine early lumenogenesis of the C. elegans excretory cell, which branches to form an H-shaped intracellular tube spanning the length of the worm. Using genetically paralyzed embryos to freeze movement, we describe lumen initiation and branching for the first time using time-lapse fluorescence microscopy. We show that the excretory cell lumen forms through a plasma membrane invasion mechanism when a nascent lumen grows from the plasma membrane into the cytoplasm. The lumen subsequently extends along the left-right axis before branching to form anterior-posterior projections. Through a genetic screen, we identify mutations in ina-1/⍺-integrin and pat-3/β-integrin that block lumenogenesis at the anterior-posterior branching step, and we show that integrin function is required within the excretory cell. Finally, we find that the excretory cell crosses the epidermal basement membrane where anterior-posterior branches form and demonstrate that basement membrane crossing fails in integrin mutant embryos. Our findings reveal how an intracellular lumen initiates and branches and identify integrins and basement membrane as key branching regulators.

Keywords:  Basement membrane; Integrin; Laminin; Lumen; Tubulogenesis

DOI:  https://doi.org/10.1242/dev.204893
Cancer Res. 2025 Dec 02.

Drink Responsibly: Cancer Cells also Like Sugary Drinks.

Fabio Zani, Julianna Blagih.

Sugar-sweetened beverages (SSBs), which contain both glucose and fructose, have been linked to an increased incidence of colorectal cancer (CRC). Their effects on CRC progression, however, are unclear. In their recent work, Feng and colleagues investigated how exposure to SSBs affects CRC metastasis. They discovered that several CRC cell lines showed enhanced migration when exposed to glucose and fructose together, compared to cells exposed to glucose or fructose alone. Similarly, in mouse models of CRC liver metastasis, mice fed with both glucose and fructose developed more liver metastases, suggesting that SSBs promote CRC spread. Leveraging on metabolomic analyses, they discovered that in the presence of both glucose and fructose, the enzyme SORD converts fructose to sorbitol, regenerating NAD⁺ from NADH. Deleting SORD reduced the NAD+/NADH ratio and CRC cell migration and metastasis. Restoring the NAD⁺/NADH ratio rescued migration, suggesting that SORD-driven NAD⁺ regeneration promotes metastatic behaviour. Furthermore, they demonstrated that increased NAD⁺/NADH levels have a profound effect on cell metabolism, supporting glycolysis, the TCA cycle, and the mevalonate pathway. Interestingly, pharmacologic inhibition of the mevalonate pathway with statins reduced cell migration and liver metastasis in mice consuming SSBs. Together, these findings demonstrate that SSBs enhance CRC metastasis through SORD-dependent metabolic reprogramming. By regenerating NAD⁺ and glycolysis and the mevalonate pathway, SORD links SSB consumption to increased tumor cell migration and metastatic potential.

DOI: https://doi.org/10.1158/0008-5472.CAN-25-5296
J Vis Exp. 2025 Nov 14.

Live-cell Imaging of Lysosomal Membrane Permeabilization During Necroptosis.

Katia S G Andrade, John Mably, Da-Zhi Wang, Zhigao Wang.

Necroptosis, a form of regulated necrosis, culminates in cell membrane rupture. Our lab and others have discovered that lysosomal membrane permeabilization (LMP) is an early and crucial event in this process, preceding membrane rupture. Rapid LMP releases potent lysosomal enzymes, particularly proteases, into the cytosol, actively promoting cell death. Live-cell imaging provides an invaluable tool for detecting LMP during necroptosis in real-time. Several fluorescent dyes are highly effective: (1) pH-sensitive LysoTracker dyes track changes in lysosomal pH. A decrease in fluorescence signal indicates a loss of the lysosomal pH gradient, a primary sign of lysosomal dysfunction, which may be a precursor or direct consequence of LMP. (2) Fluorescein-labeled dextran beads are internalized and accumulate in lysosomes. Their release into the cytosol signals complete LMP and cargo leakage. Here, we observed a progressive loss of Lysotracker fluorescence, with diffusing Dextran fluorescence into the cytosol after necroptosis induction. Thus, the live-cell imaging methodology enables researchers to precisely track the timing and extent of lysosomal dysfunction, contributing to a more comprehensive understanding of necroptosis mechanisms and illuminating potential therapeutic interventions.

DOI: https://doi.org/10.3791/69495
Proc Natl Acad Sci U S A. 2025 Dec 09. 122(49): e2508707122

Precancer exercise capacity and metabolism during tumor development coordinate the skeletal muscle-tumor metabolic competition.

Brooks P Leitner, Andin E Fosam, Won D Lee, Kaylee Zilinger, Susana C B R Nakandakari, Xinyi Zhang, Rafael C Gaspar, Wanling Zhu, Curtis J Perry, Joshua D Rabinowitz, Rachel J Perry.

  Higher exercise capacity and regular exercise training improve cancer prognosis at all stages of disease. However, the metabolic adaptations to aerobic exercise training that mediate tumor-host interactions are poorly understood. Here, we demonstrate that voluntary wheel running slows tumor growth and repartitions glucose uptake and oxidation to skeletal and cardiac muscle and away from breast and melanoma tumors in mice. Further, prehabilitation induces repartitioning of glucose metabolism in obese mice: Uptake and oxidation of glucose are enhanced in skeletal and cardiac muscle, and reduced in tumors. These increases in muscle glucose metabolism and reductions in tumor glucose metabolism, correlated with slower tumor progression. Using [U-13C6] glucose infusion, we show that exercise increases the fractional contribution of glucose to oxidative metabolism in muscle while reducing it in tumors, suggesting that aerobic exercise shifts systemic glucose metabolism away from the tumor microenvironment and toward metabolically active tissues. Transcriptional analysis revealed downregulation of mTOR signaling in tumors from exercised mice. Collectively, our findings suggest that voluntary exercise may suppress tumor progression by enhancing host tissue glucose oxidation and limiting tumor glucose availability, supporting a model in which exercise-induced metabolic competition constrains tumor energetics.

Keywords:  breast cancer; exercise; melanoma; tumor metabolism

DOI:  https://doi.org/10.1073/pnas.2508707122
Nat Metab. 2025 Dec 03.

Chaperone-mediated autophagy sustains muscle stem cell regenerative functions but declines with age.

Ignacio Ramírez-Pardo, Silvia Campanario, Bhakti Chavda, Olaya Santiago-Fernández, Marta Flández, Mercedes Grima-Terrén, Andrés Cisneros, Aina Calls-Cobos, Daniel N Itzhak, Bryan Ngo, Sudha Janaki-Raman, Edward D Kantz, Laura Ortet, Antonio Diaz, Kristen Lindenau, Julio Doménech-Fernández, Mari Carmen Gómez-Cabrera, Emilio Camafeita, Jesús Vázquez, Marta Martinez-Vicente, Antonio L Serrano, Eusebio Perdiguero, Joan Isern, Ana Maria Cuervo, Pura Muñoz-Cánoves.

Proteostasis supports stemness, and its loss correlates with the functional decline of diverse stem cell types. Chaperone-mediated autophagy (CMA) is a selective autophagy pathway implicated in proteostasis, but whether it plays a role in muscle stem cell (MuSC) function is unclear. Here we show that CMA is necessary for MuSC regenerative capacity throughout life. Genetic loss of CMA in young MuSCs, or failure of CMA in aged MuSCs, causes proliferative impairment resulting in defective skeletal muscle regeneration. Using comparative proteomics to identify CMA substrates, we find that actin cytoskeleton organization and glycolytic metabolism are key processes altered in aged murine and human MuSCs. CMA reactivation and glycolysis enhancement restore the proliferative capacity of aged mouse and human MuSCs, and improve their regenerative ability. Overall, our results show that CMA is a decisive stem cell-fate regulator, with implications in fostering muscle regeneration in old age.

DOI: https://doi.org/10.1038/s42255-025-01411-w
bioRxiv. 2025 Nov 17. pii: 2025.11.17.688927. [Epub ahead of print]

Recurrent Breast Cancer Cells Depend on De novo Pyrimidine Biosynthesis to Suppress Ferroptosis.

Kelley R McCutcheon, Josh Wu, Yasemin Ceyhan Ozdemir, Brock J McKinney, Sharan Srinivasan, Ayaha Itokawa, Oliver J Newsom, Anna Vigil, Douglas B Fox, Lucas B Sullivan, James V Alvarez.

Breast cancer recurrence remains a major clinical challenge, often associated with therapy resistance and altered metabolic states. To define metabolic vulnerabilities of recurrent disease, we performed a CRISPR knockout screen targeting 421 metabolic genes in paired primary and recurrent HER2-driven breast cancer cell lines. While both primary and recurrent tumors shared dependencies on core metabolic pathways, recurrent tumors exhibited selective essentiality for the de novo pyrimidine synthesis pathway, including Cad , Dhodh , and Ctps . Pharmacologic inhibition of the rate-limiting enzyme DHODH with BAY-2402234 selectively impaired the growth of recurrent tumor cells, while primary tumor cells were relatively resistant. BAY treatment robustly inhibited pyrimidine synthesis in all lines, but only recurrent cells underwent iron-dependent lipid peroxidation and ferroptotic cell death. Lipidomic profiling revealed enrichment of polyunsaturated ether phospholipids in recurrent cells, which may predispose them to ferroptosis. A sensitizer CRISPR screen in primary cells further identified nucleotide salvage and lipid metabolic pathways as modifiers of DHODH inhibitor sensitivity. Stable isotope tracing and nutrient depletion experiments showed that primary cells can compensate for DHODH inhibition through nucleotide salvage, whereas recurrent cells exhibit impaired salvage capacity, likely due to reduced expression of Slc28 / Slc29 nucleoside transporters. Together, these findings reveal that breast cancer recurrence is associated with increased dependence on de novo pyrimidine synthesis to suppress ferroptosis, highlighting a therapeutically actionable metabolic vulnerability in recurrent disease.

DOI: https://doi.org/10.1101/2025.11.17.688927
Trends Cancer. 2025 Nov 28. pii: S2405-8033(25)00280-8. [Epub ahead of print]

Neural hijacking in cancer metabolism: from nutrients to organelles.

Songhui Shin, Su Yeon Myoung, Hye Jin Cho, Seongjun Kim, Namgyu Lee, Sung Jin Park.

  Tumors dynamically interact with the central and peripheral nervous systems, hijacking neural plasticity and reprogramming metabolism in a bidirectional manner to drive cancer progression. Neural inputs reshape the metabolism of cancer cells and their microenvironment - glycolysis, oxidative phosphorylation, and lipid metabolism - while tumors exploit neuronal nutrients and mitochondria to thrive under metabolic stress. This review explores neurocancer metabolic crosstalk through multiple mechanisms by three principal modes of interaction, highlighting how targeting these metabolic interdependencies could disrupt tumor progression. By integrating cancer metabolism and neuroscience, it offers a conceptual framework for understanding neural-tumor metabolic circuits in malignancy and identifies potential therapeutic vulnerabilities.

Keywords:  cancer; crosstalk; metabolism; neuron; therapy

DOI:  https://doi.org/10.1016/j.trecan.2025.11.006
Res Sq. 2025 Nov 19. pii: rs.3.rs-7983397. [Epub ahead of print]

Dietary Polyunsaturated Fatty Acids Regulate Dendritic Cell Function via Nrf2-dependent Control of Ferroptosis.

Juan Cubillos-Ruiz, Deepika Awasthi, Erin McMinn, Camilla Salvagno, Sung-Min Hwang, Tito Sandoval, Chang-Suk Chae, Wiam Madani, Jacqueline Crater, Kaushik Sen, Daniel Min, Alexander Emmanuelli, Chen Tan, Andrew Dannenberg, Diana Morales, Evelyn Cantillo, Eloise Chapman-Davis, William Zhang, Suzanne Cloonan.

Dendritic cells (DCs) orchestrate adaptive immune responses to pathogens and tumors, yet how dietary lipids influence DC metabolism and function remains largely unexplored. Here we show that dietary polyunsaturated fatty acids (PUFAs) govern DC activity via Nuclear factor erythroid 2-like 2 (Nrf2)-dependent control of ferroptosis. In mice, an n-6 PUFA-enriched diet suppressed DC Nrf2 signaling, depleted glutathione, and induced lipid peroxidation and ferroptosis, thereby compromising antigen presentation. By contrast, dietary n-3 PUFAs enhanced Nrf2 signaling and redox homeostasis, preserving DC integrity and T cell priming. Pharmacologic Nrf2 activation or ferroptosis inhibition restored the function of DCs from n-6 PUFA-fed mice. Notably, adoptive immunotherapy with DCs conditioned by a diet rich in n-3 PUFAs-but not n-6 PUFAs-elicited durable, T cell-dependent control of metastatic ovarian cancer. These findings identify dietary PUFAs as key modulators of the Nrf2-glutathione-ferroptosis axis in DCs and reveal a redox-sensitive metabolic checkpoint that can be leveraged to improve cancer immunotherapy.

DOI: https://doi.org/10.21203/rs.3.rs-7983397/v1
Nat Cell Biol. 2025 Dec 01.

RASH3D19 mediates RAS activation through a positive feedback loop in KRAS-mutant cancer.

Warapen Treekitkarnmongkol, Hiroshi Katayama, Deivendran Sankaran, Mei-Chee Tai, Sanchita Rauth, Hanxiao Chen, Tristian Nguyen, Kieko Hara, Fredrik I Thege, Moorthy P Ponnusamy, Surinder K Batra, Huamin Wang, Ignacio I Wistuba, Thomas D Schmittgen, John V Heymach, Scott Kopetz, Tony Hu, Wantong Yao, Anirban Maitra, Subrata Sen.

Therapeutic targeting of mutant KRAS pathways driving cancers is being actively investigated to identify feedback mechanisms responsible for the development of adaptive resistance to mutant KRAS inhibitors undergoing clinical trials. Here we report RASH3D19 as a mediator of RAS pathway activation through a positive feedback loop involving the KRAS-microRNA signalling axis. KRAS-induced miR-222 represses ETS1 expression and downstream transactivation of miR-301a leading to elevation of its target RASH3D19. RASH3D19 facilitates activation of RAS pathways by promoting dimerization and interaction of EGFR with the SOS2, GRB2, SHP2 and GAB1 complex. Genetic deletion of RASH3D19 in mutant KRAS-expressing cancer cells exhibits growth retardation in vitro, in vivo and sensitized pancreatic ductal adenocarcinoma and colorectal cancer cells, organoids and xenografts to mutant KRAS inhibitors, suppressing feedback reactivation of RAS pathways. Therapeutic targeting of RASH3D19 is expected to lead to tumour debulking and alleviating resistance to KRAS inhibitors in mutant KRAS-expressing cancers.

DOI: https://doi.org/10.1038/s41556-025-01816-5
Cell Rep Med. 2025 Dec 01. pii: S2666-3791(25)00544-0. [Epub ahead of print] 102471

A low-protein diet drives short- and long-term improvements in metabolic health in a mouse model of sleeve gastrectomy.

Julia Illiano, Cara L Green, Alina Chao, Grace Zhu, Luiz Lopez, Odin Schaepkens, Cholsoon Jang, Dudley W Lamming, David A Harris.

  Despite the beneficial impact of bariatric surgery on obesity and metabolic disease, continued post-surgical obesity and weight recurrence are common, but may be impacted by diet. While guidelines recommend a post-operative high-protein diet to preserve lean mass, emerging evidence suggests that humans and mice are metabolically healthier on low-protein diets. Here, we assess the effect of varying dietary protein on post-surgical metabolism in a mouse model of sleeve gastrectomy. We find that a low-protein diet optimally drives post-surgical weight loss, boosts energy expenditure, and improves blood glucose regulation, likely, in part, due to the induction of FGF21. Through multi-omics, we identified clusters of differentially expressed genes and metabolites that correlate with these phenotypes and find that diet heavily influences the liver's molecular response to sleeve gastrectomy. These results suggest that current post-surgical high-protein diets may limit the short- and long-term benefits of surgery and warrant human clinical trials.

Keywords:  FGF21; bariatric surgery; body composition; diet; energy expenditure; glucose metabolism; liver; low-protein diet; multi-omics; sleeve gastrectomy

DOI:  https://doi.org/10.1016/j.xcrm.2025.102471
J Natl Cancer Inst. 2025 Dec 01. pii: djaf345. [Epub ahead of print]

NQO1 as a predictor of response to adjuvant GemCap treatment for pancreatic cancer.

Dylan Williams, Chandni Patel, Kate Murray, Lucy Oldfield, Benjamin Small, Lawrence N Barrera, Rachel O'Sullivan, James Birch-Ford, Anthony Evans, Fiona Campbell, Pedro A Perez-Mancera, Christopher M Halloran, Daniel Palmer, William Greenhalf, Ian M Copple, Chris Goldring, Thilo Hackert, Richard Jackson, John P Neoptolemos, Christoph Springfeld, Markus W Büchler, Christoph W Michalski, Paula Ghaneh, Eithne Costello.

   BACKGROUND: NAD(P)H Quinone Dehydrogenase 1 (NQO1), a detoxification enzyme regulated by the Nrf2 cytoprotective pathway, is overexpressed in pancreatic ductal adenocarcinoma (PDAC). NQO1 levels are also influenced by the C609T single nucleotide polymorphism (SNP). We hypothesised that elevated NQO1 would confer chemoresistance in PDAC and predict poor patient outcome.
METHODS: NQO1 tumor levels and germline C609T SNP status were assessed in archival samples from the European Study Group for Pancreatic Cancer (ESPAC) trials. NQO1 expression (H-score) was treated as continuous for survival regression analyses and dichotomised for visual summaries. Nrf2 or downstream gene induction was assessed in Nrf2 reporter mice or in PDAC cells following exposure to gemcitabine (Gem), 5-fluorouracil (5-FU) or the capecitabine (Cap) metabolite 5-Fluoro-5'-deoxyuridine (5'-DFUR). Colony formation following NQO1 depletion was assessed.
RESULTS: NQO1 tumor levels correlated with germline C609T SNP status (p < .001). Contrary to our hypothesis, high NQO1 expression was associated with improved survival in ESPAC-4 patients randomised to GemCap (HR 0.87 (0.751, 0.999); P = .049), and had no association to outcome in the Gem-only treated arm [HR: 0.98 (0.78, 1.23) P = .867]. Including genotype data did not improve predictive model performance. Neither Gem nor 5-FU induced Nrf2 in vivo. At high concentrations they suppressed Nrf2/NQO1 in PDAC cells, an effect not mitigated by co-treatment with 5'-DFUR. NQO1 depletion experiments revealed that NQO1 inhibits colony formation. The strongest inhibition was observed when NQO1-positive cells were co-treated with Gem and 5'-DFUR, supporting our clinical data from ESPAC.
CONCLUSION: High tumor NQO1 predicts better outcome following GemCap therapy.

Keywords:  Gem; GemCap; NQO1; Nrf2; biomarker; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1093/jnci/djaf345
bioRxiv. 2025 Nov 18. pii: 2025.11.17.688722. [Epub ahead of print]

Differential regulation of p62-ubiquitin conjugates in neurons versus astrocytes during cellular stress.

David K Sidibe, Erin M Smith, Maeve L Spivey, Maria C Vogel, Sandra Maday.

Sequestosome 1/p62 (hereafter referred to as p62) is a multifunctional protein that orchestrates various cellular stress response pathways including autophagy, proteasome-mediated degradation, antioxidant defense, nutrient sensing, and inflammatory signaling. Mutations in distinct functional domains of p62 are linked with the neurodegenerative disease amyotrophic lateral sclerosis (ALS), underscoring its importance in neural cells. Neurons and astrocytes perform distinct roles in brain physiology and thus encounter a unique landscape of cellular stress. However, how p62 is regulated in these cell types in response to various stress modalities remains largely unexplored. Several functions for p62 depend on engagement with ubiquitinated substrates. Thus, we investigated how the regulation of p62-ubiquitin conjugates differs between neurons and astrocytes exposed to two stress modalities: lysosomal membrane damage and metabolic stress. Lysosomal damage triggered ubiquitin-dependent assembly of p62 puncta in both neurons and astrocytes. In contrast, nutrient deprivation elicited different responses between neurons and astrocytes. Neurons formed p62-ubiquitin structures more prominently and displayed a greater dependence on ubiquitin for p62 clustering. Together, these findings reveal cell-type-specific and stress-specific regulation of p62-ubiquitin conjugates, indicating that neurons and astrocytes can deploy distinct quality control strategies.

DOI: https://doi.org/10.1101/2025.11.17.688722
Cell. 2025 Dec 02. pii: S0092-8674(25)01253-X. [Epub ahead of print]

Membrane potential mediates the cellular response to mechanical pressure.

Avik Mukherjee, Yanqing Huang, Jens Elgeti, Seungeun Oh, Jose G Abreu, Leander Ammar, Anjali R Neliat, Janik Schüttler, Dan-Dan Su, Christophe Dupre, Nina Catherine Benites, Xili Liu, Leonid Peshkin, Mihail Barboiu, Hugo Stocker, Marc W Kirschner, Markus Basan.

  Mechanical forces influence cellular decisions to grow, die, or differentiate, through largely mysterious mechanisms. Separately, changes in resting membrane potential have been observed in development, differentiation, regeneration, and cancer. We demonstrate that membrane potential is an important mediator of cellular response to mechanical pressure. We show that mechanical forces acting on the cell change cellular biomass density, which, in turn, alters membrane potential. Membrane potential then regulates cell number density in epithelia by controlling cell growth, proliferation, and cell elimination. Mechanistically, we show that changes in membrane potential control signaling through the Hippo and mitogen-activated protein kinase (MAPK) pathways and potentially other signaling pathways that originate at the cell membrane. While many molecular interactions are known to affect Hippo signaling, the upstream signal that activates the canonical Hippo pathway at the membrane has previously been elusive. Our results establish membrane potential as an important regulator of growth and tissue homeostasis.

Keywords:  Hippo; YAP; biomass density; growth control; mapk; mechanotransduction; membrane potential; tissue homeostasis

DOI:  https://doi.org/10.1016/j.cell.2025.11.004
Proc Natl Acad Sci U S A. 2025 Dec 09. 122(49): e2523039122

A targeted combination therapy achieves effective pancreatic cancer regression and prevents tumor resistance.

Vasiliki Liaki, Sara Barrambana, Myrto Kostopoulou, Carmen G Lechuga, Elena Zamorano-Dominguez, Domingo Acosta, Lucia Morales-Cacho, Ruth Álvarez, Pian Sun, Blanca Rosas-Perez, Rebeca Barrero, Silvia Jiménez-Parrado, Alejandra López-García, Marta San Roman, Juan Carlos López-Gil, Matthias Drosten, Bruno Sainz, Monica Musteanu, Eduardo Caleiras, Nelson Dusetti, Valeria Poli, Francisco Sánchez-Bueno, Carmen Guerra, Mariano Barbacid.

  Pancreatic ductal adenocarcinoma (PDAC) has one of the lowest cancer survival rates. Recent studies using RAS inhibitors have opened the door to more efficacious therapies, although their beneficial effect is still limited mainly due to the rapid appearance of tumor resistance. Here, we demonstrate that genetic ablation of three independent nodes involved in downstream (RAF1), upstream (EGFR), and orthogonal (STAT3) KRAS signaling pathways leads to complete and permanent regression of orthotopic PDACs induced by KRAS/TP53 mutations. Likewise, a combination of selective inhibitors of KRAS (RMC-6236/daraxonrasib), EGFR family (afatinib), and STAT3 (SD36) induced the complete regression of orthotopic PDAC tumors with no evidence of tumor resistance for over 200 d posttreatment. This combination therapy also led to significant regression of genetically engineered mouse tumors as well as patient-derived tumor xenografts (PDX) in the absence of tumor relapses. Of importance, this combination therapy was well tolerated. In sum, these results should guide the development of new clinical trials that may benefit PDAC patients.

Keywords:  KRAS, RAF1, EGFR, STAT3; MRTX1133, RMC-6236/daraxonrasib, afatinib, SD36; Pancreatic Ductal Adenocarcinoma (PDAC); targeted therapy; tumor regression and resistance

DOI:  https://doi.org/10.1073/pnas.2523039122
Biophys J. 2025 Dec 03. pii: S0006-3495(25)03453-8. [Epub ahead of print]

A Versatile GPMV-Imaging Platform for Quantitative Analysis of Receptor Binding and Membrane Fusion.

Inbar Yosibash, Suman Khan, Alisa Vaknin, Raviv Dharan, Alexandra Lichtenstein, Gonen Golani, Susan Daniel, Ori Avinoam, Raya Sorkin.

Membrane fusion is central to biological processes such as viral entry, fertilization and cell-to-cell fusion. Gaining a mechanistic understanding of fusion requires the ability to visualize and quantify the dynamic interaction between two membranes and their associated protein machineries at high temporal and spatial resolution. However, studying these processes in live cells remains challenging due to the complexity of the cellular environment. Here we demonstrate a versatile cell-free platform based on giant plasma membrane vesicles (GPMVs) that enables controlled, quantitative analysis of receptor binding and membrane fusion kinetics in a native membrane context. As proof of concept, we reconstitute the SARS-CoV-1 Spike-ACE2 interaction, capturing specific receptor engagement and accumulation at the membrane interface using confocal microscopy and micropipette aspiration. Fusion was induced by proteolytic activation and quantified using both high-resolution microscopy and high-throughput Imaging Flow Cytometry. The platform also reveals the influence of membrane composition on fusion efficiency, demonstrated by the impact of cholesterol depletion. This approach provides a broadly applicable system for dissecting membrane fusion and protein-protein interactions across membranes, with compatibility for biophysical, imaging and structural analysis. It offers new opportunities for mechanistic studies and inhibitor screening in a biologically relevant yet experimentally accessible context.

DOI: https://doi.org/10.1016/j.bpj.2025.11.2687
Autophagy Rep. 2025 ;4(1): 2593061

Involvement of ACSL3 in the formation of autophagosomes and lipid droplets during starvation conditions.

Shun Kato, Mitsuo Tagaya.

  Acyl-CoA synthetase long-chain (ACSL) catalyzes the conversion of fatty acids into acyl-CoA, which is used for neutral lipid and phospholipid synthesis. Previous studies revealed that yeast Faa1 and mammalian ACSL4 play a crucial role in phagophore expansion by locally synthesizing phospholipids. We found that another member of ACSL protein family, ACSL3, which is involved in lipid droplet biogenesis under energy-rich conditions and is regulated by SYNTAXIN17, also participates in autophagosome formation, but in a different manner. Knockdown of ACSL3 suppressed punctum formation of early autophagosomal marker proteins such as FIP200 and WIPI2 in starved cells, generating nonfunctional multi-membrane autophagosome-like structures. In contrast, ACSL4 suppression blocked autophagosome formation without affecting punctum formation of early autophagosomal marker proteins. Mechanistic analysis revealed that ACSL3 functions independently of its enzymatic activity, while catalytic activity of ACSL4 is required for autophagosome formation as well as LC3 (known as MAP1LC3 proteins) protein lipidation. Furthermore, ACSL3 has been shown to be essential for lipid droplet biogenesis during starvation. These findings establish ACSL3 as a key player in two events in early autophagy: formation of autophagosomes and lipid droplets.

Keywords:  ACSL3; ACSL4; autophagy; lipid droplet; syntaxin 17

DOI:  https://doi.org/10.1080/27694127.2025.2593061
Anal Chem. 2025 Dec 04.

Polarized Distribution of Lipid Droplets with Long Acyl Chains and Unsaturation are Hallmarks of Human Intestinal Enteroid Differentiation.

Patrik K Johansson, Yueming Liu, Katarina C Klett, Sarah C Heilshorn, Annika Enejder.

Cell polarization and differentiation require increased energy mobilization and cell membrane synthesis, whereby mitochondria and lipid droplets (LDs) play key roles. However, how these metabolic organelles organize at the subcellular level to efficiently meet energy demands in human intestinal organoids is unclear. To address this, we introduce coherent anti-Stokes Raman scattering (CARS) microscopy multiplexed with confocal fluorescence microscopy to spatially map LDs and mitochondria throughout cell differentiation in human intestinal enteroids. The results show an overall decrease in LDs over time, though less pronounced for cells positive for proliferation or stemness markers. The LD depletion was observed in the apical region, resulting in a polarized distribution to the basal side. A similar mitochondrial polarization pattern was also observed in differentiated enteroids. Spectral CARS further shows that LDs postdifferentiation contain lipids with signatures of longer acyl chains and a higher degree of unsaturation. These observations demonstrate that polarized metabolic and lipid supply infrastructures are formed to support intestinal cell differentiation in organoid cultures.

DOI: https://doi.org/10.1021/acs.analchem.5c02648
Cell Metab. 2025 Dec 02. pii: S1550-4131(25)00489-9. [Epub ahead of print]37(12): 2298-2300

Tumor acidosis: Fusing mitochondrial dynamics and lipid metabolism.

Sébastien Ibanez, Olivier Feron.

Cancer cells experience multiple stresses within tumors, stemming from elevated metabolic activity, including nutrient shortage, waste buildup, hypoxia, and acidosis. According to Groessl et al.,1 acidosis is the dominant environmental factor offering metabolic flexibility to support tumor fitness and resilience to the other stresses by promoting mitochondria fusion and enhancing respiration capacity.

DOI: https://doi.org/10.1016/j.cmet.2025.11.005
Proc Natl Acad Sci U S A. 2025 Dec 09. 122(49): e2516288122

Oxidative pentose phosphate pathway is required for T cell activation and antitumor immunity.

Zihong Chen, Kellen L Olszewski, Rolf-Peter Ryseck, Xincheng Xu, Jacob A Boyer, Christian G Peace, Yihui Shen, Caroline R Bartman, Lydia Lynch, Joshua D Rabinowitz.

  Glucose is catabolized by two major metabolic pathways, glycolysis and the oxidative pentose phosphate pathway (oxPPP). The oxPPP generates nicotinamide adenine dinucleotide phosphate (NADPH) at two steps, glucose-6-phosphate dehydrogenase (G6PD), the most common enzyme deficiency in humans, and 6-phosphogluconate dehydrogenase (PGD). Previous literature suggests that G6PD supports but PGD limits T cell-mediated immunity. Here, we use T cell-specific knockout mouse models to show that both enzymes are required for antitumor immunity and response to immunotherapy. PGD knockout depletes mature T cells systemically, while G6PD loss does not reduce basal T cell populations but results in apoptosis upon activation. Such apoptosis is not reversed by major downstream products of the oxPPP, including antioxidants, nucleosides, or fatty acids. Instead, T cells are partially rescued by removal of media cystine, whose reduction requires NADPH. G6PD loss induces an oxidative stress response that upregulates cystine import, which together with low NADPH leads to fatal disulfide stress. Overall, these results highlight an essential role for the oxidative pentose phosphate pathway in cystine homeostasis and T cell-mediated immunity.

Keywords:  NADPH; T cell activation; T cell antitumor immunity; disulfide stress; oxidative pentose phosphate pathway

DOI:  https://doi.org/10.1073/pnas.2516288122
Dig Liver Dis. 2025 Nov 28. pii: S1590-8658(25)01206-X. [Epub ahead of print]

A phase III randomized clinical trial of Gemcitabine and Nab-Paclitaxel as switch maintenance versus continuation of modified FOLFIRINOX as first-line chemotherapy in patients with advanced pancreatic cancer: The PANThEON Study.

Carolina Sciortino, Federico Nichetti, Francesca Bergamo, Federica Palermo, Stefano Tamberi, Caterina Vivaldi, Elena Ongaro, Giuseppina Arcangeli, Silvia Marchesi, Elisa Giommoni, Chiara Alessandra Cella, Chiara Pircher, Anna Chiaramonte, Katia Bencardino, Elisa Sottotetti, Antonia Martinetti, Ilario Giovanni Rapposelli, Salvatore Corallo, Samantha Di Donato, Roberto Murialdo, Laura Delliponti, Lisa Salvatore, Silvia Bozzarelli, Emanuela Dell'Aquila, Rosalba Miceli, Carlo Carnaghi, Gianluca Tomasello, Piero Rivizzigno, Maria Bonomi, Francesco Mannavola, Laura Forti, Ingrid Garajovà, Laura Attademo, Barbara Galassi, Rita Chiari, Francesco Leone, Silvio Ken Garattini, Emiliano Tamburini, Filippo Pietrantonio, Monica Niger.

   BACKGROUND: Advanced pancreatic ductal adenocarcinoma (PDAC) remains among the most lethal cancers, with >95 % of patients dying from the disease. Chemotherapy is the standard of care in advanced stages, with FOLFIRINOX and Gemcitabine-Nab-Paclitaxel (Gem-NabP) as the main first-line regimens. Both show moderate efficacy and significant toxicity. Except for the PASS-01 trial, no direct comparison exists, though observational studies suggest that specific subgroups may benefit differently. Given the modest outcomes and rapid clinical decline, most patients are ineligible for second-line therapy after progression. The PANThEON study evaluates whether switching from modified FOLFIRINOX (mFOLFIRINOX) to Gem-NabP after three months of induction with mFOLFIRINOX improves outcomes for PDAC.
METHODS: PANThEON is a no-profit, phase III, randomized, open-label, multicenter trial. The primary endpoint is overall survival (OS). Secondary endpoints include progression-free survival (PFS), time to treatment failure (TTF), overall response rate (ORR), and quality of life (QoL). Exploratory analyses will assess tumor profiling, circulating tumor DNA (ctDNA), and radiomics to identify predictive markers. A total of 220 patients will be randomized 1:1 to Gem-NabP (arm B) or continued mFOLFIRINOX (arm A).
DISCUSSION: The PANThEON trial addresses two challenges: improving efficacy while reducing toxicity. Switching to Gem-NabP may enhance tolerability without compromising benefit, prolonging survival and refining PDAC treatment strategies.
TRIAL REGISTRATION: PANThEON is registered at ClinicalTrials.gov (NCT06897644) and EuCT (2024-515214-41-00).

Keywords:  Chemotherapy; Clinical trial; Gemcitabine plus Nabpaclitaxel; Pancreatic cancer; Switch maintenance; mFOLFIRINOX

DOI:  https://doi.org/10.1016/j.dld.2025.11.007
bioRxiv. 2025 Nov 20. pii: 2025.11.19.689204. [Epub ahead of print]

Lymphotoxin-driven cancer cell eradication by tumoricidal CD8 + TIL.

Hongyan Xie, Aiping Jiang, Aonkon Dey, Joseph W Dean, Jonathan J Perera, Neal P Smith, Alex C Y Chen, Seth Anderson, Angelina M Cicerchia, Yi Sun, William A Michaud, Maria Florentin, Jacy Fang, Or-Yam Revach, Tatyana Sharova, Aleigha Lawless, Katherine H Xu, Yuhui Song, Bidish Patel, Jonathan D Stevens, William J Lane, Derin B Keskin, Sonia Cohen, Donald P Lawrence, Ryan J Sullivan, Keith T Flaherty, Genevieve M Boland, Linda T Nieman, Moshe Sade-Feldman, Nir Hacohen, Debattama R Sen, Catherine Wu, Brian Gastman, Rongsu Qi, Hequn Yin, Alexandra-Chloé Villani, Robert T Manguso, Russell W Jenkins.

Tumor-infiltrating lymphocyte (TIL) therapy is FDA-approved for patients with treatment-resistant advanced melanoma, but the TIL subpopulations critical for tumor eradication remains incompletely understood. Using patient-derived TIL-melanoma co-cultures, we identified and characterized a novel subset of CD8 + TIL, capable of class I HLA-independent cancer cell lysis. The lymphotoxin β receptor (LTβR) and interferon (IFN) sensing pathways were nominated as key determinants of TIL-mediated cancer cell killing from a whole-genome, loss-of-function CRISPR screen. Validation studies confirmed that dual LTβR and IFN sensing is necessary and sufficient for cancer cell lysis, and that expanded CD8 + TIL express high lymphotoxin β ( LTB ) and upregulate lymphotoxin α ( LTA ) upon coculture with cancer cells. Leveraging paired scRNA-seq and scTCR-seq data, we confirmed that enrichment of LTB + CD8 + T cells is associated with clinical response to TIL, and that LTB + CD8 + TIL are expanded from putative neoantigen-reactive, LTB lo CD8 + T cells in resected tumors.
Significance: We have uncovered a previously unrecognized mechanism of TIL-mediated tumor eradication, providing mechanistic insights into the role of LTBR/IFN signaling in TIL-mediated cancer cell killing, and potentially offering insights into novel strategies to isolate, enrich, and expand tumoricidal TIL or augment specific TIL functions to enhance tumor control.

DOI: https://doi.org/10.1101/2025.11.19.689204
Nat Protoc. 2025 Dec 03.

Bioengineering mini-colons for ex vivo colorectal cancer research.

L Francisco Lorenzo-Martín, Tania Hübscher, Jakob Langer, Mikhail Nikolaev, Matthias P Lutolf.

Tumor initiation remains one of the least understood events in cancer biology, largely due to the challenge of dissecting the intricacy of the tumorigenic process in laboratory settings. The insufficient biological complexity of conventional in vitro systems makes animal models the primary experimental approach to study tumorigenesis. Despite providing valuable insights, these in vivo models function as experimental black boxes with limited spatiotemporal resolution of cellular dynamics during oncogenesis. In addition, their use raises ethical concerns, further underscoring the need for alternative ex vivo systems. Here we provide a detailed protocol to integrate state-of-the-art microfabrication, tissue engineering and optogenetic approaches to generate topobiologically complex miniature colons ('mini-colons') capable of undergoing tumorigenesis in vitro. We describe the key methodology for the generation of blue light-inducible oncogenic cells, the establishment of hydrogel-based mini-colon scaffolds within microfluidic devices, the development of mini-colons and the induction of spatiotemporally controlled tumorigenesis. This protocol enables the formation and long-term culture of complex cancerous tissues that capture in vivo-like tumoral biology while offering real-time and single-cell resolution analyses. It can be implemented in 4-6 weeks by researchers with prior experience in 3D cell culture techniques. We anticipate that these methodological guidelines will have a broad impact on the cancer research community by opening new avenues for tumorigenesis studies.

DOI: https://doi.org/10.1038/s41596-025-01292-z
Br J Cancer. 2025 Dec 04.

Efficacy and safety of garsorasib in patients with KRAS G12C-mutated advanced pancreatic cancer.

Noboru Yamamoto, Dong Yan, Vinod Ganju, Xinfang Hou, Hongming Pan, Jianzhen Shan, Liwei Wang, Sang-We Kim, Gary Richardson, Rachel E Sanborn, Jingdong Zhang, Ziyong Xiang, Wenjia Wang, Zhe Shi, Ling Zhang, Yaolin Wang, Rui-Hua Xu.

BACKGROUND: Garsorasib (D-1553), a highly selective, oral KRASG12C inhibitor, has shown clinical efficacy in NSCLC and CRC and is under evaluation in pancreatic cancer.
METHODS: Pancreatic cancer patients with KRAS G12C mutation were enroled and received garsorasib 600 mg twice daily treatment in two international, multicenter, open-label phase 1/2 trials (NCT04585035 and NCT05383898) with similar eligibility criteria. Their data were pooled for analyses of efficacy and safety endpoints.
RESULTS: As of April 30, 2024, 24 KRAS G12C-mutated pancreatic cancer patients were enroled with a median follow-up of 8.9 months (range 1.1-22.9). Among 22 evaluable patients, the confirmed objective response rate (ORR) was 45.5% (95% CI, 24.4 to 67.8) with a median duration of response (DOR) of 6.4 months (95% CI, 4.2 to 16.4). The median progression-free survival (PFS) was 7.6 months (95% CI, 3.3 to 8.5) and the 6-month OS rate was 79.2% (95% CI, 57.0, 90.8). Treatment-related adverse events (TRAEs) occurred in 18 (75.0%) patients, including 6 (25.0%) with grade ≥3 events. No TRAEs led to treatment discontinuation. The safety profile was consistent with previous reports of garsorasib.
CONCLUSION: Garsorasib demonstrated encouraging antitumor activity and a tolerable safety profile in patients with KRAS G12C-mutated advanced pancreatic cancer.

DOI: https://doi.org/10.1038/s41416-025-03286-w
Proc Natl Acad Sci U S A. 2025 Dec 09. 122(49): e2509534122

Deciphering precursor cell dynamics in esophageal preneoplasia via genetic barcoding and single-cell transcriptomics.

Jinho Jang, Kyung-Pil Ko, Jie Zhang, Sohee Jun, Jae-Il Park.

  Although histologically normal, esophageal preneoplastic cells harbor early genetic alterations and likely exhibit lineage plasticity. However, their origins and trajectories remain unclear. To address this, we combined genetic barcoding with single-cell RNA sequencing to trace the lineage of esophageal preneoplastic cells. We identified a distinct progenitor-like cell population with high plasticity. Through a scoring system, these high-plasticity cells are mapped, revealing their contributions to proliferative and basal cell populations. This approach uncovers molecular markers, including Nfib and Qk, that define these precursor cells, validated by spatial transcriptomics and a Trp53 Cdkn2a Notch1 mouse model. These findings provide critical insights into early tumorigenesis, highlighting the potential of precursor cells as biomarkers for early detection and therapeutic targets of esophageal squamous cell cancer. By elucidating the cellular dynamics underlying esophageal preneoplasia, this research lays the foundation for strategies to prevent malignant progression, offering broader implications for improving cancer diagnostics and treatment approaches.

Keywords:  cell lineage tracing; esophageal squamous cell cancer; genetic barcoding; preneoplasia; single-cell transcriptomics

DOI:  https://doi.org/10.1073/pnas.2509534122
BMJ Oncol. 2025 ;4(1): e000946

KRAS-targeted therapies in cancer: novel approaches and overcoming resistance.

Daolin Tang, Guido Kroemer, Rui Kang.

  KRAS, once considered undruggable, has become actionable across specific alleles, with KRAS-G12C inhibitors now approved and next-generation approaches-including pan-KRAS/pan-RAS inhibitors, targeted degraders and RNA-based strategies-progressing rapidly. However, clinical benefit remains limited due to the frequent emergence of resistance. Escape mechanisms include on-target secondary mutations, pathway reactivation, epithelial-mesenchymal transition, lineage plasticity and metabolic rewiring within an immunosuppressive tumour microenvironment. Emerging evidence supports rational combination strategies, including parallel inhibition of epidermal growth factor receptor, protein tyrosine phosphatase non-receptor type 11 or SOS1 and vertical blockade of the mitogen-activated protein kinase-extracellular signal-regulated kinase or phosphatidylinositol 3-kinase-mechanistic target of rapamycin cascades; immunotherapies such as checkpoint blockade, T-cell receptor (TCR)-T cells, bispecific T-cell engagers or cytokine-armed oncolytic viruses; metabolic interventions targeting macropinocytosis or autophagy; as well as radiotherapy. Such combination therapies can transform primarily cytostatic effects into more durable antitumour responses, although with potential toxicity constraints. Precision approaches that integrate multiomics profiling with longitudinal circulating tumour DNA analysis enable biomarker-guided patient selection (eg, based on STK11 and KEAP1 comutations) and support therapeutic adaptations, including sequencing strategies and intermittent dosing. Thus, network-level KRAS interception combined with biomarker-driven, clonal evolution-informed trial design offers a path towards sustained control of KRAS-driven cancers.

Keywords:  Cancer of unknown primary

DOI:  https://doi.org/10.1136/bmjonc-2025-000946