bims-cagime 2025-08-10 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–08–10
43 papers selected by
Kıvanç Görgülü, Technical University of Munich

Senescent cell heterogeneity and responses to senolytic treatment are related to cell cycle status during senescence induction.
A cholesterol-dependent switch controls organ-specific metastasis in pancreatic cancer.
Cancer therapy and cachexia.
Lysosomal membrane homeostasis and its importance in physiology and disease.
Stromal senescence contributes to age-related increases in cancer.
Cooperativity in septin polymerization is tunable by ionic strength and membrane adsorption.
Saturated lipid stress attenuates mitochondrial genome synthesis in human cells.
In vivo screening reveals cell-intrinsic mediators of solid tumor resistance to CAR T cell-therapy.
Plasma membrane asymmetry and lipid homeostasis: general discussion.
Investigation of simvastatin and fluvastatin permeation across cell membrane models using molecular dynamics simulations.
Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove.
Vagal blockade of the brain-liver axis deters cancer-associated cachexia.
Baseline expression of c-Myc defines the tissue specificity of oncogenic K-Ras.
Unravelling cellular interactions using flow cytometry.
Netrin-1 promotes pancreatic tumorigenesis and innervation through NEO1.
TGF-β1-mediated downregulation of L1CAM in pancreatic ductal adenocarcinoma drives upregulation of collagen 17A1 and MMP2, facilitating tumor invasiveness and metastasis.
Two Shots on Goal: Combination of RAS Inhibition and Immunotherapy Drives Long-term Remission in Pancreatic Cancer.
Pancreatic Cancer Progression Involves Increased Lysyl Oxidase-Mediated Collagen Cross-Links as Part of the Desmoplastic Reaction.
Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns.
Autophagy activator AA-20 improves proteostasis and extends Caenorhabditis elegans lifespan.
Integrated real-time imaging of executioner caspase dynamics, apoptosis-induced proliferation, and immunogenic cell death using a stable fluorescent reporter platform.
The Lipid Interactome: An interactive and open access platform for exploring cellular lipid-protein interactomes.
The intrinsically disordered regions of organellophagy receptors are interchangeable and control organelle fragmentation, ER-phagy and mitophagy flux.
Targeting Ferroptosis to Eliminate Senescent Cells: Mechanisms and Therapeutic Potential.
Ultra-high-scale cytometry-based cellular interaction mapping.
Publisher Correction: NINJ1 regulates plasma membrane fragility under mechanical strain.
Activation of PP2A-B56α leads to aberrant EGFR signaling and proliferative phenotypes in PDAC.
NSD2 inhibitors rewire chromatin to treat lung and pancreatic cancers.
NADH reductive stress drives metabolic reprogramming.
Capillary constrictions prime cancer cell tumorigenicity through PIEZO1.
Emerging roles of lipid transfer protein dimerization.
ALDH1A3 promotes aggressive basal-like pancreatic cancer through an AP-1/RUNX2 enhancer network.
Hallmarks and mechanisms of cellular senescence in aging and disease.
A breathless brake on ferroptosis.
Fibrin as the mediator of tumor cell interaction with platelets.
Classically activated macrophages undergo functionally significant nucleotide metabolism remodelling driven by nitric oxide.
Using the Cancer Epitope Database and Analysis Resource (CEDAR).
Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues.
NAC controls nascent chain fate through tunnel sensing and chaperone action.
The Plasma Membrane may Serve as a Drug Depot to Drive the Extreme Potency of Fentanyl.
CytoAnalyst web platform facilitates comprehensive single cell RNA sequencing analysis.
Morphological map of under- and overexpression of genes in human cells.
Gut microbiota-derived formate exacerbates pulmonary metastasis in cancer.

Aging (Albany NY). 2025 Aug 07. 17

Senescent cell heterogeneity and responses to senolytic treatment are related to cell cycle status during senescence induction.

Francesco Neri, Shuyuan Zheng, Mark A Watson, Pierre-Yves Desprez, Akos A Gerencser, Judith Campisi, Denis Wirtz, Pei-Hsun Wu, Birgit Schilling.

  Cellular senescence has been strongly linked to aging and age-related diseases. It is well established that the phenotype of senescent cells is highly heterogeneous and influenced by their cell type and senescence-inducing stimulus. Recent single-cell RNA-sequencing studies identified heterogeneity within senescent cell populations. However, proof of functional differences between such subpopulations is lacking. To identify functionally distinct senescent cell subpopulations, we employed high-content image analysis to measure senescence marker expression in primary human endothelial cells and fibroblasts. We found that G2-arrested senescent cells feature higher senescence marker expression than G1-arrested senescent cells. To investigate functional differences, we compared IL-6 secretion and response to ABT263 senolytic treatment in G1 and G2 senescent cells. We determined that G2-arrested senescent cells secrete more IL-6 and are more sensitive to ABT263 than G1-arrested cells. We hypothesize that cell cycle dependent DNA content is a key contributor to the heterogeneity within senescent cell populations. This study demonstrates the existence of functionally distinct senescent subpopulations even in culture. This data provides the first evidence of selective cell response to senolytic treatment among senescent cell subpopulations. Overall, this study emphasizes the importance of considering the senescent cell heterogeneity in the development of future senolytic therapies.

Keywords:  cell cycle; cellular senescence; heterogeneity; imaging; senolytics

DOI:  https://doi.org/10.18632/aging.206299
Dev Cell. 2025 Aug 04. pii: S1534-5807(25)00439-3. [Epub ahead of print]60(15): 2029-2031

A cholesterol-dependent switch controls organ-specific metastasis in pancreatic cancer.

Julie Haenlin, Almut Schulze.

As different organs offer distinct chemical microenvironments, cancer cells require unique metabolic adaptation to colonize distant sites. In a recent issue of Nature, Rademaker et al. identify PCSK9 as a predictive factor for metastatic colonization of different organs, showing adaptation of cancer cells to different environments by regulating cholesterol metabolism.

DOI: https://doi.org/10.1016/j.devcel.2025.07.001
J Clin Invest. 2025 Aug 01. pii: e191934. [Epub ahead of print]135(15):

Cancer therapy and cachexia.

Tuba Mansoor Thakir, Alice R Wang, Amanda R Decker-Farrell, Miriam Ferrer, Rohini N Guin, Sam Kleeman, Llewelyn Levett, Xiang Zhao, Tobias Janowitz.

A central challenge in cancer therapy is the effective delivery of anticancer treatments while minimizing adverse effects on patient health. The potential dual impact of therapy is clearly illustrated in cancer-associated cachexia, a multifactorial syndrome characterized by involuntary weight loss, systemic inflammation, metabolic dysregulation, and behavioral alterations such as anorexia and apathy. While cachexia research often focuses on tumor-driven mechanisms, the literature indicates that cancer therapies themselves, particularly chemotherapies and targeted treatments, can initiate or exacerbate the biological pathways driving this syndrome. Here, we explore how therapeutic interventions intersect with the pathophysiology of cachexia, focusing on key organ systems including muscle, adipose tissue, liver, heart, and brain. We highlight examples such as therapy-induced upregulation of IL-6 and growth-differentiation factor 15, both contributing to reduced nutrient intake and a negative energy balance via brain-specific mechanisms. At the level of nutrient release and organ atrophy, chemotherapies also converge with cancer progression, for example, activating NF-κB in muscle and PKA/CREB signaling in adipose tissue. By examining how treatment timing and modality align with the natural trajectory of cancer cachexia, we underscore the importance of incorporating physiological endpoints alongside tumor-centric metrics in clinical trials. Such integrative approaches may better capture therapeutic efficacy while preserving patient well-being.

DOI: https://doi.org/10.1172/JCI191934
Nat Rev Mol Cell Biol. 2025 Aug 04.

Lysosomal membrane homeostasis and its importance in physiology and disease.

Maja Radulovic, Chonglin Yang, Harald Stenmark.

Lysosomes are membranous organelles that are crucial for cell function and organ physiology. Serving as the terminal stations of the endocytic pathway, lysosomes have fundamental roles in the degradation of endogenous and exogenous macromolecules and particles as well as damaged or superfluous organelles. Moreover, the lysosomal membrane is a docking and activation platform for several signalling components, including mTOR complex 1 (mTORC1), which orchestrates metabolic signalling in the cell. The integrity of their membrane is crucial for lysosomes to function as hubs for the regulation of cell metabolism. Various agents, including pathogens, nanoparticles and drugs, can compromise lysosomal membrane integrity. Membrane permeabilization causes leakage of proteases and cations into the cytosol, which can induce cell death pathways and innate immunity signalling. Multiple pathways repair damaged lysosomes, and severely damaged lysosomes are degraded by an autophagic process, lysophagy. Moreover, lysosome damage activates transcriptional programmes that orchestrate lysosome biogenesis to replenish the cellular lysosome pool. In this Review, we discuss recent insights into the mechanisms that ensure the maintenance of lysosomal membrane homeostasis, including novel mechanisms of lysosomal membrane repair and the interplay between lysosome damage, repair, lysophagy and lysosome biogenesis. We highlight the importance of lysosomal membrane homeostasis in cell function, physiology, disease and ageing, and discuss the potential for therapeutic exploitation of lysosomal membrane permeabilization.

DOI: https://doi.org/10.1038/s41580-025-00873-w
Nat Rev Cancer. 2025 Aug 04.

Stromal senescence contributes to age-related increases in cancer.

Jiayu Ye, Anupama Melam, Sheila A Stewart.

Ageing is a process characterized by a wide array of cellular and systemic changes that together increase the risk of developing cancer. While cell-autonomous mutations within incipient tumour cells are important, age-related changes in the microenvironment are critical partners in the transformation process and response to therapy. However, aspects of ageing that are important and the degree to which they contribute to cancer remain obscure. One of the factors that impacts ageing is increased cellular senescence but it is important to note that ageing and cellular senescence are not synonymous. We highlight open questions, including if senescent cells have phenotypically distinct impacts in aged versus young tissue, or if it is the cell type that dictates the impact of senescence on tissue homeostasis and disease. Finally, it is probable that our current definition of cellular senescence encompasses more than one mechanistically distinct cellular state; thus, we highlight phenotypic differences that have been noted across cell types and tissues of origin. This Review focuses on the role that senescent stromal cells have in cancer, with a particular emphasis on fibroblasts given the amount of work that has focused on them.

DOI: https://doi.org/10.1038/s41568-025-00840-9
Biophys J. 2025 Aug 07. pii: S0006-3495(25)00498-9. [Epub ahead of print]

Cooperativity in septin polymerization is tunable by ionic strength and membrane adsorption.

Ellysa J D Vogt, Ian Seim, Wilton T Snead, Brandy N Curtis, Amy S Gladfelter.

Cells employ cytoskeletal polymers to move, divide, and pass information inside and outside of the cell. Previous work on eukaryotic cytoskeletal elements such as actin, microtubules, and intermediate filaments investigating the mechanisms of polymerization have been critical to understand how cells control the assembly of the cytoskeleton. Most biophysical analyses have considered cooperative versus isodesmic modes of polymerization; this framework is useful for specifying functions of regulatory proteins that control nucleation and understanding how cells regulate elongation in time and space. The septins are considered a fourth component of the eukaryotic cytoskeleton, but they are poorly understood in many ways despite their conserved roles in membrane dynamics, cytokinesis, and cell shape, and in their links to a myriad of human diseases. Because septin function is intimately linked to their assembled state, we set out to investigate the mechanisms by which septin polymers elongate under different conditions. We used simulations, in vitro reconstitution of purified septin complexes, and quantitative microscopy to directly interrogate septin polymerization behaviors in solution and on synthetic lipid bilayers of different geometries. We first used reactive Brownian dynamics simulations to determine if the presence of a membrane induces cooperativity to septin polymerization. We then used fluorescence correlation spectroscopy (FCS) to assess septins' ability to form filaments in solution at different salt conditions. Finally, we investigated septin membrane adsorption and polymerization on planar and curved supported lipid bilayers. Septins clearly show signs of salt-dependent cooperative assembly in solution, but cooperativity is limited by binding a membrane. Thus, septin assembly is dramatically influenced by extrinsic conditions and substrate properties and can show properties of both isodesmic and cooperative polymers. This versatility in assembly modes may explain the extensive array of assembly types, functions, and subcellular locations in which septins act.

DOI: https://doi.org/10.1016/j.bpj.2025.08.005
bioRxiv. 2025 Jul 29. pii: 2025.07.28.667051. [Epub ahead of print]

Saturated lipid stress attenuates mitochondrial genome synthesis in human cells.

Casadora Boone, Sophie Judge, Ahmad Shami, Bezawit Danna, Andrea B Ball, Tejashree Pradip Waingankar, Hera Saqub, Ajit S Divakaruni, Samantha C Lewis.

Fatty acids are trafficked between organelles to support membrane biogenesis and act as signaling molecules to rewire cellular metabolism in response to starvation, overnutrition, and environmental cues. Mitochondria are key cellular energy converters that harbor their own multi-copy genome critical to metabolic control. In homeostasis, mitochondrial DNA (mtDNA) synthesis is coupled to mitochondrial membrane expansion and division at sites of contact with the endoplasmic reticulum (ER). Here, we provide evidence from cultured hepatocytes that mtDNA synthesis and lipid droplet biogenesis occur at spatially and functionally distinct ER-mitochondria membrane contact sites. We find that, during saturated lipid stress, cells pause mtDNA synthesis and mitochondrial network expansion secondary to rerouted fatty acid trafficking through the ER and lipid droplet biogenesis, coincident with a defect in soluble protein import to the ER lumen. The relative composition of fatty acid pools available to cells is critical, as monounsaturated fatty acid supplementation rescued both ER proteostasis and mtDNA synthesis, even in the presence of excess saturated fat. We propose that shutoff of mtDNA synthesis conserves mtDNA-to-mitochondrial network scaling until cells can regain ER homeostasis.
Summary: Overnutrition of cultured human cells causes endoplasmic reticulum dysfunction, which downregulates mitobiogenesis in turn by constraining mtDNA synthesis.

DOI: https://doi.org/10.1101/2025.07.28.667051
bioRxiv. 2025 Jul 29. pii: 2025.07.24.666408. [Epub ahead of print]

In vivo screening reveals cell-intrinsic mediators of solid tumor resistance to CAR T cell-therapy.

Julia Fröse, Charles A Whittaker, Paul Leclerc, Evelyn Chen, Sean Doherty, Adam Langenbucher, Riley D Hellinger, Daniel Goulet, Tuomas Tammela, Michael T Hemann.

Chimeric antigen receptor (CAR) T-cell therapy has transformed the treatment of hematologic cancers. However, its efficacy in solid tumors, including pancreatic ductal adenocarcinoma (PDAC), has been limited. By integrating modular CRISPR screening with immunocompetent orthotopic models of PDAC, we identified unknown tumor-intrinsic modulators of CAR T-cell therapy response. Disruption of genes involved in oxidative and proteotoxic stress, particularly the Nrf2 target Slc33a1 , sensitizes PDAC tumors to CAR T-cell killing. Single cell gene expression analyses revealed that CAR-T resistant tumors exhibit reduced Nrf2 pathway activity. Mechanistically, we show that Nrf2 pathway hyperactivation by genetic ablation of Keap1 or expression of a tumor-derived Keap1 allele sensitized PDAC tumors to CAR T-cell therapy. Thus, cell-intrinsic molecular states accompanying malignant progression can sensitize tumor cells to cell-based immunotherapies. These molecular mechanisms could be exploited to augment both the efficacy of CAR-T cell therapy in solid malignancies, and may allow patient stratification by tumor genotype.
Statement of significance: CAR T-cell therapy remains an unsolved challenge for pancreatic cancer. The discovery of tumor-intrinsic mechanisms of resistance has been largely limited by current experimental models. Using large-scale genomic screening in an orthotopic, immunocompetent model of pancreatic cancer, we uncover a role for cell-intrinsic metabolic states in regulating CAR T-cell response.

DOI: https://doi.org/10.1101/2025.07.24.666408
Faraday Discuss. 2025 Aug 04.

Plasma membrane asymmetry and lipid homeostasis: general discussion.

Francisco Barerra, Manuel Bibrowski, John Conboy, Niclas Paul Decker, Markus Deserno, Rumiana Dimova, Milka Doktorova, Thais Enoki, Oded Farago, Gerald W Feigenson, Alexander P Fellows, Gonen Golani, Carlo Guardiani, Heiko Heerklotz, Shinako Kakuda, Neha P Kamat, Manpreet Kaur, Sarabjeet Kaur, Michael M Kozlov, Kandice R Levental, Ilya Levental, Reinhard Lipowsky, Erwin London, Joseph Lorent, Edward Lyman, Madan Rao, Tyler Reagle, Raya Sorkin, Malavika Varma, Axel Voigt.

DOI: https://doi.org/10.1039/d5fd90018b
J Chem Phys. 2025 Aug 14. pii: 065101. [Epub ahead of print]163(6):

Investigation of simvastatin and fluvastatin permeation across cell membrane models using molecular dynamics simulations.

Daniele Belletto, Tania F G G Cova, Gloria Mazzone, Alberto A C C Pais, Emilia Sicilia.

The chief motivation for the failure of drugs in clinical trials is their low bioavailability caused by the inability to cross the cell membrane. Understanding drug-membrane interactions is crucial for improving therapeutic efficacy. In this work, molecular dynamics simulations were employed to investigate the permeation of simvastatin and fluvastatin across three lipid bilayer models representing normal and cancer cell membranes. Free energy profiles reveal that simvastatin, due to its higher lipophilicity, interacts more strongly with lipid environments, preferentially permeating cancer-like symmetric membranes. Fluvastatin, in contrast, shows less selective behavior across different membrane types, consistent with its charged nature. Statin insertion perturbs membrane structure, increasing area per lipid and decreasing bilayer thickness and lipid order. These findings highlight how membrane composition and asymmetry govern passive drug diffusion and suggest that selective membrane interactions may reflect the differential anticancer potential of statins. The results provide mechanistic insights into structure-permeability relationships and support the strategic use of realistic membrane models in drug discovery and repurposing efforts.

DOI: https://doi.org/10.1063/5.0280981
Elife. 2025 Aug 06. pii: RP105111. [Epub ahead of print]14

Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove.

Christina Alexandra Stephens, Niek van Hilten, Lisa Zheng, Michael Grabe.

  Biological membranes are complex and dynamic structures with different populations of lipids in their inner and outer leaflets. The Ca2+-activated TMEM16 family of membrane proteins plays an important role in collapsing this asymmetric lipid distribution by spontaneously and bidirectionally scrambling phospholipids between the two leaflets, which can initiate signaling and alter the physical properties of the membrane. While evidence shows that lipid scrambling can occur via an open hydrophilic pathway (groove) that spans the membrane, it remains unclear if all family members facilitate lipid movement in this manner. Here, we present a comprehensive computational study of lipid scrambling by all TMEM16 members with experimentally solved structures. We performed coarse-grained molecular dynamics (MD) simulations of 27 structures from five different family members solved under activating and non-activating conditions, and we captured over 700 scrambling events in aggregate. This enabled us to directly compare scrambling rates, mechanisms, and protein-lipid interactions for fungal and mammalian TMEM16s, in both open (Ca2+-bound) and closed (Ca2+-free) conformations with statistical rigor. We show that all TMEM16 structures thin the membrane and that the majority of scrambling (>90%) occurs at the groove only when TM4 and TM6 have sufficiently separated. Surprisingly, we also observed 60 scrambling events that occurred outside the canonical groove, over 90% of which took place at the dimer-dimer interface in mammalian TMEM16s. This new site suggests an alternative mechanism for lipid scrambling in the absence of an open groove.

Keywords:  TMEM16; coarse-grained simulations; membrane deformation; membrane transport; molecular biophysics; mouse; scramblases; structural biology

DOI:  https://doi.org/10.7554/eLife.105111
Cell. 2025 Jul 29. pii: S0092-8674(25)00805-0. [Epub ahead of print]

Vagal blockade of the brain-liver axis deters cancer-associated cachexia.

Aliesha Garrett, Naama Darzi, Ashlesha Deshmukh, Nataly Rosenfeld, Omer Goldman, Lital Adler, Elizabeta Bab-Dinitz, Oded Singer, Alireza Hassani Najafabadi, Chi Wut Wong, Shree Bose, Peggy M Randon, Francisco Bustamante, Rene Larios, Alexander Brandis, Tevie Mehlman, Brandon Smaglo, Ping Chang, Jacqueline Oliva, Cara Haymaker, Laukik Nagawekar, Sophie R Wu, Yixuan Huang, Aidan Shen, Ahana Vora, Jon Floyd Padilla, Alissa Pfeffer, Gary Sutherland, Mark Starr, Teresa Zimmers, Yangzhi Zhu, James Morizio, Ayelet Erez, Xiling Shen.

  Cancer-associated cachexia (CAC) is a multifactorial and currently incurable syndrome responsible for nearly one-third of cancer-related deaths. It contributes to therapy resistance and increases mortality among affected patients. In this study, we show that cancer-induced systemic inflammation alters vagal tone in CAC mouse models. This vagal dysregulation disrupts the brain-liver vagal axis, leading to a reprogramming of hepatic protein metabolism through the depletion of HNF4α, a key transcriptional regulator of liver function. The loss of HNF4α disrupts hepatic metabolism and promotes systemic inflammation, resulting in cachectic phenotypes. Interventions targeting the right cervical vagus nerve surgically, chemically, electrically, or through a non-invasive transcutaneous device attenuate CAC progression, alleviate its clinical manifestations, and synergize with chemotherapy to improve overall health and survival in mice.

Keywords:  HNF4α; cancer-associated cachexia; liver; metabolism; neuromodulation; vagus nerve

DOI:  https://doi.org/10.1016/j.cell.2025.07.016
bioRxiv. 2025 Jul 25. pii: 2025.07.21.665965. [Epub ahead of print]

Baseline expression of c-Myc defines the tissue specificity of oncogenic K-Ras.

Olesja Popow, Qing Yu, Clarance Yapp, Shannon Hull, João A Paulo, Benjamin Hanna, Shidong Xu, Yanan Kuang, Carlie Sigel, Cloud P Paweletz, Steven P Gygi, Kevin M Haigis.

KRAS is among the most frequently mutated oncogenes in cancer. Yet, mutations in KRAS are common only in tumors originating from a subset of tissues. It is critical to understand the molecular mechanisms underlying this oncogene tissue specificity. Utilizing genetically engineered mouse models carrying a conditional oncogenic allele of Kras , we expressed activated K-Ras in adult tissues to investigate its specificity. We discovered that the ability of K-Ras G12D to influence the fitness of cells in a given tissue is not determined by its canonical signaling through MAPK. Instead, low baseline expression of c-Myc renders tissues non-permissive to oncogenic K-Ras, a context that can be reversed in the liver by ectopically expressing c-Myc. This functions independently of the proliferative index of the tissue or the induction of cell cycle arrest or apoptosis. Our findings reveal the importance of the basal state of the tissue-inherent signaling network for determining oncogene specificity.

DOI: https://doi.org/10.1101/2025.07.21.665965
Nat Methods. 2025 Aug 07.

Unravelling cellular interactions using flow cytometry.

DOI: https://doi.org/10.1038/s41592-025-02743-x
bioRxiv. 2025 Jul 26. pii: 2025.07.22.666009. [Epub ahead of print]

Netrin-1 promotes pancreatic tumorigenesis and innervation through NEO1.

Yosuke Ochiai, Hiroki Kobayashi, Masaki Sunagawa, Taisuke Baba, Ermanno Malagola, Feijing Wu, Takayuki Tanaka, Masahiro Hata, Junya Arai, Zhengyu Jiang, Ruth A White, Xiaofei Zhi, Jin Qian, Quin T Waterbury, Ruhong Tu, Biyun Zheng, Yi Zeng, Hualong Zheng, Puran Zhang, Shuang Li, Leah B Zamechek, Jonathan S LaBella, Takahiro Sugie, Tadashi Iida, Atsushi Enomoto, Holger K Eltzschig, Carmine F Palermo, Iok In Christine Chio, Kenneth P Olive, Timothy C Wang.

Nerves have been shown to regulate cancer progression. However, a clear demonstration of a role for axon guidance molecules in pancreatic tumorigenesis, innervation, and metastasis has been lacking. Using murine Kras G12D -mutant pancreatic organoids, we screened axon guidance molecules by qRT-PCR, identified Ntn1 upregulation, and then verified its in vivo upregulation during pancreatic tumorigenesis in humans and mice. NTN1 and its receptor NEO1 were upregulated in epithelial cells by the Kras mutation and β-adrenergic signaling, in part, through the MAPK pathway. Ex-vivo culture of celiac ganglia showed that NTN1 promoted the axonogenesis of sympathetic neurons through the nerve NEO1 receptor. In the Pdx1-Cre;LSL-Kras G12D/+ model, Ntn1 knockout decreased sympathetic innervation and the development of pancreatic intraepithelial neoplasia. Treatment of pancreatic tumor organoids with recombinant NTN1 enhanced cell growth, epithelial-mesenchymal transition (EMT), and cancer stemness with the upregulation of ZEB1 and SOX9 through NEO1-mediated activation of focal adhesion kinase (FAK). In Pdx1-Cre;LSL-Kras G12D/+ ;LSL-Trp53 R172H/+ mice, Ntn1 knockout reduced innervation, FAK phosphorylation, and the features of EMT and stemness to extend mouse survival. In a liver metastasis model of PDAC (pancreatic ductal adenocarcinoma), treatment with a NTN1-neutralizing antibody or tumoral knockdown of Neo1 reduced ZEB1 and SOX9 and decreased tumor progression. In contrast, Ntn1 overexpression promoted innervation and the progression of PDAC liver metastasis. These data suggest that the NTN1/NEO1 axis is a key regulator of PDAC progression, directly influencing cancer cell stemness and EMT, while indirectly promoting tumor growth through nerves. Inhibiting the NTN1/NEO1 axis could represent a potential therapeutic approach for PDAC.
Statement of Significance: NTN1 promotes pancreatic tumorigenesis and metastasis directly and indirectly through nerves, highlighting the importance of tumor cell-nerve crosstalk in cancer. NTN1 blockade could represent a promising strategy for treating PDAC liver metastasis.

DOI: https://doi.org/10.1101/2025.07.22.666009
Cell Death Dis. 2025 Aug 06. 16(1): 592

TGF-β1-mediated downregulation of L1CAM in pancreatic ductal adenocarcinoma drives upregulation of collagen 17A1 and MMP2, facilitating tumor invasiveness and metastasis.

Donatella Delle Cave, Annalisa Di Domenico, Marco Fantuz, Marianna Ciotola, Maria Mangini, Silvia Buonaiuto, Brunella Corrado, Marco Corona, Federica Saracino, Gennaro Andolfi, Ilaria Di Biase, Antonio Cucciardi, Alessandro Carrer, Bruno Sainz, Teresa Pirozzi, Daniele Lo Re, Vincenza Colonna, Gabriella Minchiotti, Anna Chiara De Luca, Enza Lonardo.

The highly fibrotic microenvironment of pancreatic ductal adenocarcinoma (PDAC) poses significant challenges for effective treatment, particularly in drug delivery and tumor progression. Our study investigates the role of collagen dynamics in PDAC, revealing that TGF-β1 negatively regulates the expression of L1 cell adhesion molecule (L1CAM), leading to a more invasive tumor phenotype. We identify a subset of PDAC cells with low L1CAM expression (L1low) that actively influences collagen deposition and remodeling, as evidenced by the upregulation of collagen 17A1 (COL17A1) and matrix metalloproteinase 2 (MMP2), both associated with poor prognosis. In vivo studies demonstrate that L1low cells correlate with increased collagen deposition, reduced sensitivity to gemcitabine, and heightened liver metastasis. The secretion of COL17A1 and MMP2 by these cells enhances their migratory capabilities and contributes to the formation of a fibrotic stroma that facilitates tumor progression. This interaction underscores the critical role of collagen in shaping the tumor microenvironment and promoting aggressive tumor behavior. Notably, treatment with Tranilast significantly reduced collagen deposition and MMP2 levels while promoting L1CAM expression, suggesting a therapeutic avenue for counteracting the aggressive characteristics of L1low cells. By modulating collagen dynamics and enhancing drug delivery, Tranilast may improve treatment outcomes for patients with low L1CAM-expressing tumors. Understanding the mechanisms by which L1low cells contribute to collagen secretion and tumor aggressiveness is essential for developing effective interventions in pancreatic cancer.

DOI: https://doi.org/10.1038/s41419-025-07859-8
Cancer Discov. 2025 Aug 04. 15(8): 1537-1539

Two Shots on Goal: Combination of RAS Inhibition and Immunotherapy Drives Long-term Remission in Pancreatic Cancer.

Emily L Lasse Opsahl, Marina Pasca di Magliano.

Oncogenic KRAS is a hallmark of pancreatic cancer, one of the deadliest malignancies, and inhibition of oncogenic KRAS alone is, in most patients, not sufficient to eradicate the tumor. The two studies by Stanger and colleagues and Lowe and colleagues propose combination therapy approaches to leverage the power of the immune system, together with KRAS inhibition, to achieve long-term remission. See related article by Orlen et al., p. 1697 See related article by Broderick et al., p. 1717.

DOI: https://doi.org/10.1158/2159-8290.CD-25-0878
Biochemistry. 2025 Aug 08.

Pancreatic Cancer Progression Involves Increased Lysyl Oxidase-Mediated Collagen Cross-Links as Part of the Desmoplastic Reaction.

Alex Barrett, Mark D Maslanka, Zsuzsanna Darula, Maxwell C McCabe, Anthony J Saviola, Lauren R Schmitt, Valerie Weaver, Todd M Pitts, Wells A Messersmith, Kirk C Hansen.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive and lethal disease characterized by extensive extracellular matrix (ECM) remodeling and fibrosis. In general, the formation of a desmoplastic stroma is associated with dynamic ECM remodeling and resistance to most standard-of-care treatments, such as conventional chemotherapy. Here, we report on alterations to core ECM and ECM remodeling enzymes, which include significant changes in levels of lysyl hydroxylase and oxidase enzymes that modulate collagen cross-linking reactions. Amino acid analysis and a novel cross-linking proteomics approach were employed to further explore these structural changes, revealing significantly elevated levels of collagen cross-linked products and several type I collagen cross-linked N-terminal telopeptides (NTX). Our findings suggest that these modifications not only enhance tumor stiffness and facilitate cancer cell invasion but also present potential biomarkers for early PDAC detection. This research contributes to the evolving landscape of PDAC treatment strategies, proposing new avenues for therapeutic intervention targeting ECM remodeling.

DOI: https://doi.org/10.1021/acs.biochem.5c00125
PLoS Comput Biol. 2025 Aug 04. 21(8): e1013351

Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns.

Bengi Ruken Yavuz, Ugur Sahin, Hyunbum Jang, Ruth Nussinov, Nurcan Tuncbag.

Effective identification of oncogenic mutations is essential for diagnosis, forecasting resistance, and metastasis in remission. It is required for an optimal drug regimen. We develop a framework to discover mutations that co-exist in different oncoproteins, and those that are excluded, likely encoding oncogene-induced senescence. For the first, mapping the proteins onto pathways assist combinatorial drug selections and help detect metastases. The second provides the molecular basis for synthetic lethality, to date investigated at the genome level. Our pan-cancer profiles of ~60,000 tumor sequences, detect 3424 co-existing tumor-specific mutations. Mapping them onto pathways indicates that they preferentially promote specific primary tumors. We uncover metastatic mutations and provide metastatic breast-cancer markers. This work not only clarifies the mechanistic basis of intratumor mutational diversity but usefully reveals markers for metastasis in patients' genomes and introduces a novel computational framework for detecting metastasis based on tumor mutational profiles. Mapping the mutations onto pathways provides an invaluable metastasis-targeting resource, guiding drug combinations.

DOI: https://doi.org/10.1371/journal.pcbi.1013351
Proc Natl Acad Sci U S A. 2025 Aug 12. 122(32): e2423455122

Autophagy activator AA-20 improves proteostasis and extends Caenorhabditis elegans lifespan.

Ee Phie Tan, Nora Lyang, Saam Doroodian, Pablo Sanz-Martinez, Jin Xu, Sviatlana Zaretski, José L Nieto-Torres, Hiroshi Ebata, Shaun H Y Lim, William C Hou, Khalyd J Clay, Leonard Yoon, Lynée A Massey, Derek Rhoades, Danny Garza, Kristen A Johnson, Alan To, Lydia Ambaye, Emily P Bentley, Michael Petrascheck, Alexandra Stolz, Jeffery W Kelly, Malene Hansen.

  The degradation of cellular components through autophagy is essential for longevity and healthy aging. However, autophagy function decreases with aging, contributing to age-related diseases. In this study, we characterized a small-molecule activator of autophagy called AA-20 that enhances autophagy and lipid droplet clearance in human cells and in the nematode Caenorhabditis elegans. AA-20 reduces polyglutamine aggregation in an autophagy-dependent manner in both human cells and C. elegans, where it also promotes fitness. Consistently, we found that AA-20 extends lifespan in WT C. elegans, but not in autophagy-deficient mutants. Interestingly, our findings suggest that AA-20 acts, at least in part, through a mechanism involving the transcription factor EB, but without inhibiting the protein kinase mammalian target of rapamycin complex 1. Collectively, our results identify an autophagy activator AA-20, which may have potential therapeutic implications for aging-related proteinopathies and lipid storage disorders.

Keywords:  C. elegans; autophagy activator; healthspan; lifespan; lipophagy

DOI:  https://doi.org/10.1073/pnas.2423455122
Cell Death Discov. 2025 Aug 06. 11(1): 368

Integrated real-time imaging of executioner caspase dynamics, apoptosis-induced proliferation, and immunogenic cell death using a stable fluorescent reporter platform.

Selen Selcen, Lena Wieland, Tiago De Oliveira, Michael Ghadimi, Lena-Christin Conradi, Günter Schneider, Leonie Witte, Matthias Wirth.

Regulated cell death plays a central role in tissue homeostasis, disease progression, and therapeutic responses. However, tools to study these processes with high spatiotemporal resolution in physiologically relevant systems remain limited. Here, we present a fluorescent reporter cell system that enables real-time visualization of caspase-3/-7 activity via a DEVD-based biosensor, alongside a constitutive fluorescent marker for assessing successful transduction and cell presence. We generated stable cell lines expressing this reporter and adapted them to both 2D and 3D culture systems, including organoids. This platform allowed dynamic tracking of apoptotic events and viability loss at single-cell resolution. Using a proliferation dye, we also detected apoptosis-induced proliferation in neighboring cells. Furthermore, the system enabled simultaneous detection of immunogenic cell death via an endpoint measurement of surface calreticulin exposure by flow cytometry, supporting its application in studying immunogenic signaling. By measuring and integrating multiple cell death readouts by live-cell imaging, our system is well-suited for high-content screening and mechanistic dissection of different modes of cell death. When combined with complementary markers of pyroptosis and necroptosis, this platform may also be extended to investigate more complex, integrated forms of cell death.

DOI: https://doi.org/10.1038/s41420-025-02662-y
ArXiv. 2025 Jul 30. pii: arXiv:2507.23101v1. [Epub ahead of print]

The Lipid Interactome: An interactive and open access platform for exploring cellular lipid-protein interactomes.

Gaelen Guzman, André Nadler, Frank Stein, Jeremy M Baskin, Carsten Schultz, Fikadu Tafesse.

Lipid-protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has long been hindered by the inherent biochemical properties of lipids. Recent advances in functionalized lipid probes -- equipped with photoactivatable crosslinkers, affinity handles, and photocleavable protecting groups -- have enabled proteomics-based identification of lipid interacting proteins with unprecedented specificity and resolution. Despite the growing number of published lipid interactomes, there remains no centralized effort to harmonize, compare, or integrate these datasets. The Lipid Interactome addresses this gap by providing a structured, interactive web portal that adheres to FAIR data principles -- ensuring that lipid interactome studies are Findable, Accessible, Interoperable, and Reusable. Through standardized data formatting, interactive visualizations, and direct cross-study comparisons, this resource enables researchers to systematically explore the protein-binding partners of diverse bioactive lipids. By consolidating and curating lipid interactome proteomics data from multiple studies, the Lipid Interactome database serves as a critical tool for deciphering the biological functions of lipids in cellular systems.
Nat Cell Biol. 2025 Aug 04.

The intrinsically disordered regions of organellophagy receptors are interchangeable and control organelle fragmentation, ER-phagy and mitophagy flux.

Mikhail Rudinskiy, Carmela Galli, Andrea Raimondi, Maurizio Molinari.

Organellophagy receptors control the generation and delivery of portions of their homing organelle to acidic degradative compartments to recycle nutrients, remove toxic or aged macromolecules and remodel the organelle upon physiologic or pathologic cues. How they operate is not understood. Here we show that organellophagy receptors are composed of a membrane-tethering module that controls organellar and suborganellar distribution and by a cytoplasmic intrinsically disordered region (IDR) with net cumulative negative charge that controls organelle fragmentation and displays an LC3-interacting region (LIR). The LIR is required for lysosomal delivery but is dispensable for organelle fragmentation. Endoplasmic reticulum (ER)-phagy receptors' IDRs trigger DRP1-assisted mitochondrial fragmentation and mitophagy when transplanted at the outer mitochondrial membrane. Mitophagy receptors' IDRs trigger ER fragmentation and ER-phagy when transplanted at the ER membrane. This offers an interesting example of function conservation on sequence divergency. Our results imply the possibility to control the integrity and activity of intracellular organelles by surface expression of organelle-targeted chimeras composed of an organelle-targeting module and an IDR module with net cumulative negative charge that, if it contains a LIR, eventually tags the organelle portions for lysosomal clearance.

DOI: https://doi.org/10.1038/s41556-025-01728-4
Aging Dis. 2025 Jul 19.

Targeting Ferroptosis to Eliminate Senescent Cells: Mechanisms and Therapeutic Potential.

Sanjay Kumar Kureel, Blake B Rasmussen.

Cellular senescence is involved in early development, wound healing, and tumor suppression. However, the accumulation of senescent cells (SCs) drives tissue dysfunction and many age associated pathologies such as cancer and neurodegeneration. SCs demonstrate irreversible cessation of cell cycle, overexpression of anti-apodotic proteins, and senescence associated secretory phenotype (SASP), cause tissue dysfunction. Traditional senolytics induces apoptosis but have poor selectivity, uncertain long-term efficacy, and resistant SCs, limiting their use. Ferroptosis, an iron-dependent, non-apoptotic form of programmed cell death, has emerged as a promising alternative. SCs bypass the apoptosis by overexpression of an anti-apoptotic pathway, but ferroptosis uses oxidative damage to overcome these defenses, thus, making it effective for eliminating SCs. This review critically evaluates ferroptosis-mediated processes such as elevated level of iron, polyunsaturated fatty acids (PUFAs) and oxidative damages in elimination of SCs and its therapeutic potential for age related pathologies including fibrosis, cancer and neurodegenerative diseases. This review highlights the molecular mechanisms underlying ferroptosis and its potential for treating age-related diseases such as fibrosis, atherosclerosis, osteoarthritis, and neurodegeneration. By addressing the translational challenges of ferroptosis-based therapies, we emphasize its potential as a next generation senolytic for targeting senescence and aging-related pathologies.

DOI: https://doi.org/10.14336/AD.2025.0141
Nat Methods. 2025 Aug 07.

Ultra-high-scale cytometry-based cellular interaction mapping.

Dominik Vonficht, Lea Jopp-Saile, Schayan Yousefian, Viktoria Flore, Inés Simó Vesperinas, Ruth Teuber, Bogdan Avanesyan, Yanjiang Luo, Caroline Röthemeier, Florian Grünschläger, Mirian Fernandez-Vaquero, Vincent Fregona, Diana Ordoñez-Rueda, Laura K Schmalbrock, Luca Deininger, Angelo Jovin Yamachui Sitcheu, Zuguang Gu, Maja C Funk, Ralf Mikut, Mathias Heikenwälder, Angelika Eggert, Arend von Stackelberg, Sebastian Kobold, Jan Krönke, Ulrich Keller, Andreas Trumpp, Ahmed N Hegazy, Cornelia Eckert, Daniel Hübschmann, Simon Haas.

Cellular interactions are of fundamental importance, orchestrating organismal development, tissue homeostasis and immunity. Recently, powerful methods that use single-cell genomic technologies to dissect physically interacting cells have been developed. However, these approaches are characterized by low cellular throughput, long processing times and high costs and are typically restricted to predefined cell types. Here we introduce Interact-omics, a cytometry-based framework to accurately map cellular landscapes and cellular interactions across all immune cell types at ultra-high resolution and scale. We demonstrate the utility of our approach to study kinetics, mode of action and personalized response prediction of immunotherapies, and organism-wide shifts in cellular composition and cellular interaction dynamics following infection in vivo. Our scalable framework can be applied a posteriori to existing cytometry datasets or incorporated into newly designed cytometry-based studies to map cellular interactions with a broad range of applications from fundamental biology to applied biomedicine.

DOI: https://doi.org/10.1038/s41592-025-02744-w
Nature. 2025 Aug 06.

Publisher Correction: NINJ1 regulates plasma membrane fragility under mechanical strain.

Yunfeng Zhu, Fang Xiao, Yiling Wang, Yufang Wang, Jialin Li, Dongmei Zhong, Zhilei Huang, Miao Yu, Zhirong Wang, Joshua Barbara, Christopher Plunkett, Mengxue Zeng, Yiyan Song, Tian Tan, Ruibin Zhang, Kezhen Xu, Zhongxing Wang, Changjie Cai, Xiangdong Guan, Scott Hammack, Liang Zhang, Zheng Shi, Fu-Li Xiang, Feng Shao, Jie Xu.

DOI: https://doi.org/10.1038/s41586-025-09444-7
bioRxiv. 2025 Jul 31. pii: 2025.07.18.665598. [Epub ahead of print]

Activation of PP2A-B56α leads to aberrant EGFR signaling and proliferative phenotypes in PDAC.

Claire M Pfeffer, Sydney J Clifford, Saadia A Karim, Ella Rose D Chianis, Brittany N Heil, Lauren E Gartenhaus, Emma F Kay, Garima Baral, Elizabeth G Hoffman, Sagar M Utturkar, Harish Kothandaraman, Whitney Smith-Kinnaman, Kasi Hansen, Emily G Smith, Elisabeth Porter, Fuping Zhang, Nadia Atallah Lanman, Jukka Westermarck, Emma H Doud, Amber L Mosley, Jennifer P Morton, Brittany L Allen-Petersen.

Pancreatic ductal adenocarcinoma (PDAC) stands to become the second most deadly cancer by 2030. The small GTPase, KRAS, is mutated in over 90% of PDAC patients and considered the primary driver mutation. Despite being an almost ubiquitous event, KRAS mutations have been difficult to target therapeutically, particularly KRAS G12D , the most common mutation in PDAC. In addition to these pharmacological challenges, KRAS mutations have been shown to drive signaling plasticity and therapeutic resistance through phosphorylation cascades in most cancers. Protein phosphatases are master regulators of kinase signaling, however the contribution of phosphatase deregulation to mutant KRAS cancer phenotypes is poorly understood. Protein phosphatase 2A (PP2A) inhibits effectors downstream of KRAS, placing this family of enzymes as key regulators of PDAC oncogenic signaling. However, our previous studies utilizing small molecule activating compounds of PP2A show a heterogeneous response in PDAC, with some cell lines displaying increased oncogenic signaling despite induction of phosphatase activity. Similarly, specific PP2A subunits exhibit both tumor suppressive and oncogenic functions depending on the cellular context. Therefore, understanding the role of PP2A in regulating cancer phenotypes is critical for the future development of therapeutic strategies that leverage this phosphatase. Here, we determined the impact of the specific PP2A subunit, B56α, on PDAC phenotypes using both genetic and pharmacological activation strategies in human PDAC cell lines and genetic mouse models. We demonstrate that while PP2A-B56α suppresses specific oncogenic pathways, B56α activation exacerbates PDAC proliferative phenotypes and decreases overall survival in vivo , potentially through increased epidermal growth factor receptor (EGFR) signaling. EGFR is a critical signaling node in PDAC as inhibition or loss of EGFR prevents KRAS-driven tumorigenesis and increased EGFR activity is associated with poor patient outcome. The activation of EGFR by PP2A-B56α is in part mediated through increased expression and processing of EGFR ligands, specifically amphiregulin, heparin-binding EGF-like growth factor (HB-EGF), and epiregulin. Furthermore, pharmacological PP2A activation in combination with EGFR inhibitors mitigates this signaling and increases cell death. Together, these studies implicate a previously undescribed non-canonical role for PP2A-B56α in EGFR signaling that contributes to PDAC progression.

DOI: https://doi.org/10.1101/2025.07.18.665598
Nature. 2025 Aug 06.

NSD2 inhibitors rewire chromatin to treat lung and pancreatic cancers.

Jinho Jeong, Simone Hausmann, Hanyang Dong, Kacper Szczepski, Natasha M Flores, Andy Garcia Gonzalez, Liyang Shi, Xiaoyin Lu, Joanna Lempiäinen, Moritz Jakab, Liyong Zeng, Tourkian Chasan, Eric Bareke, Rui Dong, Emma Carlson, Reinnier Padilla, Dylan Husmann, Julia Thompson, Gerry A Shipman, Emily Zahn, Courtney A Barnes, Laiba F Khan, Liz Marie Albertorio-Sáez, Eva Brill, Vishnu Udayakumar Sunita Kumary, Matthew R Marunde, Danielle N Maryanski, Cheryl C Szany, Bryan J Venters, Carolina Lin Windham, Michal Eligiusz Nowakowski, Iwona Czaban, Mariusz Jaremko, Michael-Christopher Keogh, Kang Le, Michael J Soth, Benjamin A Garcia, Łukasz Jaremko, Jacek Majewski, Pawel K Mazur, Or Gozani.

NSD2 catalyses the epigenetic modification H3K36me2 (refs. 1,2) and is a candidate convergent downstream effector of oncogenic signalling in diverse malignancies3-5. However, it remains unclear whether the enzymatic activity of NSD2 is therapeutically targetable. Here we characterize a series of clinical-grade small-molecule catalytic NSD2 inhibitors (NSD2i) and show that the pharmacological targeting of NSD2 constitutes an epigenetic dependency with broad therapeutic efficacy in KRAS-driven preclinical cancer models. NSD2i inhibits NSD2 with single-digit nanomolar half-maximal inhibitory concentration potency and high selectivity over related methyltransferases. Structural analyses reveal that the specificity of NSD2i for NSD2 is due to competitive binding with S-adenosylmethionine and catalytic disruption through a binary-channel obstruction mechanism. Proteo-epigenomic and single-cell strategies in pancreatic and lung cancer models support a mechanism in which sustained NSD2i exposure reverses pathological H3K36me2-driven chromatin plasticity, re-establishing silencing at H3K27me3-legacy loci to curtail oncogenic gene expression programs. Accordingly, NSD2i impairs the viability of pancreatic and lung cancer cells and the growth of patient-derived xenograft tumours. Furthermore, NSD2i, which is well-tolerated in vivo, prolongs survival in advanced-stage autochthonous KRASG12C-driven pancreatic and lung tumours in mouse models to a comparable level as KRAS inhibition with sotorasib6. In these models, treatment with both a NSD2 inhibitor and sotorasib synergize to confer sustained survival with extensive tumour regression and elimination. Together, our work uncovers targeting of the NSD2-H3K36me2 axis as an actionable vulnerability in difficult to treat cancers and provides support for the evaluation of NSD2 and KRAS inhibitor combination therapies in a clinical setting.

DOI: https://doi.org/10.1038/s41586-025-09299-y
Trends Cell Biol. 2025 Aug 05. pii: S0962-8924(25)00157-6. [Epub ahead of print]

NADH reductive stress drives metabolic reprogramming.

Ronghui Yang, Zihao Guo, Binghui Li.

  Cellular metabolism is intricately regulated by redox signaling, with the NADH/NAD+ couple serving as a central hub. Emerging evidence reveals that NADH reductive stress, marked by NADH accumulation, is not merely a passive byproduct of metabolic dysfunction but an active regulatory signal driving metabolic reprogramming. In this Review, we synthesize recent advances in understanding NADH reductive stress, including its origins, regulatory mechanism, and manipulation. We examine its broad impact on cellular metabolism, its interplay with oxidative and energy stress, and its pathogenic roles in a range of diseases. By integrating these findings, we propose NADH reductive stress as a master regulator for metabolic reprogramming and highlight new avenues for mechanistic exploration and therapeutic intervention.

Keywords:  NADH reductive stress; NADH-reductive-stress-associated diseases; energy stress; metabolic reprogramming; oxidative stress

DOI:  https://doi.org/10.1016/j.tcb.2025.07.005
bioRxiv. 2025 Jul 26. pii: 2025.07.22.666218. [Epub ahead of print]

Capillary constrictions prime cancer cell tumorigenicity through PIEZO1.

G Silvani, C Kopecky, S Romanazzo, V Rodriguez, A Das, E Pandzic, J G Lock, C Chaffer, K Poole, K A Kilian.

Metastasis is a hallmark of cancer and is responsible for the majority of cancer-related deaths. Evidence suggests that even a single cancer cell can spread and seed a secondary tumour. However, not all circulating tumour cells have this ability, which implies that dissemination and distal growth require adaptative mechanisms during circulation. Here we report that constriction during microcapillary transit will trigger reprogramming of melanoma cells to a tumorigenic cancer stem cell-like state. Using a microfluidic device mimicking physiological flow rates and gradual capillary narrowing, we showed that compression through narrow channels lead to cell and nuclear deformation, rapid changes in chromatin state and increased calcium handling through the mechanosensor PIEZO1. Within minutes of microcapillary transit, cells show increased regulation of transcripts associated with metabolic reprogramming and metastatic processes, which culminates in the adoption of cancer stem cell-like properties. Squeezed cells displayed elevated melanoma stem cell markers, increased propensity for trans-endothelium invasion, and characteristics of enhanced tumorigenicity in vitro and in vivo . Pharmacological disruption of channel activity inhibited the stem cell-like state, while the selective PIEZO1 activator Yoda1 primed this state irrespective of constriction. Finally, deletion of PIEZO1 led to complete abrogation of the constriction-induced stem cell-like state. Together, this work demonstrates that compressive forces during circulation can reprogram circulating cancer cells to tumorigenic stem cell-like states that are primed for extravasation and metastatic colonization.

DOI: https://doi.org/10.1101/2025.07.22.666218
J Cell Sci. 2025 Aug 01. pii: jcs263971. [Epub ahead of print]138(15):

Emerging roles of lipid transfer protein dimerization.

Shalom Borst Pauwels, Jacques Neefjes, Birol Cabukusta.

  The unique lipid composition of organelles defines their identity and is fundamental to their function. Lipid transfer proteins perform non-vesicular trafficking of lipids among cellular membranes to maintain their lipid compositions. Lipid transfer protein-mediated lipid trafficking is also essential for creating sub-organellar nano-domains that can recruit functional proteins or change the biophysical properties of membranes. The latest research focusing on the homo- and hetero-dimerization of lipid transfer proteins highlights the functional implications and the clinical significance of these events. Dimerization promotes lipid transfer protein localization at membrane contact sites and mediates the assembly of lipid transfer protein super-complexes to synchronize the transfer of different lipid types between organelles. Meanwhile, abnormal lipid flows caused by disarrangements in lipid transfer protein dimerization disturb organelle lipid landscapes, which has clinical consequences. This Review discusses the latest developments regarding the dimerization of lipid transfer proteins and their adaptor proteins that are critical for lipid trafficking between the organelles of the cell.

Keywords:  Dimerization; Lipid transfer proteins; Membrane contact sites; Non-vesicular trafficking

DOI:  https://doi.org/10.1242/jcs.263971
Oncogene. 2025 Aug 08.

ALDH1A3 promotes aggressive basal-like pancreatic cancer through an AP-1/RUNX2 enhancer network.

Xiaoping Zou, Shuang Nie, Jing Cao, Mengyue Shi, Kathleen Schuck, Zhao Shi, Lingling Zhang, Hongzhen Li, Yifeng Sun, Chao Fang, Jingxiong Hu, Yiqi Niu, Yuanyuan Yu, Zhiheng Zhang, Chao Li, Mingyue Hu, Lei Wang, Kuirong Jiang, Zipeng Lu, Jan Akkan, Susanne Raulefs, Christoph Kahlert, Susanne Roth, Ingrid Herr, Yuan Wan, Andre Mihaljevic, Xuetian Qian, Qi Zhang, Maggie Haitian Wang, Jörg Kleeff, Helmut Friess, Zuguang Gu, Christoph W Michalski, Shanshan Shen, Bo Kong.

The basal-like transcriptional subtype of pancreatic ductal adenocarcinoma (PDAC) is linked to therapy resistance and poor prognosis. The cancer stem cell marker aldehyde dehydrogenase 1A3 (ALDH1A3) is a critical enzyme in acetaldehyde metabolism, but the interconnection to the basal-like subtype is poorly understood. Here, we identified ALDH1A3 as a key gene, which correlates with reduced survival and increased tumor growth. Functional studies revealed interaction of ALDH1A3 with genes like FAM3C, MCC, PMEPA1, and IRS2, forming a network driving PDAC progression. Chromatin profiling showed that ALDH1A3 affects acetylation of histone 3, mediating AP-1 activity, particularly via FOS family members, activating oncogenic pathways such as MAPK and TNF signaling. RUNX2 emerged as a therapeutic target within this network, as its knockdown disrupted MAPK signaling and reduced tumor growth. These findings emphasize the role of ALDH1A3 in linking nuclear metabolic-epigenetic programming in basal-like PDAC, highlighting it as a promising therapeutic target for novel treatment strategies.

DOI: https://doi.org/10.1038/s41388-025-03530-w
Cell Death Discov. 2025 Aug 04. 11(1): 364

Hallmarks and mechanisms of cellular senescence in aging and disease.

Amir Ajoolabady, Domenico Pratico, Suhad Bahijri, Basmah Eldakhakhny, Jaakko Tuomilehto, Feng Wu, Jun Ren.

Cellular senescence, often referred to simply as "senescence", is a complex intracellular process with diverse biological, physiological, and pathological roles. Biologically, it is essential for embryogenesis and development. Physiologically, senescence acts as a safeguard against tumorigenesis by preventing the proliferation of damaged or defective cells. However, persistent activation of senescence can contribute to various pathological conditions, particularly those associated with aging, cancer, and other chronic diseases such as liver and pulmonary diseases. Growing evidence links aging to heightened activation of cellular senescence, leading to the accumulation of senescent cells. Here in this perspective, we aim to decipher the latest molecular mechanisms and regulatory pathways of cellular senescence in the context of aging and aging-related diseases. Additionally, we discuss emerging research directions, highlighting current limitations and gaps in the field. Addressing these challenges may not only advance our understanding of senescence but also uncover new therapeutic opportunities.

DOI: https://doi.org/10.1038/s41420-025-02655-x
Mol Cell. 2025 Aug 07. pii: S1097-2765(25)00609-4. [Epub ahead of print]85(15): 2815-2817

A breathless brake on ferroptosis.

Mingchuang Sun, Li Zhuang, Boyi Gan.

In this issue of Molecular Cell, Minikes et al.1 reveal that hypoxia suppresses ferroptosis independently of HIF signaling via inhibition of the oxygen-sensitive histone demethylase KDM6A, linking hypoxia-mediated chromatin regulation to phospholipid metabolism and ferroptosis resistance in cancer.

DOI: https://doi.org/10.1016/j.molcel.2025.07.008
J Mol Med (Berl). 2025 Aug 05.

Fibrin as the mediator of tumor cell interaction with platelets.

Ivan Tesakov, Anna D Korneichuk, Aleksandra A Filkova, Anna E Boldova, Anna A Deputatova, Anatoly U Kokhan, Yuliya D Korol, Kristina A Mazova, Viktoria A Pakina, Anna G Poleshko, Vladislav A Shumskiy, Ekaterina V Blinova, Dmitrii S Blinov, Ekaterina V Shamova, Mikhail A Panteleev, Anastasia N Sveshnikova.

  Metastasis, a major complication in cancer, is known to depend on the interaction of tumor cells with platelets. However, anti-platelet therapy does not reliably increase survival rates. To address this, here we use light transmission aggregometry, flow cytometry, and confocal microscopy for characterization of human platelets interaction with six lines of tumor cell cultures. A murine model of Lewis carcinoma was used to test the effects of antiplatelet and anticoagulation therapy. Tumor-cell-induced platelet aggregation (TCIPA) correlated with the cell line invasive potential, required calcium and plasma proteins, and was only mildly suppressed by platelet inhibition. However, TCIPA was completely abolished by heparin, rivaroxaban, or dabigatran. For pre-fixed platelets, TCIPA was completely inhibited by the fibrin polymerization inhibitor GPRP. Tumor cells directly induced spatial fibrin polymerization in a factor X-dependent manner. Confocal microscopy confirmed platelet entrapment in the fibrin mesh formed around tumor cells. In the murine model of tumor cell injection, both anticoagulation and antiplatelet treatment reduced lung metastasis. These data suggest that formation of the fibrin mesh associated with a circulating tumor cell, with platelet entrapped in it (not necessarily in the activated state), could be an important early step in the metastasis development. KEY MESSAGES: Platelet-tumor cell heteroaggregates are stabilized by the fibrin network. Thrombin formation is induced by tumor cells, while platelet activation is less essential. Anticoagulant treatment prevents this interaction and may suppress metastasis.

Keywords:  Hemostasis; Metastasis; Platelets; Thrombin; Tissue factor; Tumor cell-induced platelet aggregation

DOI:  https://doi.org/10.1007/s00109-025-02580-7
Nat Metab. 2025 Aug 04.

Classically activated macrophages undergo functionally significant nucleotide metabolism remodelling driven by nitric oxide.

Steven V John, Gretchen L Seim, Billy J Erazo-Flores, James A Votava, Uzziah S Urquiza, Nicholas L Arp, John Steill, Jack Freeman, Lauren N Carnevale, Isaiah Roberts, Xin Qing, Stuart A Lipton, Ron Stewart, Laura J Knoll, Jing Fan.

During an immune response, macrophages specifically reprogramme their metabolism to support functional changes. Here, we revealed that nucleotide metabolism is one of the most significantly reprogrammed pathways upon classical activation. Specifically, de novo synthesis of pyrimidines is maintained up to uridine monophosphate, but blocked at cytidine triphosphate and deoxythymidine monophosphate synthesis; de novo synthesis of purines is shut off at the last step (catalysed by AICAR transformylase/IMP cyclohydrolase, ATIC), and cells switch to increased purine salvage. Nucleotide degradation to nitrogenous bases is upregulated but complete oxidation of purine bases (catalysed by xanthine oxidoreductase, XOR) is inhibited, diverting flux into salvage. Mechanistically, nitric oxide was identified as a major regulator of nucleotide metabolism, simultaneously driving multiple key changes, including the transcriptional downregulation of Tyms and profound inhibition of ATIC and XOR. Inhibiting purine salvage using Hgprt knockout or inhibition alters the expression of many stimulation-induced genes, suppresses macrophage migration and phagocytosis, and increases the proliferation of the intracellular parasite Toxoplasma gondii. Together, these results thoroughly uncover the dynamic reprogramming of macrophage nucleotide metabolism upon classical activation and elucidate the regulatory mechanisms and functional significance of such reprogramming.

DOI: https://doi.org/10.1038/s42255-025-01337-3
Methods Mol Biol. 2025 ;2932 75-91

Using the Cancer Epitope Database and Analysis Resource (CEDAR).

Zeynep Koşaloğlu-Yalçın, Randi Vita, Nina Blazeska, Bjoern Peters, Alessandro Sette.

  The Cancer Epitope Database and Analysis Resource (CEDAR) is a freely accessible catalog of cancer epitope and receptor data linked to the biological, immunological, and clinical contexts in which they were described. CEDAR data is populated by manual curation of the cancer literature and provides a central resource for researchers to access information about cancer antigens and their specific epitopes, which is relevant to our understanding of the role that the immune system plays in cancer progression, prevention, and treatment. In this chapter, we aim to provide a comprehensive overview of the database section of CEDAR. This includes a detailed description of all available query parameters, guidance on navigating through the query results, and a demonstration of how CEDAR can aid cancer research, featuring example research scenarios and queries.

Keywords:  Cancer immunology; Database; Epitopes; Immunotherapy; Neoantigens; Tumor antigens

DOI:  https://doi.org/10.1007/978-1-0716-4566-6_3
Proc Natl Acad Sci U S A. 2025 Aug 12. 122(32): e2504578122

Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues.

Johannes Stein, Maria Ericsson, Michel Nofal, Lorenzo Magni, Sarah Aufmkolk, Ryan B McMillan, Laura Breimann, Conor P Herlihy, S Dean Lee, Andréa Willemin, Jens Wohlmann, Laura Arguedas-Jimenez, Peng Yin, Ana Pombo, George M Church, Chao-Ting Wu.

  DNA-points accumulation for imaging in nanoscale topography (DNA-PAINT) enables nanoscale imaging with virtually unlimited multiplexing and molecular counting. Here, we address challenges, such as variable imaging performance and target accessibility, that can limit its broader applicability. Specifically, we enhance its capacity for robust single-protein imaging and molecular counting by optimizing the integration of total internal reflection fluorescence microscopy with physical sectioning, in particular, Tokuyasu cryosectioning. Our method, tomographic and kinetically enhanced DNA-PAINT (tkPAINT), achieves 3 nm localization precision across diverse samples, enhanced imager binding, and improved cellular integrity. tkPAINT can facilitate molecular counting with DNA-PAINT inside the nucleus, as demonstrated through its quantification of the in situ abundance of RNA Polymerase II in both HeLa cells as well as mouse tissues. Anticipating that tkPAINT could become a versatile tool for the exploration of biomolecular organization and interactions across cells and tissues, we also demonstrate its capacity to support multiplexing, multimodal targeting of proteins and nucleic acids, and three-dimensional (3D) imaging.

Keywords:  DNA-PAINT; TIRF; nuclear organization; single-molecule localization microscopy; super-resolution microscopy

DOI:  https://doi.org/10.1073/pnas.2504578122
bioRxiv. 2025 Jul 31. pii: 2025.07.27.667080. [Epub ahead of print]

NAC controls nascent chain fate through tunnel sensing and chaperone action.

Jae Ho Lee, Laurenz Rabl, Martin Gamerdinger, Vaishali Goyal, Katrin Michaela Khakzar, Natalia Moreira Barbosa, Juliana Abramovich, Fabian Morales-Polanco, Ann-Kathrin Köhler, Ekaterina Samatova, Marina V Rodnina, Elke Deuerling, Judith Frydman.

The nascent polypeptide-associated complex (NAC) is a conserved ribosome-bound factor with essential yet incompletely understood roles in protein biogenesis. Here, we show that NAC is a multifaceted regulator that coordinates translation elongation, cotranslational folding, and organelle targeting through distinct interactions with nascent polypeptides both inside and outside the ribosome exit tunnel. Using NAC-selective ribosome profiling in C. elegans , we identify thousands of sequence-specific NAC binding events across the nascent proteome, revealing broad cotranslational engagement with hydrophobic and helical motifs in cytosolic, nuclear, ER, and mitochondrial proteins. Unexpectedly, we discover an intra-tunnel sensing mode, where NAC engages ribosomes with extremely short nascent polypeptides inside the exit tunnel in a sequence-specific manner. These early NAC interactions induce an early elongation slowdown that tunes ribosome flux and prevent ribosome collisions, linking NAC's chaperone activity to kinetic control of translation. We propose that NAC action protects aggregation-prone intermediates by shielding amphipathic helices thus promoting cytonuclear folding and supporting mitochondrial membrane protein biogenesis and ER targeting by early recognition of signal sequences and transmembrane domain. Our findings establish NAC as an early-acting, multifaceted orchestrator of cotranslational proteostasis, with distinct mechanisms of action on nascent chains depending on their sequence features and subcellular destinations.

DOI: https://doi.org/10.1101/2025.07.27.667080
bioRxiv. 2025 Jul 26. pii: 2025.07.22.666146. [Epub ahead of print]

The Plasma Membrane may Serve as a Drug Depot to Drive the Extreme Potency of Fentanyl.

Joseph Clayton, George J Farmer, Jackie Glenn, Shailesh N Mistry, J Robert Lane, Lei Shi, Lidiya Stavitskaya, Meritxell Canals, Jana Shen.

The drug overdose crisis in the United States is driven largely by the ultrapotent synthetic (UPS) opioid fentanyl; however, fentanyl's extreme potency is poorly understood. Here we used state-of-the-art molecular dynamics simulations and experiments to test a hypothesis that fentanyl's extreme potency is driven by its ability to partition into the plasma membrane, creating a drug reservoir near the receptor. The estimated effective permeability of fentanyl at pH 7.5 is on the order of 10 -7 cm/s - at least two orders of magnitude faster than morphine. In contrast, isotonitazene (a newly emerged UPS opioid) and naloxone (an antagonist) effectively do not partition into the membrane under the same conditions. The simulations captured the proton-coupled permeation processes, challenging the long-standing pH-partition hypothesis. Subsequent reporter cell line experiments demonstrated that cells exposed to fentanyl, but not morphine, reactivated the receptor even after washout and addition of naloxone. Immobilized affinity membrane chromatography confirmed that fentanyl has significantly higher phospholipid affinity than morphine. Our findings strongly support the drug depot hypothesis and highlight the importance of membrane-dependent opioid pharmacology for understanding toxicity and guiding the design of more effective antagonists. The simulation methodology enables detailed analysis of membrane permeation by ionizable inhibitors, supporting ADME optimization in drug development.

DOI: https://doi.org/10.1101/2025.07.22.666146
Sci Rep. 2025 Aug 06. 15(1): 28736

CytoAnalyst web platform facilitates comprehensive single cell RNA sequencing analysis.

Phi Bya, Duy Tran, Khoi Nguyen, Sorin Draghici, Tin Nguyen.

  Single-cell technologies have revolutionized our ability to study cellular heterogeneity and dynamics at unprecedented resolutions. In this fast-growing field, it becomes increasingly challenging to navigate the vast number of tools and steps for analysis. It is particularly difficult to integrate and analyze large datasets that require extensive collaborations and customized pipelines to obtain robust results. We present CytoAnalyst, a web-based platform that offers a number of important advantages over existing tools for single-cell analysis. First, the platform enables custom pipeline configuration using an efficient study management system and a broad range of analysis modules. Second, the platform supports parallel analysis instances, facilitating the comprehensive comparison of different methods or parameter settings available at each analysis step. Third, the advanced sharing system facilitates real-time synchronization among team members and seamless analysis continuation across different devices. Finally, the grid-layout visualization system supports simultaneous displays of different data aspects, allowing for the comparison of multiple labels and plots side-by-side for comprehensive data insights, with the ability to save and reload visualization settings at any analysis step. The platform incorporates multiple blending modes, allowing users to combine plots in various ways for comprehensive data exploration. CytoAnalyst supports a high level of analytical rigor while providing user-friendly and flexible operations through its carefully designed interface and extensive documentation. The platform supports all major web browsers and is freely available at https://cytoanalyst.tinnguyen-lab.com .

Keywords:  AI-guided cell annotation; Cell type annotation; Clustering analysis; Embedding analysis; Interactive visualization; Single-cell analysis

DOI:  https://doi.org/10.1038/s41598-025-14398-x
Nat Methods. 2025 Aug;22(8): 1742-1752

Morphological map of under- and overexpression of genes in human cells.

Srinivas Niranj Chandrasekaran, Eric Alix, John Arevalo, Adriana Borowa, Patrick J Byrne, William G Charles, Zitong S Chen, Beth A Cimini, Boxiong Deng, John G Doench, Jessica D Ewald, Briana Fritchman, Colin J Fuller, Jedidiah Gaetz, Amy Goodale, Marzieh Haghighi, Yu Han, Zahra Hanifehlou, Holger Hennig, Desiree Hernandez, Christina B Jacob, Tim James, Tomasz Jetka, Alexandr A Kalinin, Ben Komalo, Maria Kost-Alimova, Tomasz Krawiec, Brittany A Marion, Glynn Martin, Nicola Jane McCarthy, Lisa Miller, Arne Monsees, Nikita Moshkov, Alán F Muñoz, Arnaud Ogier, Magdalena Otrocka, Krzysztof Rataj, David E Root, Francesco Rubbo, Simon Scrace, Douglas W Selinger, Rebecca A Senft, Peter Sommer, Amandine Thibaudeau, Sarah Trisorus, Rahul Valiya Veettil, William J Van Trump, Sui Wang, Michał Warchoł, Erin Weisbart, Amélie Weiss, Michael Wiest, Agata Zaremba, Andrei Zinovyev, Shantanu Singh, Anne E Carpenter.

Cell Painting images offer valuable insights into a cell's state and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUMP Cell Painting Consortium perturbed roughly 75% of the protein-coding genome in human U-2 OS cells, generating a rich resource of single-cell images and extracted features. These profiles capture the phenotypic impacts of perturbing 15,243 human genes, including overexpressing 12,609 genes (using open reading frames) and knocking out 7,975 genes (using CRISPR-Cas9). Here we mitigated technical artifacts by rigorously evaluating data processing options and validated the dataset's robustness and biological relevance. Analysis of phenotypic profiles revealed previously undiscovered gene clusters and functional relationships, including those associated with mitochondrial function, cancer and neural processes. The JUMP Cell Painting genetic dataset is a valuable resource for exploring gene relationships and uncovering previously unknown functions.

DOI: https://doi.org/10.1038/s41592-025-02753-9
Theranostics. 2025 ;15(15): 7693-7708

Gut microbiota-derived formate exacerbates pulmonary metastasis in cancer.

Ray Putra Prajnamitra, Chaw Yee Beh, Wen-Hung Tang, Shu-Chian Ruan, Yuan-Yuan Cheng, Pei-Teng Kuo, Yu-Wen Tien, Patrick Ching-Ho Hsieh.

  Rationale: The gut microbiota and its metabolites significantly influence cancer development and metastasis. Among these, formate, the simplest short-chain fatty acid (SCFA), remains underexplored in the context of metastasis. This study investigates the role of microbiota-derived formate in exacerbating pulmonary metastasis in melanoma and pancreatic ductal adenocarcinoma (PDAC), aiming to elucidate its mechanistic contributions to cancer progression. Methods: Using antibiotics-induced dysbiosis in mice, we quantified plasma formate levels via nuclear magnetic resonance (NMR) metabolomics and identified gut bacterial contributors through 16S rRNA sequencing. Formate's effects on melanoma and PDAC lung metastases were evaluated through in vivo supplementation experiments. Cellular assays, metabolomics, and gene expression analyses further elucidated its mechanistic impact. Results: Dysbiosis significantly increased circulating formate levels, with Enterobacterales identified as key contributors. Formate supplementation enhanced melanoma and PDAC lung metastases by promoting cancer cell proliferation, migration, and nucleotide synthesis. Mechanistic studies revealed that formate upregulated one-carbon metabolism, critical for tumor aggressiveness, and increased the production of metabolites like glutathione, facilitating oxidative stress resistance. Conclusion: Microbiota-derived formate plays a critical role in enhancing pulmonary metastasis by modulating cancer cell metabolism. These findings highlight the therapeutic potential of targeting formate production or its associated metabolic pathways to mitigate cancer spread. Additionally, microbiome modulation emerges as a promising complementary approach to improving cancer treatment outcomes.

Keywords:  Melanoma; formate; lung metastasis; metabolomics; microbiota

DOI:  https://doi.org/10.7150/thno.108873