bims-cagime 2025-11-23 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–11–23
37 papers selected by
Kıvanç Görgülü, Technical University of Munich

Hypoxia-induced metastatic heterogeneity in pancreatic cancer.
NINJ1.
Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane.
CRISPR-Cas9 Screening Identifies Resistance Mechanisms to KRAS Inhibition in Pancreatic Cancer.
The canonical ER stress IRE1α/XBP1 pathway mediates skeletal muscle wasting during pancreatic cancer cachexia.
Systematic analysis of immune cell motility leveraging the open intravital microscopy database Immunemap.
How one nutrient controls cell size.
Tumor-intrinsic dichotomy shapes cellular heterogeneity in pancreatic cancer.
Collagen nanofiber alignment attenuates leader-follower energetic and metabolic differences during collective migration in pancreatic cancer.
FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer.
ATG2A-mediated DAG transfer recruits DGAT2 for lipid droplet growth.
Branched chain amino acids and their aberrant metabolism in cancer.
A health-system-scale, episode-resolved multimodal atlas of cancer cachexia.
Tumour-reactive heterotypic CD8 T cell clusters from clinical samples.
HNF1A is a novel BRD4 target and critical for BET-inhibitor response in pancreatic ductal adenocarcinoma.
The Reactome Knowledgebase 2026.
Triggering ferroptosis to tackle cancer.
Revisiting Cancer Cachexia Staging: Introducing an "At Risk" Category Based on AWGC Components.
The Physiology Of the WEight Reduced State (POWERS) study: assessing energy balance.
Estrogen Production in Pancreatic Cancer Shapes a Tumor Suppressive Stromal Microenvironment.
Subcellular cartography of the phosphoinositide multiverse.
Membrane Remodeling by the Collective Action of Caveolin-1.
Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer.
ZAK activation at the collided ribosome.
HSP90 buffers deleterious genetic variations in BRCA1.
Autophagy regulation by phase separation, avidity, and wetting.
ricePSP: a database of rice phase separation-associated proteins.
Mitochondrial Transfer Rescues Respiration to Support De Novo Pyrimidine Biosynthesis and Tumor Progression.
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale.
NimbusImage: a cloud-computing platform for image analysis.
Engineering a spatiotemporal macrophage circuit via STING phase separation to override immune suppression in pancreatic cancer.
Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models.
Targeting cancer-associated fibroblasts for real-time intraoperative tumor identification with a spray-on fluorescent probe.
Enrichment-Free, Targeted Covalent Drug Discovery in Live Cells.
OmniPath: integrated knowledgebase for multi-omics analysis.
Multiplexed genetic tags for electron and fluorescence microscopy.
Redefining the concept of erythrocyte senescence: is eryptosis fundamentally different from erythrocyte senescence.

Res Sq. 2025 Oct 01. pii: rs.3.rs-7394295. [Epub ahead of print]

Hypoxia-induced metastatic heterogeneity in pancreatic cancer.

Shin-Heng Chiou, Pradeep Gunasekaran, Qianqian Wang, Yoke-Chen Chang, Polina Guseva, Rajika Chauhan, Alexander Kley, Gene Lee, Siddharth Roy, Yousef Masoudpoor, Arthur Roberts, Kelly Walton, Lucyann Franciosa, Shafiq Bhat, Emmanuel Zachariah, Kishan Patel, Zhongren Zhou, Wenjin Chen, Zhouli Ni, Guoping Gu, Cristina Montagna.

In most solid tumors, hypoxia is a critical physical attribute that reprograms malignant cells into a highly metastatic state. Specifically, hypoxia is a well-established inducer of cellular plasticity, which is associated with treatment resistance and metastasis. Furthermore, hypoxia exacerbates chromosomal instability (CIN), a hallmark of cancer that can be initiated by the loss of Trp53 and a key contributor to metastasis. Despite this, the mechanisms by which malignant cells concurrently co-opt these elements of hypoxic adaptation to promote metastasis remains unknown. Here we report that hypoxia promotes metastasis by suppressing the JmjC-containing histone lysine demethylase Kdm8. CRISPR/Cas9-mediated targeting of Kdm8 in a Kras;Trp53-driven mouse model of pancreatic ductal adenocarcinoma robustly rewires the malignant cell transcriptomic programs, leading to a profound loss of the epithelial morphology and widespread metastatic disease. Mechanistically, Kdm8 suppression in normoxia recapitulates major aspects of the global epigenetic changes and the transcriptomic rewiring induced by hypoxia. Moreover, Kdm8 deficiency leads to mitotic defects, increased micronuclei formation, Kras copy number gains, and enhanced CIN. Of note, disruption of Kdm8's demethylase function phenocopies the effects of Kdm8 loss, whereas expression of hypermorphic Kdm8 variants that are resistant to hypoxic suppression reduces metastasis beyond the levels achieved by the wildtype counterpart. Through the suppression of Kdm8 demethylase activity, hypoxia unleashes a potent metastatic program by simultaneously advancing cellular plasticity and CIN.

DOI: https://doi.org/10.21203/rs.3.rs-7394295/v1
Curr Biol. 2025 Nov 17. pii: S0960-9822(25)01338-7. [Epub ahead of print]35(22): R1072-R1073

NINJ1.

Elliott M Bernard, Ella Hartenian, Petr Broz.

Bernard, Hartenian, and Broz introduce NINJ1, a transmembrane protein that mediates plasma membrane rupture during lytic cell death.

DOI: https://doi.org/10.1016/j.cub.2025.10.030
bioRxiv. 2025 Oct 02. pii: 2025.09.30.679611. [Epub ahead of print]

Phosphatidylserine and RhoB connect phosphatidylinositol 4-phosphate and phosphatidic acid metabolism at the plasma membrane.

Shiying Huang, Yeun Ju Kim, Xiaofu Cao, Timothy W Bumpus, Mira Sohn, Matthew Tyler Menold, Ryan S Dale, Jin Joo Kang, Saori Uematsu, Shagun Gupta, Shu-Bing Qian, Haiyuan Yu, Tamas Balla, Jeremy M Baskin.

Cells tightly control the homeostatic levels and subcellular localizations of membrane phospholipids through the regulation of the activities of numerous lipid-metabolizing enzymes and lipid transfer proteins. Yet, the mechanisms by which lipid imbalances are sensed and corrected to establish and maintain homeostasis are, in most cases, unknown. Here we present an expanded view of plasma membrane (PM) phosphoinositide metabolism by revealing an unexpected metabolic connection between two key anionic lipids in this membrane, phosphatidylinositol 4-phosphate (PI4P) and phosphatidic acid (PA). PM pools of PI4P are generated by PI 4-kinase Type IIIα (PI4KIIIα/PI4KA), an essential enzyme whose partial dysfunction leads to numerous hereditary human diseases. We find that depletion of PI4P by pharmacological inhibition of PI4KA increases the activity of phospholipase Ds (PLDs) and the levels of their lipid product, PA, in the PM. Guided by RNA-seq analysis and proximity labeling proteomics, we elucidate how cells connect this PI4P decrease to a compensatory increase in PA levels. Loss of PM PI4P induces a concomitant decrease of phosphatidylserine (PS) levels, and this metabolic rewiring activates a reciprocal relationship between PS synthesis and PLD-mediated PA generation. These metabolic changes also lead to transcriptional and translational upregulation of the small GTPase RhoB, which enhances PLD-mediated PA synthesis and subsequent actin cytoskeletal remodeling. Our study reveals how disease-relevant perturbation of phosphoinositide synthesis induces an integrated response that ultimately boosts levels of PA, a key anionic lipid and metabolic intermediate in phosphoinositide resynthesis.

DOI: https://doi.org/10.1101/2025.09.30.679611
Cancer Res. 2025 Nov 17.

CRISPR-Cas9 Screening Identifies Resistance Mechanisms to KRAS Inhibition in Pancreatic Cancer.

Szu-Aun Long, Haley Todd, Grace Goodhart, Wen-Hsuan Chang, Amber M Amparo, Rachel Bridgens, Julien Dilly, Se Jun Park, Robert M Beal, Sara M Shehadeh, Megan A Satyadi, Vidushi K Trivedi, Sarah E Ackermann, Raivath Mukherjee, Craig M Goodwin, A Cole Edwards, Clint A Stalnecker, Kenneth D Greis, Andrew J Aguirre, G Aaron Hobbs, Kirsten L Bryant, Syed A Ahmad, Adrienne D Cox, Channing J Der, Andrew M Waters.

KRAS inhibitors (KRASi) targeting various KRAS mutations have entered clinical trials for pancreatic cancer. Despite promising preliminary clinical responses, most patients relapse due to intrinsic or acquired resistance. Thus, combination treatments are essential to extend the efficacy of KRAS-targeted therapies. To further determine genetic mechanisms of KRASi resistance, we performed KRASi-anchored CRISPR-Cas9 loss-of-function screens in KRASG12D, KRASG12C, KRASG12R, and KRASQ61H mutant PDAC cell lines, using six KRASi, to identify genes that modulate sensitivity to KRAS inhibition. Several hits from the screens, including EGFR, CK2, p110α and p110γ, and YAP were validated by combining targeted inhibitors with KRASi. KRASQ61H-mutant PDAC cell lines were intrinsically less dependent on KRAS for survival than other KRAS mutational subtypes. Further, EGFR inhibitor erlotinib synergized with the RAS(ON) multi-selective inhibitor RMC-7977 in KRASQ61H-mutant PDAC cell lines and in cell lines with highly active EGFR by mitigating ERK rebound activity. KRASi-resistant cell lines featured sustained ERK/MAPK dependence despite decreased ERK activity. Together, these findings enhance the understanding of intrinsic and acquired resistance to KRASi and identify therapeutic vulnerabilities that can potentially be exploited for KRASi combination therapies in pancreatic cancer patients.

DOI: https://doi.org/10.1158/0008-5472.CAN-25-1835
EMBO Mol Med. 2025 Nov 17.

The canonical ER stress IRE1α/XBP1 pathway mediates skeletal muscle wasting during pancreatic cancer cachexia.

Aniket S Joshi, Meiricris Tomaz da Silva, Anh Tuan Vuong, Bowen Xu, Ravi K Singh, Ashok Kumar.

  Cancer cachexia is a debilitating syndrome characterized by the progressive loss of skeletal muscle mass with or without fat loss. Recent studies have implicated dysregulation of the endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) pathways in skeletal muscle under various conditions, including cancer. In this study, we demonstrate that the IRE1α/XBP1 branch of the UPR promotes activation of the ubiquitin-proteasome system, autophagy, JAK-STAT3 signaling, and fatty acid metabolism in the skeletal muscle of the KPC mouse model of pancreatic cancer cachexia. Moreover, we show that the IRE1α/XBP1 pathway is a key contributor to muscle wasting. Skeletal muscle-specific deletion of the XBP1 transcription factor significantly attenuates tumor-induced muscle atrophy. Mechanistically, transcriptionally active XBP1 binds to the promoter regions of genes such as Map1lc3b, Fbxo32, and Il6, which encode proteins known to drive muscle proteolysis. Pharmacological inhibition of IRE1α using 4µ8C in KPC tumor-bearing mice attenuates cachexia-associated molecular changes and improves muscle mass and strength. Collectively, our findings suggest that targeting IRE1α/XBP1 pathway may offer a therapeutic strategy to counteract muscle wasting during pancreatic cancer-induced cachexia.

Keywords:  ER Stress; Fatty Acid Oxidation; JAK-STAT; Muscle Wasting; Unfolded Protein Response

DOI:  https://doi.org/10.1038/s44321-025-00337-w
EMBO J. 2025 Nov 20.

Systematic analysis of immune cell motility leveraging the open intravital microscopy database Immunemap.

Immunemap Consortium

  Understanding the spatiotemporal dynamics of immune cells in living organisms is a major goal in bioimaging. Intravital microscopy enables direct observation of cellular behavior over time with tissue-to-subcellular resolution, making it essential for investigating immune responses across tissues, conditions, and disease contexts. However, most intravital microscopy data remain siloed in individual labs, limiting reuse, standardization, and large-scale analysis. To address these limitations, we present Immunemap, an open-data platform and interactive atlas of immune cell motility. Immunemap currently provides access to over 58,000 curated single-cell tracks and more than 1,049,000 cell-centroid annotations from 400 intravital microscopy videos in murine models, spanning diverse tissues and conditions. The platform supports both exploratory and quantitative research. We show here how unsupervised learning identifies distinct motility patterns, and how large-scale mapping enables comparisons across stimuli, imaging setups, and organs. Its cloud-based architecture offers an interactive web interface and public APIs for integration with computational pipelines. By adhering to FAIR principles (Findability, Accessibility, Interoperability, and Reuse) and fostering cross-disciplinary studies, Immunemap supports reproducible research and provides a benchmark for bioimage analysis and tool development in intravital imaging.

Keywords:  Bioimage Data Analysis; Cell Tracking; Immune Response; Intravital Microscopy; Spatiotemporal Dynamics

DOI:  https://doi.org/10.1038/s44318-025-00629-4
Elife. 2025 Nov 19. pii: e109482. [Epub ahead of print]14

How one nutrient controls cell size.

Angela Montero, Lydia W S Finley.

  The metabolic fate of a nutrient called pyruvate determines how big cells become.

Keywords:  D. melanogaster; biochemistry; cell biology; cell growth; chemical biology; genetics; hepatocytes; human; pyruvate metabolism; redox state; translation

DOI:  https://doi.org/10.7554/eLife.109482
Trends Cancer. 2025 Nov 14. pii: S2405-8033(25)00277-8. [Epub ahead of print]

Tumor-intrinsic dichotomy shapes cellular heterogeneity in pancreatic cancer.

Rebecca Diya Samuel, Shiv K Singh.

  Intratumoral heterogeneity in pancreatic cancer poses a significant challenge, contributing to disease aggressiveness and complicating treatment. A recent study by Li et al. reveals that this heterogeneity is maintained by tumor-intrinsic reciprocal signaling between SPP1 and GREM1 in the epithelial and mesenchymal cell populations of pancreatic cancer.

Keywords:  SPP1–GREM1; epithelial–mesenchymal; pancreatic cancer; tumor heterogeneity

DOI:  https://doi.org/10.1016/j.trecan.2025.11.003
Acta Biomater. 2025 Nov 19. pii: S1742-7061(25)00853-0. [Epub ahead of print]

Collagen nanofiber alignment attenuates leader-follower energetic and metabolic differences during collective migration in pancreatic cancer.

Madison R Pickett, Mohini Kamra, David A Castilla-Casadiego, Sepehr Noori, William Matsui, Adrianne M Rosales, Janet Zoldan, Sapun H Parekh.

  The extracellular matrix (ECM) is a dynamic microenvironment that influences cell behavior and fate, with changes in its architecture linked to processes such as differentiation and disease progression in cancer. Pancreatic ductal adenocarcinoma (PDAC) is an aggressive form of cancer associated with a dense ECM composed of collagen I fibers. While considerable research on PDAC metastasis has focused on single-cell migration, recent studies suggest PDAC cells undergo a process called "collective migration" as groups. This study investigates PDAC migration and metabolism on electrospun collagen I nanofiber meshes. A 3D-printed, removable insert is used to create a gap-like a scratch-that allows for analysis of cell migration on intact fibers. By tuning nanofiber orientation, this study replicates the PDAC ECM during stromal remodeling to assess cellular metabolism and the energetic state of leader and follower cells during migration. Interestingly, the data suggests that nanofiber architecture strongly modulates differences between PDAC leader and follower cells during collective migration. While leader cells require more ATP and rely more on oxidative phosphorylation in both conditions, this reliance is particularly pronounced in the random condition. These findings underscore the interplay between collective migration, ECM architecture, and metabolism in PDAC migration. STATEMENT OF SIGNIFICANCE: The role of the stromal extracellular matrix (ECM) in metastasis and migration is well studied, yet its impact on metabolic processes underlying metastasis, especially in pancreatic ductal adenocarcinoma (PDAC), remains unclear. PDAC is marked by high metastasis rates and a densely fibrotic ECM, with increased collagen alignment correlating to poor prognosis. In this study, we explore how ECM architecture, represented by near-native electrospun collagen nanofibers, influences collective migration and metabolism in PDAC. Our findings show that increased collagen alignment reduces metabolic differences, including ATP/ADP ratio, gene expression, and mitochondrial membrane potential, between leader and follower cells during migration. This is the first study to investigate leader-follower dynamics in PDAC collective migration using tunable, stromal-mimicking, fibrous substrates.

Keywords:  cancer metabolism; extracellular matrix (ECM); migration; nanofibers; pancreatic ductal adenocarcinoma (PDAC)

DOI:  https://doi.org/10.1016/j.actbio.2025.11.031
EMBO Rep. 2025 Nov 20.

FOXO1 links KRAS G12D and G12V alleles to glutamine and nitrogen metabolism in colorectal cancer.

Suzan Ber, Ming Yang, Marco Sciacovelli, Shamith Samarajiwa, Khushali Patel, Efterpi Nikitopoulou, Annie Howitt, Simon J Cook, Ashok R Venkitaraman, Christian Frezza, Alessandro Esposito.

  Mutations in KRAS, particularly at codon 12, are frequent in adenocarcinomas of the colon, lungs and pancreas, driving carcinogenesis by altering cell signalling and reprogramming metabolism. However, the specific mechanisms by which different KRAS G12 alleles initiate distinctive patterns of metabolic reprogramming are unclear. Using isogenic panels of colorectal cell lines harbouring the G12A, G12C, G12D and G12V heterozygous mutations and employing transcriptomics, metabolomics, and extensive biochemical validation, we characterise distinctive features of each allele. We demonstrate that cells harbouring the common G12D and G12V oncogenic mutations significantly alter glutamine metabolism and nitrogen recycling through FOXO1-mediated regulation compared to parental lines. Moreover, with a combination of small molecule inhibitors targeting glutamine and glutamate metabolism, we also identify a common vulnerability that eliminates mutant cells selectively. These results highlight a previously unreported mutant-specific effect of KRAS alleles on metabolism and signalling that could be potentially harnessed for cancer therapy.

Keywords:  Colorectal Cancer; FOXO Signalling; Glutamine Metabolism; Glutamine Synthase; KRAS Mutation

DOI:  https://doi.org/10.1038/s44319-025-00641-z
Nat Struct Mol Biol. 2025 Nov 17.

ATG2A-mediated DAG transfer recruits DGAT2 for lipid droplet growth.

Helin Elhan, Alicia Damm, Justin L Korfhage, Daniel Álvarez, Mehdi Zouiouich, Francesca Giordano, Stefano Vanni, Thomas J Melia, Abdou Rachid Thiam.

Lipid droplet (LD) growth mechanisms and the roles of LD-associated lipid transfer proteins remain poorly understood. Here we show that the autophagy lipid transfer protein ATG2A has an anabolic role and promotes LD expansion by transferring diacylglycerol (DAG), triacylglycerol (TAG) and phosphatidic acid, from the endoplasmic reticulum to LDs. In ATG2A deficiency, synthesized lipids are incorporated inefficiently into LDs and assemble new LDs. In addition, DAG O-acyltransferase 2 (DGAT2), which synthesizes TAG and expands LD, fails to relocate to LDs. In vitro, DAG recruits DGAT2 to LDs. These findings support the idea that ATG2A-mediated DAG transfer recruits DGAT2 to LDs, promoting LD expansion. ATG2A alone promotes LD growth by transferring TAG and DAG, but its effectiveness in LD expansion is reduced when DGAT2 is inhibited. This synergistic action with DGAT2 prevents the buildup of nonmembrane lipids within the endoplasmic reticulum and favors TAG synthesis on the LD surface.

DOI: https://doi.org/10.1038/s41594-025-01689-0
Trends Cancer. 2025 Nov 18. pii: S2405-8033(25)00255-9. [Epub ahead of print]

Branched chain amino acids and their aberrant metabolism in cancer.

Morgan L Brown, Xuanyan Cai, M Celeste Simon.

  Cancer cells require sufficient nutrients to support biomass generation, rapid proliferation, and survival. Thus, extensive reprogramming of amino acid metabolism is necessary for tumor initiation and progression under strenuous conditions. One metabolic pathway that has garnered attention is branched chain amino acid (BCAA) catabolism, a pathway that is highly altered across malignancies. This review examines current insights into how circulating BCAAs and their aberrant catabolic enzymes impact both cancer cells and the surrounding tumor microenvironment.

Keywords:  branched chain amino acids; cancer metabolism; nutrient supplementation; tumor microenvironment

DOI:  https://doi.org/10.1016/j.trecan.2025.10.004
medRxiv. 2025 Sep 30. pii: 2025.09.29.25336906. [Epub ahead of print]

A health-system-scale, episode-resolved multimodal atlas of cancer cachexia.

Venise Jan Castillon, Amy X Xie, Sonia Boscenco, Ethan Tse, Neil Ruthen, Jamie Wang, Ziad El Bakouny, Michele Waters, Chenlian Fu, Christopher Fong, Urvi A Shah, A Ari Hakimi, Justin Jee, Eileen White, Tobias Janowitz, Marcus D Goncalves, Ed Reznik.

Cancer cachexia is a wasting syndrome with outsized impact on morbidity and mortality. Neither the etiology of cachexia, nor its consequences on patient physiology and outcomes, are well-understood. Here, we repurposed longitudinal clinicogenomic data from 59,493 cancer patients to define episode-resolved trajectories of cachexia and linked them to serology, tumor genotypes, and clinical outcomes. Cachexia risk concentrated around periods of disease progression and associated with inferior outcomes in nearly all cancer types. Across cancers, cachectic episodes exhibited a consistent serologic signature characterized by low albumin and hemoglobin and high levels of liver enzymes. Numerous somatic tumor genotypes, including TP53 mutation across several diseases, were associated with elevated cachexia risk. Motivated by these observations, we developed a multivariate model to predict impending risk of cachexia in lung and colorectal cancer patients. Routine clinicogenomic data is therefore a powerful resource for discovery in cachexia and other cancer-associated pathophysiologies.

DOI: https://doi.org/10.1101/2025.09.29.25336906
Nature. 2025 Nov 19.

Tumour-reactive heterotypic CD8 T cell clusters from clinical samples.

Sofía Ibáñez-Molero, Johanna Veldman, Juan Simon Nieto, Joleen J H Traets, Austin George, Kelly Hoefakker, Anita Karomi, Rolf Harkes, Bram van den Broek, Su Min Pack, Liselotte Tas, Nils L Visser, Susan E van Hal-van Veen, Paula Alóndiga-Mérida, Maartje Alkemade, Iris M Seignette, Renaud Tissier, Marja Nieuwland, Martijn van Baalen, Joanna Poźniak, Erik Mul, Simon Tol, Sofia Stenqvist, Lisa M Nilsson, Jonas A Nilsson, John B A G Haanen, Winan J van Houdt, Daniel S Peeper.

Emerging evidence suggests a correlation between CD8+ T cell-tumour cell proximity and anti-tumour immune response1,2. However, it remains unclear whether these cells exist as functional clusters that can be isolated from clinical samples. Here, using conventional and imaging flow cytometry, we show that from 21 out of 21 human melanoma metastases, we could isolate heterotypic clusters, comprising CD8+ T cells interacting with one or more tumour cells and/or antigen-presenting cells (APCs). Single-cell RNA-sequencing analysis revealed that T cells from clusters were enriched for gene signatures associated with tumour reactivity and exhaustion. Clustered T cells exhibited increased TCR clonality indicative of expansion, whereas TCR-matched T cells showed more exhaustion and co-modulation when conjugated to APCs than when conjugated to tumour cells. T cells that were expanded from clusters ex vivo exerted on average ninefold increased killing activity towards autologous melanomas, which was accompanied by enhanced cytokine production. After adoptive cell transfer into mice, T cells from clusters showed improved patient-derived melanoma control, which was associated with increased T cell infiltration and activation. Together, these results demonstrate that tumour-reactive CD8+ T cells are enriched in functional clusters with tumour cells and/or APCs and that they can be isolated and expanded from clinical samples. Typically excluded by single-cell gating in flow cytometry, these distinct heterotypic T cell clusters are a valuable source to decipher functional tumour-immune cell interactions and may also be therapeutically explored.

DOI: https://doi.org/10.1038/s41586-025-09754-w
bioRxiv. 2025 Oct 02. pii: 2025.10.01.679805. [Epub ahead of print]

HNF1A is a novel BRD4 target and critical for BET-inhibitor response in pancreatic ductal adenocarcinoma.

Kennedy S Humphrey, Katherine J Crawford, Bharani Muppavarapu, Melanie M Mayberry, William Morris, Evan Torres, Mark D Long, Jianxin Wang, Erik S Knudsen, Agnieszka K Witkiewicz, Ethan V Abel.

Pancreatic ductal adenocarcinoma (PDAC) is an exceedingly lethal cancer that lacks actionable molecular drivers, limiting precision treatment options. We previously identified the transcription factor, HNF1A, as a novel driver of tumorigenesis and pancreatic cancer stem cell (PCSC) properties in PDAC; however, HNF1A-targeting modalities do not currently exist. Here we show that HNF1A is a direct target of the epigenetic reader protein, BRD4, and its expression is exquisitely sensitive to BET-inhibitors (BETi), which inhibit PDAC cell proliferation and block PCSC-properties in a panel of HNF1A-expressing cell lines and patient-derived xenograft cells. Remarkably, we report that the antineoplastic activity of BETi/BRD4 knockdown can be overcome by restoration of HNF1A expression, but not by re-expression of canonical BETi target MYC. RNA-sequencing analyses revealed that a subset of BETi-responsive transcripts is dependent on HNF1A expression, including receptor tyrosine kinases (RTKs), regulators and ligands. Consistent with these data, we found that HNF1A restoration rescued EGFR/ERBB3-signaling and the protective effects of HNF1A restoration could be overcome with EGFR-inhibitors. Furthermore, we found that expressions of HNF1A, BRD4, and ERBB3 were strongly correlated across PDAC patient samples using multispectral immunofluorescence, supporting a connection between these players in PDAC biology, and high expression of ERBB3 associated with better survival, supporting the clinical importance of this network in patient outcomes. These findings demonstrate that BETi can be used to ablate HNF1A expression and that the inhibition of HNF1A is critical for BETi activity, while supporting HNF1A as novel therapeutic target in PDAC.
Significance: This study demonstrates that the oncogenic transcription factor HNF1A is a direct target of BRD4, and that the ablation of HNF1A by BET-inhibitors is central to their antineoplastic activity in PDAC.

DOI: https://doi.org/10.1101/2025.10.01.679805
Nucleic Acids Res. 2025 Nov 18. pii: gkaf1223. [Epub ahead of print]

The Reactome Knowledgebase 2026.

Eliot Ragueneau, Chuqiao Gong, Pierre Sinquin, Cristoffer Sevilla, Deidre Beavers, Alexander Grentner, Johannes Griss, Gregory F J Hogue, Nancy T Li, Lisa Matthews, Bruce May, Marija Milacic, Helia Mohammadi, Robert Petryszak, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Krishna Tiwari, Joel Weiser, Adam Wright, Marc Gillespie, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio.

The Reactome Knowledgebase (https://reactome.org) is a freely accessible, expert-curated, open-source, and open-data resource that describes human biology in molecular detail. It spans normal physiology as well as disease mechanisms, including the impact of genetic variation and drug action. Reactome content is continuously expanded and revised, with automated workflows now monitoring retracted publications to maintain data integrity. To meet the needs of a growing user base, Reactome has launched a redesigned Angular-based interface with enhanced accessibility, modular architecture, and a hierarchy of visualization tools: ReacFoam for global pathway overviews, enhanced high-level diagrams for intuitive navigation, and redesigned entity level views (ELVs) enriched with chemical structures, animated protein models, and a new "compare mode" to contrast normal and disease states. New analysis tools support multi-omics integration and customizable visualizations. Recent innovations include the React-to-me chatbot for natural language interaction, community-driven tutorials, and an open Figma icon library. Reactome's sustainability and compliance with FAIR data principles were recently recognized with CoreTrustSeal certification and its designation as a Global Core Biodata and ELIXIR resource, reinforcing its role as a trusted global knowledgebase.

DOI: https://doi.org/10.1093/nar/gkaf1223
Nat Rev Drug Discov. 2025 Nov 19.

Triggering ferroptosis to tackle cancer.

Sarah Crunkhorn.

DOI: https://doi.org/10.1038/d41573-025-00189-6
Thorac Cancer. 2025 Nov;16(22): e70188

Revisiting Cancer Cachexia Staging: Introducing an "At Risk" Category Based on AWGC Components.

Tatsuma Sakaguchi, Keisuke Maeda, Makoto Yamasaki, Naoharu Mori.

  Cancer cachexia is a multifactorial syndrome characterized by progressive weight loss, muscle wasting, and systemic inflammation. Early identification of individuals at risk for cachexia is essential for timely intervention, yet a universally accepted definition of the "at risk" stage remains lacking. Building on the Asian Working Group for Cachexia (AWGC) framework, we propose that the presence of any one of the five components-low BMI (< 21 kg/m2), weight loss ≥ 2% over 3-6 months, anorexia, low handgrip strength, or elevated CRP levels-may indicate vulnerability to cachexia. We evaluated the prognostic value of this definition in a cohort of 364 patients with palliative cancer. The patients were categorized into three groups: non-cachectic, at risk, and cachectic. Survival analyses demonstrated significant differences across groups (p = 0.005), with the median overall survival not reached in the non-cachectic group, 381 days in the at-risk group, and 157 days in the cachectic group. While low BMI and weight loss were not associated with survival in patients with edema, they became evident in those without edema (HR = 1.54 and 1.58), highlighting the confounding role of fluid retention in anthropometric assessment. Anorexia, low handgrip strength, and elevated CRP levels independently predicted poor prognosis in both full and non-edematous cohorts. These findings support the clinical relevance of an "at risk" category based on AWGC components, especially in patients without edema. This simple and pragmatic definition may facilitate the early identification of patients who could benefit from supportive interventions before cachexia becomes refractory.

Keywords:  Asian Working Group for Cachexia; at risk of cachexia; cancer cachexia; precachexia

DOI:  https://doi.org/10.1111/1759-7714.70188
Int J Obes (Lond). 2025 Nov 17.

The Physiology Of the WEight Reduced State (POWERS) study: assessing energy balance.

POWERS Consortium

BACKGROUND/OBJECTIVES: We provide the rationale for and description of energy balance measures (i.e., energy intake and energy expenditure) in The Physiology Of the WEight Reduced State (POWERS) study which aims to understand the contribution of the many factors that influence weight regain following behavioral weight loss.
METHODS: The primary dependent variable is weight regain over 1 year following a 7% or greater supervised weight loss. The balance between energy intake and expenditure is the primary determinant of weight regain. Healthy adults (target n = 205), aged 25- < 60 years, with body mass index (BMI) 30- < 40 kg/m2 are being recruited. Energy intake and expenditure phenotypes are measured prior to weight loss (baseline, BL), immediately following weight loss (T0), and then four (T4) and 12 months (T12) after weight loss. Weight stability is required before BL and T0 measurement periods. Weight change at T12 from T0 is the primary outcome variable. Energy intake is measured with serial doubly labeled water (DLW) measurements combined with dual x-ray absorptiometry (DXA) to assess changes in fat and lean mass; DLW is also used to measure twenty-four-hour energy expenditure (TEE). Components of TEE including resting energy expenditure (REE) and non-resting and activity energy expenditure (NREE and AEE), as well as skeletal muscle chemomechanical efficiency and grip strength are assessed. Self-reported dietary intake is assessed with interviewer-administered multiple-pass 24-hour food recalls.
DISCUSSION: This manuscript describes the rationale for the methods chosen to assess energy balance and the analytical methods employed to normalize and express data in the setting of changes in body weight and composition immediately following behavioral weight loss and thereafter at 4- and 12-months post-weight loss.

DOI: https://doi.org/10.1038/s41366-025-01935-x
Cancer Res. 2025 Nov 19.

Estrogen Production in Pancreatic Cancer Shapes a Tumor Suppressive Stromal Microenvironment.

Paul Manoukian, Deni M van Schie, Anne-Sophie van Schelt, Nienke P M Wassenaar, Mark P G Dings, Marjolein F Lansbergen, Cynthia Waasdorp, Rodrigo Leite de Oliveira, Wjera V Wickenhagen, Annemieke C Heijboer, Jan Koster, Danny A Zwijnenburg, Arantza Farina-Sarasqueta, Geert Kazemier, Johanna W Wilmink, Jan Paul Medema, Hanneke W M van Laarhoven, Maarten F Bijlsma.

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related death due to a lack of effective therapeutic interventions. PDAC tumors are highly fibrotic, and stromal abundance is hypothesized to contribute to patient outcomes. However, stromal fibroblasts can be tumor-promoting and -restraining, which could explain the disappointing clinical results of stromal targeting therapies. Here, we observed that serum levels of stromal biomarkers associated with favorable outcomes were significantly higher in female PDAC patients compared to male patients. This was supported by in silico estimates of stromal abundance across solid cancers, as well as magnetic resonance elastography and tissue staining which revealed that female PDAC patients had stiffer tumor tissue. Gene expression analysis revealed that estrogen signaling instructs a stromal fibroblast phenotype that is associated with relatively indolent molecular subtypes and a more favorable prognosis, which is maintained by stromal expression of C-type lectin CLEC3B. Remarkably, estrogens were detected intra-tumorally, and pancreatic cancer cells expressed key enzymes for estrogen synthesis. Estrogen production in PDAC was fueled by the catabolism of stroma-derived branched chain amino acids, which ultimately resulted in the production of steroid hormone precursors. Together, these data reveal important hormone-driven factors that limit tumor progression by reprogramming the tumor microenvironment and provide leads for therapy development for PDAC.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-4707
Biochim Biophys Acta Mol Cell Biol Lipids. 2025 Nov 16. pii: S1388-1981(25)00114-3. [Epub ahead of print] 159706

Subcellular cartography of the phosphoinositide multiverse.

Morgan M C Ricci, Claire C Weckerly, Gerald R V Hammond.

  Phosphoinositides (PPIn) are low-abundance phospholipids that define membrane identity and direct compartment-specific signaling across eukaryotic cells. Marking fifty years since Michell's seminal 1975 review, we re-evaluate how the subcellular localization of these lipids informs their function. Using a historical and mechanistic framework, we survey evidence for the steady-state distribution of all eight PPIn species and their key precursor, phosphatidic acid, emphasizing live-cell biosensor studies and kinase localization. We conclude that PI(4,5)P₂ and PIP₃ signaling remain largely confined to the plasma membrane, whereas PI4P and PI3P occupy distinct but complementary domains of the Golgi and endosomal systems, and PI(3,5)P₂ marks specialized late endosomal compartments. Together, these patterns reveal PPIn as spatial rather than purely temporal signaling molecules-an ATP-derived currency maintaining the ordered heterogeneity of eukaryotic membranes. Understanding how these pathways self-regulate will define the next generation of phosphoinositide biology.

Keywords:  Inositol lipids; Phosphoinositides

DOI:  https://doi.org/10.1016/j.bbalip.2025.159706
bioRxiv. 2025 Oct 04. pii: 2025.10.03.680304. [Epub ahead of print]

Membrane Remodeling by the Collective Action of Caveolin-1.

Korbinian Liebl, Gregory A Voth.

Caveolin-1 proteins scaffold 50-100nm large invaginations in the plasma membrane to mediate critical cellular processes. As revealed recently by cryo-electron microscopy, several caveolin-1 protomers can fold into a disk-like structure that embeds in the cytoplasmic leaflet. This 8S complex represents a basal component to drive membrane curvature via higher-order interactions. The biophysical mechanisms behind the membrane remodeling, however, have remained elusive. To address this shortcoming, we have developed a new bottom-up coarse-grained model to overcome the substantial computational limitations for this large system. During simulations with the coarse-grained model, the complexes increasingly coordinate as partially mediated by attractive electrostatic interactions between scaffolding domains. The coordination of complexes strongly correlates with membrane protrusion, as approaching complexes amplify localized stress in the exoplasmic leaflet. Thus, proximity of two CAV1-8S complexes induces dynamic curvature generation that can facilitate access for signaling partners. This mechanism is further explored in clusters of multiple CAV1-8S complexes that form large-scale membrane invaginations.

DOI: https://doi.org/10.1101/2025.10.03.680304
bioRxiv. 2025 Oct 16. pii: 2025.10.01.679814. [Epub ahead of print]

Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer.

Ying Liu, Ting Miao, Alice Wang, Ezequiel Dantas, Ah-Ram Kim, Zhongjie Zhang, Xiaomei Sun, Richard Binari, John M Asara, Yanhui Hu, Marcus D Goncalves, Tobias Janowitz, Norbert Perrimon.

Paraneoplastic syndromes arise when tumor-derived cytokines reprogram distant organs. Although mediators such as Interleukin-6 have been implicated, how these signals impair host organ function remains incompletely defined. Here, we identify a cytokine-lipid axis that drives hepatic autophagy dysfunction. Specifically, in Drosophila , the gut tumor-derived interleukin-like cytokine Upd3 induces the expression of the triglyceride lipase CG5SCC , which we named " cancer-associated lipid mobilizer ( calm )", and the ceramide synthase schlank in the fat body. This upregulation rewires fat body lipid metabolism, resulting in an autophagic-flux blockade. Genetic reduction of either CG5SCC or schlank restores organelle homeostasis and mitigates paraneoplastic phenotypes. This mechanism is conserved in mammals: in mice, IL-6 upregulates the lipoprotein lipase Lpl and ceramide synthases which in turn trigger a hepatic autophagy-flux blockade; in humans, hepatic LPL and ceramide synthases expression correlates with poorer survival in hepatocellular carcinoma. Our findings position hepatic lipid metabolism rewiring, especially ceramide synthesis as a critical, conserved node coupling systemic inflammation to organelle dysfunction, and suggest this pathway as a possible therapeutic entry point for cancer-associated liver disorders.

DOI: https://doi.org/10.1101/2025.10.01.679814
Nature. 2025 Nov 19.

ZAK activation at the collided ribosome.

Vienna L Huso, Shuangshuang Niu, Marco A Catipovic, James A Saba, Timo Denk, Eugene Park, Jingdong Cheng, Otto Berninghausen, Thomas Becker, Rachel Green, Roland Beckmann.

Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK1. Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK-ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK-ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of the SAM domain in regulating kinase activity on and off the ribosome, with some mutants bypassing the ribosome requirement for ZAK activation. Collectively, our data provide a mechanistic blueprint of the kinase activity of ZAK at the collided ribosome interface.

DOI: https://doi.org/10.1038/s41586-025-09772-8
Mol Cell. 2025 Nov 19. pii: S1097-2765(25)00867-6. [Epub ahead of print]

HSP90 buffers deleterious genetic variations in BRCA1.

Brant Gracia, Xing-Han Zhang, Patricia Montes, Tin Chanh Pham, Min Huang, Junjie Chen, Georgios Ioannis Karras.

  Protein-folding chaperone heat shock protein 90 (HSP90) buffers genetic variation in diverse organisms, but the clinical significance of HSP90 buffering in human disease remains unclear. Here, we show that HSP90 buffers mutations in the BRCT domain of BRCA1. HSP90-buffered BRCA1 mutations result in protein variants that retain interactions with partner proteins and strongly rely on HSP90 for protein stability and function in cell survival. Moreover, HSP90-buffered BRCA1 variants confer poly (ADP-ribose) polymerase (PARP) inhibitor resistance in cancer cells. Low-level HSP90 inhibition overcomes this resistance, revealing a cryptic and mutant-specific HSP90-contingent synthetic lethality. Furthermore, by stabilizing metastable variants across the entirety of the BRCT domain, HSP90 reduces the clinical severity of BRCA1 mutations, allowing them to accumulate in populations. We estimate that HSP90 buffers 18% of known human BRCA1-BRCT missense mutations. Our work extends the clinical significance of HSP90 buffering to a prevalent class of variations in BRCA1, pioneering its importance in therapy resistance and cancer predisposition.

Keywords:  BRCA1; HSP90; HSP90 inhibition; PARP inhibition; breast cancer; mutational buffer; polytherapy; protein folding; structural mutations; synthetic lethality

DOI:  https://doi.org/10.1016/j.molcel.2025.10.026
Trends Biochem Sci. 2025 Nov 19. pii: S0968-0004(25)00244-0. [Epub ahead of print]

Autophagy regulation by phase separation, avidity, and wetting.

Riccardo Babic, Joachim Brenneisen, Florian Wilfling, Claudine Kraft.

  Autophagy enables cells to selectively degrade a wide range of macromolecules, and how this process achieves spatial precision within the densely packed cytosol is an active area of investigation. Recent advances suggest that phase separation provides a crucial organizational framework that converts autophagy into a spatiotemporally coordinated and self-organizing process. Biomolecular condensates formed by phase separation can create high-avidity binding platforms between autophagy receptors, scaffold proteins, and the cargo that stabilize transient molecular contacts. The formation of such condensates specifies the cargo and initiates autophagosome formation at defined cellular locations. Simultaneously, physical properties such as wetting govern how condensates interact with membranes, and thus influence engulfment efficiency. Viewing autophagy through the lens of condensate physics not only explains its molecular specificity but also highlights new therapeutic opportunities.

Keywords:  autophagy; autophagy-based therapeutics; avidity; biomolecular condensates; phase separation; wetting

DOI:  https://doi.org/10.1016/j.tibs.2025.10.003
Genome Biol. 2025 Nov 17. 26(1): 390

ricePSP: a database of rice phase separation-associated proteins.

Runxin Gao, Minrong Guo, Shiping Luan, Weizhi Ouyang, Xingwang Li.

  Multivalent interactions between proteins with intrinsically disordered regions or prion-like domains can drive liquid-liquid phase separation (LLPS) and form membraneless condensates essential for diverse cellular functions. Here, we predict phase separation scores for all annotated rice proteins and present ricePSP ( https://ricepsp.github.io/ ), a database of phase separation-associated proteins. AlphaFold structural predictions further validate the phase separation potential of these proteins. As a proof of concept, we apply ricePSP to identify flowering-related phase separation proteins, revealing insights into how LLPS may regulate flowering. Collectively, ricePSP provides a valuable resource for studying crop phase separation proteins and LLPS-related mechanisms in crop trait regulation.

Keywords:  Condensate; Flowering; IDR; Liquid–liquid phase separation; Phase separation-associated protein; Rice

DOI:  https://doi.org/10.1186/s13059-025-03842-w
Cancer Res. 2025 Nov 17.

Mitochondrial Transfer Rescues Respiration to Support De Novo Pyrimidine Biosynthesis and Tumor Progression.

Maria Dubisova, Klara Bohacova, Zuzana Nahacka, Daniel Kraus, Jaromir Novak, Sarka Dvorakova, Petra Brisudova, Natalie Danesova, Saba Selvi, Mariia Hrysiuk, Berwini B Endaya, Panagiotis Botsios, Dan-Diem Thi Le, Monika Novotna, Sona Vodenkova, Jaroslav Truksa, Karel Chalupsky, Krystof Klima, Jan Prochazka, Radislav Sedlacek, Francesco Mengarelli, Patrick Orlando, Luca Tiano, Stepana Boukalova, Michael V Berridge, Renata Zobalova, Jiri Neuzil.

Cancer cells with severe defects in mitochondrial DNA (mtDNA) can import mitochondria via horizontal mitochondrial transfer (HMT) to restore respiration. Mitochondrial respiration is necessary for the activity of dihydroorotate dehydrogenase (DHODH), an enzyme of the inner mitochondrial membrane that catalyzes the fourth step of de novo pyrimidine synthesis. Here, we investigated the role of de novo synthesis of pyrimidines in driving tumor growth in mtDNA-deficient (ρ0) cells. While ρ0 cells grafted in mice readily acquired mtDNA, this process was delayed in cells transfected with alternative oxidase (AOX), which combines the functions of mitochondrial respiratory complexes III and IV. The ρ0 AOX cells were glycolytic but maintained normal DHODH activity and pyrimidine production. Deletion of DHODH in a panel of tumor cells completely blocked or delayed tumor growth. The grafted ρ0 cells rapidly recruited tumor-promoting/stabilizing cells of the innate immune system, including pro-tumor M2 macrophages, neutrophils, eosinophils, and mesenchymal stromal cells (MSCs). The ρ0 cells recruited MSCs early after grafting, which were potential mitochondrial donors. Grafting MSCs together with ρ0 cancer cells into mice resulted in mitochondrial transfer from MSCs to cancer cells. Overall, these findings indicate that cancer cells with compromised mitochondrial function readily acquire mtDNA from other cells in the tumor microenvironment to restore DHODH-dependent respiration and de novo pyrimidine synthesis. The inhibition of tumor growth induced by blocking DHODH supports targeting pyrimidine synthesis as a potential widely applicable therapeutic approach.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-0737
Nucleic Acids Res. 2025 Nov 17. pii: gkaf1265. [Epub ahead of print]

Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale.

Mario Picciani, Armin Soleymaniniya, Julian Müller, Amirhossein Sakhteman, Konstantinos Tzanakis, Judith Bernett, Elias Kahl, Firas Hamood, Johannes Kersting, Mohsen Pourjam, Luis Augusto Eijy Nagai, Markus List, Bernhard Kuster, Matthew The, Mathias Wilhelm.

Proteomic and phenotypic cell sensitivity datasets are increasingly important for understanding chemoproteomics and the underlying drug mechanisms of action. Yet, integrating such heterogeneous datasets remains challenging due to inconsistent annotations, incompatible IDs, and variable data processing methods. Here, a major update to ProteomicsDB (https://www.proteomicsdb.org) is presented that combines over 1300 proteomic and 1000 transcriptomic profiles with phenotypic cell sensitivity data across >1500 human cancer cell lines and 1470 drugs. Harmonizing cell line and drug names and applying a standardized normalization and refitting pipeline for dose-response curves enables consistent, statistically robust analysis across studies. Three new graphical user interfaces support interactive exploration of cell sensitivity data, exploring the protein targets and dose-resolved changes in protein expression in the presence of a drug, and comparing the expression profiles of cell lines. With this update, ProteomicsDB is strengthening its future role as a central hub for proteomics and multi-omics, providing researchers with a unified framework to explore phenotypic cell sensitivity in combination with dose-resolved expression proteomics at the molecular level, supporting biomarker discovery, drug repurposing, and precision medicine applications.

DOI: https://doi.org/10.1093/nar/gkaf1265
Nat Methods. 2025 Nov 20.

NimbusImage: a cloud-computing platform for image analysis.

Zijian Niu, Thibault Bruyère, David Manthey, Jingxin Li, Aoife O'Farrell, Arjun Raj.

DOI: https://doi.org/10.1038/s41592-025-02942-6
Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2504718122

Engineering a spatiotemporal macrophage circuit via STING phase separation to override immune suppression in pancreatic cancer.

Xue Yang, Yinlu Wang, Jiaxin Zhou, Siyu Li, Jin Ye, Yu Sun, Mengning He, Kai Fan, Zixin Chen, Fangzheng Tian, Ben Zhao, Jianqiong Zhang, Jinbing Xie, Zebin Xiao, Xiaoyuan Chen, Shenghong Ju.

  Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, largely due to its highly immunosuppressive tumor microenvironment (TME), which fuels metastasis and resistance to immunotherapy. Through comprehensive analysis of single-cell RNA sequencing datasets, we identified multiple heterogeneous tumor-associated macrophage (TAMs) subpopulations as key regulators of PDAC progression, which coexpress MRC1 and exert their effects by actively suppressing antitumor immune responses. To overcome this barrier, we developed a spatiotemporal macrophage reprogramming platform that leverages STING phase separation to reprogram TAM plasticity and reshape the immune landscape. This system, MRC1-targeting peptide-M@BLZ945 (PMMB), integrates a colony-stimulating factor 1 receptor (CSF-1R) inhibitor and a STING agonist within a macrophage-mimetic nanostructure, enabling sequential, controlled reprogramming of TAMs. By leveraging STING phase separation, PMMB stabilizes TAMs in an antitumor CD80+ phenotype while preventing excessive inflammation, achieving durable immune activation. In preclinical models, PMMB not only suppresses both primary and metastatic PDAC but also enhances CD8+ T cell infiltration, reinvigorates anti-PD-1 therapy responses, and mitigates immune exhaustion. These findings establish spatiotemporal macrophage circuit engineering via STING phase separation as a cross-scale strategy to override PDAC's immune barriers and drive next-generation macrophage-targeted immunotherapy. This study paves the way for rationally designed, precision macrophage modulation strategies in solid tumors.

Keywords:  PDAC; biomimetic; tumor associated macrophages; tumor metastasis

DOI:  https://doi.org/10.1073/pnas.2504718122
J Clin Invest. 2025 Nov 17. pii: e193370. [Epub ahead of print]135(22):

Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models.

Jie Zhao, Xinghao Li, Xinyu Li, Pengfei Ren, Yilan Wu, Hao Gong, Lijian Wu, Junran Huang, Saisai Wang, Ziwei Guo, Mo Chen, Zexian Zeng, Deng Pan.

  Macrophage-mediated phagocytosis plays a critical role in the elimination of cancer cells and shaping antitumor immunity. However, the tumor-intrinsic pathways that regulate cancer cell sensitivity to macrophage-mediated phagocytosis remain poorly defined. In this study, we performed a genome-wide CRISPR screen in murine pancreatic cancer cells cocultured with primary macrophages and identified that disruption of the tumor-intrinsic pyrimidine synthesis pathway enhances phagocytosis. Mechanistically, we discovered that macrophages inhibit the pyrimidine salvage pathway in tumor cells by upregulating Upp1-mediated uridine degradation through cytokines TNF-α and IL-1. This shift increased tumor cells' reliance on de novo pyrimidine synthesis. As a result, tumor cells with impaired de novo pyrimidine synthesis showed depleted UMP and displayed enhanced exposure of phosphatidylserine (PtdSer), a major "eat-me" signal, thereby promoting macrophage-mediated phagocytosis. In multiple pancreatic cancer models, Cad-deficient tumors exhibited markedly reduced tumor burden with increased levels of phagocytosis by macrophages. Importantly, the Cad-mediated suppression of pancreatic cancer was dependent on TAMs and cytokines IL-1 and TNF-α. Pharmacological inhibition of DHODH, which blocks de novo pyrimidine synthesis, similarly decreased tumor burden with enhanced phagocytosis in pancreatic cancer models. These findings highlight the critical role of the tumor-intrinsic pyrimidine synthesis pathway in modulating macrophage-mediated antitumor immunity, with potential therapeutic implications.

Keywords:  Cancer immunotherapy; Immunology; Innate immunity; Macrophages; Metabolism; Oncology

DOI:  https://doi.org/10.1172/JCI193370
Sci Adv. 2025 Nov 21. 11(47): eaeb5810

Targeting cancer-associated fibroblasts for real-time intraoperative tumor identification with a spray-on fluorescent probe.

Riley J Deutsch-Williams, Yuxuan Xie, Zachary Rabinowitz, Marie Goemans, Pratyaksha Wirapati, Claudio Vinegoni, Jonathan Ct Carlson, Mikael Pittet, Ralph Weissleder.

Surgical tumor resection is often the only curative option for the nearly 20 million newly diagnosed patients with cancer every year. Fluorescence-guided surgery techniques are being developed in an effort to improve margin detection and surgical resection outcomes, with several systemically administered imaging agents having gained clinical approval. However, it has been challenging to overcome limited margin contrast with current approaches and to navigate procedural complexities of intravenous contrast delivery. We hypothesized that "spray-on probes" with specificity for fibroblast activation protein alpha in peritumoral fibroblasts could improve fluorescence-guided surgery, detect smaller tumors, improve imaging accuracy, and reduce the amount of times a patient is hospitalized. We show that this strategy increases achievable tumor margin contrast by 5- to 10-fold and detects even microscopic cancer deposits. These improvements have the potential to transform patient outcomes by enabling more accurate cancer surgeries, reducing the number of follow-up surgeries, and leading to personalized treatment plans.

DOI: https://doi.org/10.1126/sciadv.aeb5810
ACS Chem Biol. 2025 Nov 18.

Enrichment-Free, Targeted Covalent Drug Discovery in Live Cells.

Kevin D Dong, Qing Yu, Ka Yang, Bertrand J Wong, Hong Yue, Sipei Fu, Rebecca L Whitehouse, Eric S Fischer, Steven P Gygi.

Live-cell activity-based protein profiling (ABPP) with mass spectrometry enables the proteome-wide quantification of compound reactivity, yet resulting datasets often suffer from low data completeness for high-priority targets and do not give users the option to measure compound-induced protein changes within the same screening assay. To address these limitations, we developed CysDig, an enrichment-free chemoproteomics platform for the targeted covalent drug discovery in live cells. Using the CysDig platform, we screened 288 cysteine-reactive electrophiles against 300 functionally annotated cysteine sites. From this screen, we identified covalent binders that liganded dozens of sites and identified multiple instances of acute compound-induced protein degradation of ACAT1. We validated a molecule that engaged with the active site of HECT E3 ligase HUWE1 and showed that chemical inhibition stabilized known substrates. Together, these findings establish CysDig as a powerful, targeted platform for live-cell covalent drug screening, expanding the current repertoire of available approaches for ligand discovery in live cells.

DOI: https://doi.org/10.1021/acschembio.5c00581
Nucleic Acids Res. 2025 Nov 18. pii: gkaf1126. [Epub ahead of print]

OmniPath: integrated knowledgebase for multi-omics analysis.

Dénes Türei, Jonathan Schaul, Nicolàs Palacio-Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, Elif Çevrim, Macabe Daley, Melih Darcan, Daniel Dimitrov, Tunca Doğan, Daniel Domingo-Fernández, Aurelien Dugourd, Attila Gábor, Lejla Gul, Benjamin A Hall, Charles Tapley Hoyt, Olga Ivanova, Michal Klein, Toby Lawrence, Diego Mañanes, Dezső Módos, Sophia Müller-Dott, Márton Ölbei, Christina Schmidt, Bünyamin Şen, Fabian J Theis, Atabey Ünlü, Erva Ulusoy, Alberto Valdeolivas, Tamás Korcsmáros, Julio Saez-Rodriguez.

Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath (https://omnipathdb.org/), a database combining diverse molecular knowledge from 168 resources. It covers causal protein-protein, gene regulatory, microRNA, and enzyme-post-translational modification interactions, cell-cell communication, protein complexes, and information about the function, localization, structure, and many other aspects of biomolecules. It prioritizes literature curated data, and complements it with predictions and large scale databases. To enable interactive browsing of this large corpus of knowledge, we developed OmniPath Explorer, which also includes a large language model agent that has direct access to the database. Python and R/Bioconductor client packages and a Cytoscape plugin create easy access to customized prior knowledge for omics analysis environments, such as scverse. OmniPath can be broadly used for the analysis of bulk, single-cell, and spatial multi-omics data, especially for mechanistic and causal modeling.

DOI: https://doi.org/10.1093/nar/gkaf1126
Nat Protoc. 2025 Nov 19.

Multiplexed genetic tags for electron and fluorescence microscopy.

Oleksandr Berezin, Alberto Piovesan, Roman Graf, Eleni Samara, Felix Sigmund, Gil Gregor Westmeyer.

This protocol provides comprehensive guidance for researchers, including those with limited electron microscopy (EM) experience, on the effective use of genetically encoded, multichannel EMcapsulin reporters in both fluorescence microscopy and EM workflows. EMcapsulins are a set of modular gene reporters that manifest as distinct shapes in EM when expressed in cell culture or model organisms. This protocol encompasses detailed instructions for labeling cells or proteins of interest with fluorescent EMcapsulins, along with biochemical quality control measures. Researchers may also adapt the protocol to develop custom EMcapsulin constructs tailored to their specific experimental requirements.

DOI: https://doi.org/10.1038/s41596-025-01260-7
Geroscience. 2025 Nov 19.

Redefining the concept of erythrocyte senescence: is eryptosis fundamentally different from erythrocyte senescence.

Anton Tkachenko, Ondrej Havranek, Florian Lang, Karl S Lang, Thomas Wieder.

  In response to acute stress, nucleated cells undergo various regulated cell deaths (RCDs). Alternatively and in the long run, they permanently stop proliferating with the parallel acquisition of apoptosis resistance and the senescence-associated secretory phenotype. This particular long-term stress response is referred to as cellular senescence. Terminally differentiated, anucleate red blood cells (RBCs) cannot proliferate anymore and are incapable of synthesizing proteins. RBC senescence is therefore defined by phagocytosis-promoting age-related changes, such as band 3 protein-derived senescent erythrocyte-specific antigen (SESA)-mediated binding of autologous antibodies, desialylated glycoproteins, CD47 loss, and glycophorin depletion. Additionally, RBCs can undergo eryptosis, a Ca2+-driven RCD. Here, we consider the intracellular signals that drive RBC senescence and eryptosis to underscore how these pathways are intertwined. Our findings suggest that RBC senescence and eryptosis are distinct processes with their differences primarily lying in how fast senescent and eryptotic RBCs are removed from the circulation. Severe damage to RBCs promotes intense Ca2+ influx, oxidative and nitrosative stress, as well as activation of caspase-3. This eventually leads to phosphatidylserine externalization and eryptosis. Phosphatidylserine externalization, in turn, ensures swift erythrophagocytosis of eryptotic RBCs thus preventing hemolysis. On the other hand, suberyptotic stress stimuli are not sufficient to trigger rapid cell death. However, they mediate the gradual and inevitable accumulation of senescence-associated injuries. Clearance of senescent RBCs with low-level phosphatidylserine exposure is slow-paced, and mature RBCs possess mechanisms to eradicate senescence markers that tag cells for phagocytosis to extend their lifespan (e.g., generation of vesicles). In this review, we highlight the physiological significance of RBC senescence and eryptosis, and provide practical guidelines to distinguish them thus avoiding misinterpretation of experimental data.

Keywords:  Eryptosis; Phosphatidylserine exposure; Red blood cells; Regulated cell death; Senescence

DOI:  https://doi.org/10.1007/s11357-025-02010-z