bims-cagime 2025-07-13 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–07–13
twenty-six papers selected by
Kıvanç Görgülü, Technical University of Munich

GDF15: from biomarker to target in cancer cachexia.
Ca2+-dependent vesicular and non-vesicular lipid transfer controls hypoosmotic plasma membrane expansion.
Sensing of extracellular l-proline availability by the integrated stress response determines the outcome of cell competition.
Fluorescent probes for the visualization of membrane microdomain, deformation, and fusion.
Groove architecture controls lipid scrambling in simulations of protein and model systems.
Selective remodelling of the adipose niche in obesity and weight loss.
[Caveolin-1 stiffens the plasma membrane and limits transcellular tunnel expansion].
Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.
Collective cell migration across scales: A systems perspective.
ATG16L1 membrane recruitment in autophagy.
Labile iron pool dynamics do not drive ferroptosis potentiation in colorectal cancer cells.
Acyl-CoA-binding protein as a driver of pathological aging.
Multivalency Controls the Growth and Dynamics of a Biomolecular Condensate.
The role of ester- vs. ether-linked phospholipids in the ability of biological membranes to accept protons and support proton diffusion.
In vitro Reconstitution of Cytoskeletal Networks inside Phase Separated Giant Unilamellar Vesicles (GUVs).
Dynamic forces shape the survival fate of eliminated cells.
Extracellular Vesicles in cancer: from isolation and characterization to metastasis, drug resistance, and clinical applications.
Mendelian randomization analysis of immune cell populations, serum metabolites and hepatocellular carcinoma risk.
Oxidative Phosphorylation in Uncoupled Mitochondria.
ECM Mechanics Control Jamming-to-Unjamming Transition of Cancer Cells.
Advanced Microfluidics for Single Cell-Based Cancer Research.
Molecular recording of cellular protein kinase activity with chemical labeling.
Therapeutic targeting of FOSL1 and RELA-dependent transcriptional mechanisms to suppress pancreatic cancer metastasis.
Polyamines buffer labile iron to suppress ferroptosis.
KinoViz: A User-Friendly Web Application for High-Throughput Kinome Profiling Analysis and Visualization in Cancer Research.
A guide to characterizing the dynamic mitochondria-endoplasmic reticulum contact sites.

Trends Cancer. 2025 Jul 09. pii: S2405-8033(25)00150-5. [Epub ahead of print]

GDF15: from biomarker to target in cancer cachexia.

Max Hüllwegen, Maximilian Kleinert, Stephan von Haehling, Andreas Fischer.

  Most patients with advanced cancer suffer from cachexia, a complex metabolic disorder characterized by unintentional body weight loss that diminishes their quality of life and reduces the effectiveness of therapies. Currently, effective treatments for cachexia remain elusive. Growth differentiation factor 15 (GDF15) is a nonspecific blood biomarker of cancer, hyperemesis gravidarum, and various chronic diseases. GDF15 acts through GDNF family receptor α-like (GFRAL) receptors in the hindbrain to influence food intake, nausea, body weight, and insulin sensitivity. In this review we synthesize the current literature on the role of GDF15 in regulating metabolism and immunosuppression, and elucidate how these processes impact on cancer progression. We highlight recent clinical trials demonstrating that targeting GDF15 can overcome resistance to immunotherapy and increase physical activity, appetite, and weight gain in cancer patients.

Keywords:  GDF15; biomarker; cachexia; cancer; immunosuppression; metabolism

DOI:  https://doi.org/10.1016/j.trecan.2025.06.007
BMC Biol. 2025 Jul 09. 23(1): 207

Ca2+-dependent vesicular and non-vesicular lipid transfer controls hypoosmotic plasma membrane expansion.

Baicong Mu, David M Rutkowski, Gianluca Grenci, Dimitrios Vavylonis, Dan Zhang.

   BACKGROUND: Robust coordination of surface and volume changes is critical for cell integrity. Few studies have elucidated the plasma membrane (PM) remodeling events during drastic cell surface and volume alteration, especially regarding PM sensing and its subsequent rearrangements.
RESULTS: In this article, using fission yeast protoplasts, we reveal a Ca2+-dependent mechanism for membrane addition that ensures PM integrity and allows its expansion during acute hypoosmotic cell swelling. We show that MscS-like mechanosensitive channels activated by PM tension control extracellular Ca2+ influx, which triggers potential direct lipid transfer at endoplasmic reticulum (ER)-PM contact sites by conserved extended-synaptotagmins and accelerates exocytosis, enabling PM expansion necessary for osmotic equilibrium. Defects in any of these key events result in rapid protoplast rupture upon severe hypotonic shock. Our numerical simulations of such hypoosmotic PM expansion further propose a cellular strategy that combines instantaneous non-vesicular lipid transfer with bulk exocytic membrane delivery to maintain PM integrity for dramatic cell surface/volume adaptation.
CONCLUSIONS: We propose a cellular strategy that combines instantaneous non-vesicular lipid transfer with bulk exocytic membrane delivery to maintain PM integrity for dramatic cell surface/volume adaptation.

Keywords:  Ca2+ signaling; ER-PM contacts; Exocytosis; Extended-synaptotagmins; Fission yeast; Hypoosmotic shock; MscS-like mechanosensitive channels; Non-vesicular lipid transfer; PM expansion; PM integrity

DOI:  https://doi.org/10.1186/s12915-025-02309-5
Sci Adv. 2025 Jul 11. 11(28): eadw1883

Sensing of extracellular l-proline availability by the integrated stress response determines the outcome of cell competition.

Shruthi Krishnan, Ana Lima, Sizhe Tan, Ying Thong Low, Salvador Perez Montero, Aida Di Gregorio, Adrian Perez Barreto, Sarah Bowling, Karen Vousden, Tristan A Rodriguez.

Cell competition is a conserved fitness quality control that eliminates cells that are less fit than their neighbors. How winner cells induce the elimination of losers is poorly understood. We tackle this question by studying the onset of embryonic differentiation in mice, where cell competition eliminates 35% of embryonic cells. These loser cells have mitochondrial dysfunction, which we show causes amino acid deprivation and activation of the integrated stress response (ISR), a pathway essential for their survival. We demonstrate that l-proline is a key amino acid sensed by the ISR and that proline represses the ISR and drives their elimination. These results indicate that cell competition acts as a previously unidentified tissue-sparing mechanism, regulated by the availability of extracellular amino acids, that allows for the elimination of dysfunctional cells when amino acids are plentiful but ensures their survival in nutrient-poor environments.

DOI: https://doi.org/10.1126/sciadv.adw1883
Smart Mol. 2025 Mar;3(1): e20240059

Fluorescent probes for the visualization of membrane microdomain, deformation, and fusion.

Pei-Hong Tong, Tong-Yuan Wu, Mingle Li, Hai-Bin Wang, Feng Zheng, Lin Xu, Wei-Tao Dou.

  The cell membrane, a fluid interface composed of self-assembled phospholipid molecules, is a vital component of biological systems that maintains cellular stability and prevents the invasion of foreign toxins. Due to its inherent fluidity, the cell membrane can undergo bending, shearing, and stretching, making membrane deformation crucial in processes like cell adhesion, migration, phagocytosis, and signal transduction. Within the plasma membrane are highly ordered dynamic structures formed by lipid molecules, known as "lipid rafts," whose dynamic dissociation and reorganization are prerequisites for membrane deformation. Fluorescent probes have emerged as vital tools for studying these dynamic processes, offering a non-destructive, in situ, and real-time imaging method. By strategically designing these probes, researchers can image not only the microdomains of cell membranes but also explore more complex processes such as membrane fusion and fission. This review systematically summarizes the latest advancements in the application of fluorescent probes for cell membrane imaging. It also discusses the current challenges and provides insights into future research directions. We hope this review inspires further studies on the dynamic processes of complex cell membranes using fluorescent probes, ultimately advancing our understanding of the mechanisms underlying membrane dissociation, reorganization, fusion, and separation, and fostering research and therapeutic development for membrane-associated diseases.

Keywords:  deformation; fluorescent probes; fusion; membrane microdomain

DOI:  https://doi.org/10.1002/smo.20240059
bioRxiv. 2025 Jul 01. pii: 2025.06.27.662058. [Epub ahead of print]

Groove architecture controls lipid scrambling in simulations of protein and model systems.

Harper E Smith, Travis Harrison-Rawn, Wang Zheng, Angela Ballesteros, Marcos Sotomayor.

Lipid bilayers are essential to life as they surround most cells and membrane-bound organelles. The integrity and fate of cells depend on the asymmetric makeup of lipid bilayers with various membrane proteins regulating the lipid composition of a bilayer's two leaflets. Lipids scramblases are one of the primary regulators of lipid asymmetry in bilayers, spontaneously transferring lipids between membrane leaflets. Members of the TMEM16, OSCA/TMEM63, and TMC families have been suggested to be lipid scramblases. Despite significant differences, these proteins share a common structural architecture that features a membrane-exposed groove. The "credit card" mechanism proposes that lipids switch leaflets by moving their polar head groups either inside (partially dry) or on the surface of (wet) membrane-exposed, open hydrophilic grooves. However, emerging evidence of closed-groove scrambling challenges this model. Given the sequence diversity of groove-lining amino acids in TMEM16, OSCA/TMEM63, and TMC proteins, we hypothesized that lipid scrambling is primarily determined by groove architecture. To test this hypothesis and the credit card mechanism, we used coarse-grained molecular dynamics simulations of experimental structures and AlphaFold-generated models of six different scramblases in closed and open states. In these simulations, we observed little scramblase activity in most closed-state configurations but robust scrambling by all open-state models. We then built simplified TMEM16-based scramblases with only three bead types uniformly set for solvent-facing, transmembrane, and groove regions. We used this and further simplified models to vary groove surface hydrophilicity, groove surface geometry, and groove architecture. Our models support the partially dry and wet credit card mechanisms and suggest that groove architecture plays a more important role in facilitating lipid scrambling than the detailed sequence of groove-lining amino acids.

DOI: https://doi.org/10.1101/2025.06.27.662058
Nature. 2025 Jul 09.

Selective remodelling of the adipose niche in obesity and weight loss.

Antonio M A Miranda, Liam McAllan, Guianfranco Mazzei, Ivan Andrew, Iona Davies, Meryem Ertugrul, Julia Kenkre, Hiromi Kudo, Joana Carrelha, Bhavik Patel, Sophie Newton, Weihua Zhang, Alice Pollard, Amy Cross, Oliver McCallion, Mikyung Jang, Ka Lok Choi, Scarlett Brown, Yasmin Rasool, Marco Adamo, Mohamed Elkalaawy, Andrew Jenkinson, Borzoueh Mohammadi, Majid Hashemi, Robert Goldin, Laurence Game, Joanna Hester, Fadi Issa, Dylan G Ryan, Patricia Ortega, Ahmed R Ahmed, Rachel L Batterham, John C Chambers, Jaspal S Kooner, Damir Baranasic, Michela Noseda, Tricia Tan, William R Scott.

Weight loss significantly improves metabolic and cardiovascular health in people with obesity1-3. The remodelling of adipose tissue (AT) is central to these varied and important clinical effects4. However, surprisingly little is known about the underlying mechanisms, presenting a barrier to treatment advances. Here we report a spatially resolved single-nucleus atlas (comprising 171,247 cells from 70 people) investigating the cell types, molecular events and regulatory factors that reshape human AT, and thus metabolic health, in obesity and therapeutic weight loss. We discover selective vulnerability to senescence in metabolic, precursor and vascular cells and reveal that senescence is potently reversed by weight loss. We define gene regulatory mechanisms and tissue signals that may drive a degenerative cycle of senescence, tissue injury and metabolic dysfunction. We find that weight loss reduces adipocyte hypertrophy and biomechanical constraint pathways, activating global metabolic flux and bioenergetic substrate cycles that may mediate systemic improvements in metabolic health. In the immune compartment, we demonstrate that weight loss represses obesity-induced macrophage infiltration but does not completely reverse activation, leaving these cells primed to trigger potential weight regain and worsen metabolic dysfunction. Throughout, we map cells to tissue niches to understand the collective determinants of tissue injury and recovery. Overall, our complementary single-nucleus and spatial datasets offer unprecedented insights into the basis of obese AT dysfunction and its reversal by weight loss and are a key resource for mechanistic and therapeutic exploration.

DOI: https://doi.org/10.1038/s41586-025-09233-2
Med Sci (Paris). 2025 Jun-Jul;41(6-7):41(6-7): 558-560

[Caveolin-1 stiffens the plasma membrane and limits transcellular tunnel expansion].

Emmanuel Lemichez, Camille Morel, Cécile Leduc, Patricia Bassereau.

DOI: https://doi.org/10.1051/medsci/2025093
bioRxiv. 2025 Jul 04. pii: 2025.06.30.662412. [Epub ahead of print]

Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism.

Orion S Willoughby, Anna S Nichenko, Matthew H Brisendine, Niloufar Amiri, Shelby N Henry, Daniel S Braxton, John R Brown, Kalyn S Specht, Adele K Addington, Alexey V Zaitsev, Steven T Burrows, Ryan P McMillan, Haiyan Zhang, Spencer A Tye, Charles P Najt, Siobhan M Craige, Timothy W Rhoads, Junco S Warren, Joshua C Drake.

Metabolic flexibility, the capacity to adapt fuel utilization in response to nutrient availability, is essential for maintaining energy homeostasis and preventing metabolic disease. Here, we investigate the role of Ulk1 phosphorylation at serine 555 (S555), a site regulated by AMPK, in coordinating metabolic switching following short-term caloric restriction and fasting. Using Ulk1(S555A) global knock-in mice, we show loss of S555 phosphorylation impairs glucose oxidation in skeletal muscle and liver during short-term CR, despite improved glucose tolerance. Metabolomic, transcriptomic, and mitochondrial respiration analyses reveal a compensatory reliance on glucogenic amino acids, particularly alanine and serine, in Ulk1(S555A) mice, with sustained amino acid oxidation during fasting and blunted mitochondrial response to energetic stress. These findings establish Ulk1(S555) phosphorylation as a critical regulatory event linking nutrient stress to substrate switching and highlights an underappreciated role of Ulk1 in maintaining metabolic flexibility.

DOI: https://doi.org/10.1101/2025.06.30.662412
Semin Cell Dev Biol. 2025 Jul 08. pii: S1084-9521(25)00038-2. [Epub ahead of print]173 103628

Collective cell migration across scales: A systems perspective.

Zimeng Wu, Mie Wong.

  Collective cell migration is a key tissue shaping process fundamental to development, wound healing and cancer invasion. The sensing, integration, transduction and propagation of guidance signals and the resulting generation of collective cell responses during collective cell migration can occur at several different length scales from molecular to cellular to supracellular. Furthermore, we have become aware that the cell-environment relationship during migration is bi-directional, where cells not only receive guidance cues from the environment, but also dynamically remodel the environment via their migratory behaviours. Such complex interplay of internal (i.e. intracellular) and external (i.e. cell-cell and cell-environment) interactions makes predicting the emergent output behaviours of cell groups challenging. Here, we propose a framework that combines interdisciplinary experimental and theoretical approaches to bridge the gap between molecular-level mechanisms and tissue-level phenomena during collective cell migration in complex environments. We will review recent works on both in vitro and in vivo migratory models that successfully employ some of these approaches to identify general principles explaining the input-output relationships of robustly tuneable migratory systems. By integrating in vitro with in vivo observations, we will develop more comprehensive models of how collective cell migration is orchestrated in living organisms, which will also pave the way for more effective applications in tissue engineering and disease therapeutics in the future.

Keywords:  Collective cell migration; Development; Feedback; GPCR; Live imaging; Modelling; Systems biology

DOI:  https://doi.org/10.1016/j.semcdb.2025.103628
Crit Rev Biochem Mol Biol. 2025 Jul 11. 1-16

ATG16L1 membrane recruitment in autophagy.

Fujing Wei, Nan Qin, Yunling Chen, Zhenzhen Liu, Xiaozhu Zhao, Xiaoying Yu, Ziling Feng, Yu Wang, Aimin Yang, Hongjuan Cui.

  Autophagy, a highly conserved catabolic pathway in eukaryotes, is essential for cellular survival during starvation and for maintaining cellular homeostasis. Central to autophagy is the de novo formation of double-membrane autophagosomes, which requires the orchestrated action of a set of autophagy-related (ATG) proteins. ATG16L1 is a core autophagy protein involved in distinct phases of autophagosome biogenesis, including membrane remodeling and the formation of phagophore-like membrane cups. It interacts with the ATG12-ATG5 conjugate to form the ATG12-ATG5-ATG16L1 complex, which functions as an E3-like enzyme to catalyze LC3 lipidation. The membrane targeting of the ATG12-ATG5-ATG16L1 complex is crucial for regulating autophagy and preventing ectopic membrane engagement. In this review, we summarize and discuss the potential mechanisms underlying ATG16L1 membrane recruitment, focusing on its intrinsic membrane-binding properties and partner-mediated recruitment pathways. We critically explore how these multiple mechanisms collectively ensure the proper localization and function of ATG16L1, thereby regulating the initiation of autophagy, LC3 lipidation, and the sequestration of bacteria during xenophagy.

Keywords:  ATG12–ATG5-ATG16L1 complex; ATG16L1; Autophagy; autophagosome; membrane targeting

DOI:  https://doi.org/10.1080/10409238.2025.2521321
bioRxiv. 2025 Jul 05. pii: 2025.07.01.662602. [Epub ahead of print]

Labile iron pool dynamics do not drive ferroptosis potentiation in colorectal cancer cells.

Varun Ponnusamy, Deahzana R Randall, Zheng Hong Lee, Nupur K Das, Liang Zhao, Kathryn Buscher, Sumeet Solanki, Adam R Renslo, Peggy P Hsu, Yatrik M Shah.

Colorectal cancer (CRC) is the second leading cause of cancer-related mortality in the United States. CRC tumors exhibit aberrant iron accumulation, which supports tumor cell proliferation through multiple metabolic pathways. However, the oncogenic benefits of elevated iron must be counterbalanced by its potential to catalyze oxidative damage via reactive oxygen species generated from labile, redox-active iron. Ferroptosis is a regulated, non-apoptotic form of cell death characterized by iron-dependent lipid peroxidation. This process is tightly controlled by the selenoenzyme glutathione peroxidase 4 (GPX4), which reduces lipid peroxides and can be pharmacologically inhibited by agents such as RSL3 and JKE1674. A key source of redox-active iron is the labile iron pool (LIP), yet its role in regulating ferroptosis remains incompletely defined. To examine this, we supplemented CRC cells with exogenous iron following pharmacologic induction of ferroptosis. Iron supplementation significantly reduced cell viability, suggesting that expansion of the LIP potentiates ferroptotic cell death. However, whether ferroptosis is accompanied by dynamic changes in the LIP, and if such changes are mechanistically required for its potentiation, was unknown. To further characterize this response, we profiled the expression of iron regulatory genes under ferroptotic conditions and observed no change in transcriptional response in iron homeostasis genes. When using a fluorescent probe for labile iron, we found that the LIP did not measurably increase during ferroptosis induction. These findings suggest that the LIP itself does not expand after the initiation of ferroptosis to become the primary driver of ferroptotic potentiation.

DOI: https://doi.org/10.1101/2025.07.01.662602
Proc Natl Acad Sci U S A. 2025 Jul 15. 122(28): e2501584122

Acyl-CoA-binding protein as a driver of pathological aging.

Léa Montégut, Flavia Lambertucci, Lucas Moledo-Nodar, Carmen Fiuza-Luces, Carlos Rodríguez-López, Jose Antonio Serra-Rexach, Sylvie Lachkar, Omar Motiño, Mahmoud Abdellatif, Sylvère Durand, Fanny Aprahamian, Vincent Carbonnier, Delphine Le Corre, Sophie Mouillet-Richard, Hui Chen, Allan Sauvat, Yanbing Dong, Sijing Li, Yan Rong, Federico Pietrocola, Pierre Laurent-Puig, Carlos López-Otín, Isabelle Martins, Clea Barcena, Alejandro Lucia, Guido Kroemer.

  The tissue hormone acyl coenzyme A-binding protein (ACBP, encoded by the gene diazepam-binding inhibitor, DBI) has been implicated in various facets of pathological aging. Here, we show that ACBP plasma concentrations are elevated in (close-to-)centenarians (mean ± SD age 99.5 ± 4.5 y) commensurate with their health deterioration, correlating with a reduced glomerular filtration rate and a surge in senescence-associated cytokines. ACBP neutralization by means of a monoclonal antibody (mAb) improved health span in a strain of progeroid mice. In a mouse model of chronic kidney injury induced by cisplatin, anti-ACBP mAb administration counteracted both histopathological and functional signs of organ failure. ACBP inhibition also prevented the senescence of tubular epithelial cells and glomerular podocytes induced by cisplatin or doxorubicin, respectively, as measurable by the immunohistochemical detection of cyclin-dependent kinase inhibitor 1A (CDKN1A, best known as p21). Senescence was also prevented by anti-ACBP mAb treatment in additional mouse models of accelerated aging. This applied to liver damage induced by a combination of high-fat diet and carbon tetrachloride, where hepatic cells become senescent. Moreover, administration of anti-ACBP mAb prevented natural and doxorubicin-accelerated cardiomyocyte senescence. We performed single-nucleus RNA sequencing to study the transcriptome of hearts that had been exposed to doxorubicin and/or anti-ACBP in vivo. In cardiomyocytes, doxorubicin caused an anti-ACBP-reversible dysregulation of mRNAs coding for cardioprotective proteins involved in autophagy, fatty acid oxidation, mitochondrial homeostasis, and oxidative phosphorylation. Altogether, these findings plead in favor of a broad age-promoting effect of ACBP across different organ systems.

Keywords:  aging; autophagy; chemotherapy; kidney injury; senescence

DOI:  https://doi.org/10.1073/pnas.2501584122
J Am Chem Soc. 2025 Jul 08.

Multivalency Controls the Growth and Dynamics of a Biomolecular Condensate.

Julian von Hofe, Jatin Abacousnac, Mechi Chen, Moeka Sasazawa, Ida Javér Kristiansen, Soren Westrey, David G Grier, Saumya Saurabh.

Biomolecular condensates are essential for cellular organization and function, yet understanding how chemical and physical factors govern their formation and dynamics has been limited by a lack of noninvasive measurement techniques. Conventional microscopy methods often rely on fluorescent labeling and substrate immobilization, which can perturb the intrinsic properties of condensates. To overcome these challenges, we apply label-free, contact-free holographic video microscopy to study the behavior of a condensate-forming protein in vitro. This technique enables rapid, high-throughput, and precise measurements of individual condensate diameters and refractive indexes, providing unprecedented insight into size distributions and dense-phase macromolecular concentrations over time. Using this method, we investigate the kinetics of droplet growth, aging, and equilibrium dynamics in the model condensate-forming protein PopZ. By systematically varying the concentration and valence of cations, we uncover how multivalent ions influence condensate organization and dynamics, a hypothesis we further test using super-resolution microscopy. Our findings reveal that PopZ droplet growth deviates from classical models such as Smoluchowski coalescence and Ostwald ripening. Instead, we show that condensate growth is consistent with gelation at the critical overlap concentration. Holographic microscopy offers significant advantages over traditional techniques, such as differential interference contrast microscopy, delivering reproducible measurements and capturing condensate dynamics with unparalleled precision. This work highlights the power of holographic microscopy to probe the material properties and mechanistic underpinnings of biomolecular condensates, paving the way for deeper insights into their roles in synthetic systems.

DOI: https://doi.org/10.1021/jacs.5c02947
Biophys J. 2025 Jul 08. pii: S0006-3495(25)00424-2. [Epub ahead of print]

The role of ester- vs. ether-linked phospholipids in the ability of biological membranes to accept protons and support proton diffusion.

Ambili Ramanthrikkovil Variyam, Mario Mencía, Nadav Amdursky.

  In biology, the distribution of ester-linked vs. ether-linked phospholipids is meaningful, such as in the abundance of ether-linked phospholipids in archaea vs. ester-linked phospholipids in bacteria/eukarya, and the presence of ether-linked phospholipids in some tissues of higher eukaryotes. Owing to biological membranes' capability of proton acceptance and supporting proton diffusion (PD) on their surface, e.g., in bioenergetics, it was envisioned that the phospholipid linkage might condition the proton transfer (PT) and PD properties. Here, we explore how and if such differences in membrane composition result in attenuation in the PT/PD properties of biological membranes by using a light-gated membrane-tethered proton donor. We reveal that the PT/PD properties differ between the membranes and between the two phases of the membranes (liquid vs. gel phase). At the liquid phase, we found that the headgroup dominates the PT/PD properties, whereas the ester-/ether-linkage has no substantial role. However, at the gel solid phase, such linkage has a significant role in determining both the PT from the probe to the membrane and the subsequent PD properties. Surprisingly, we found that the PT from the probe to the surface of the ether-linked lipid membrane was faster than that of the ester-linked lipid membrane. We explain this finding by the extracted dimensionality of PD. We show that in the gel phase, the ester-linked lipids create a proton pathway with PD dimensionality close to unity, resulting in poor PT, whereas the ether-linked lipids allow lateral PD and a faster PT. The PT/PD properties of the ether-linked lipid membranes also appear mostly insensitive to exterior bulk protons, which might be ascribed to the inner polar part of such membranes. Since bioenergetics is fundamental within cells, the different capabilities of the membranes to support PT/PD might explain the evolutionary constraints of their formation and their presence in certain mammalian tissues.

Keywords:  Archaeal membranes; Bacterial membranes; Lateral diffusion; Photoacids; Proton transport

DOI:  https://doi.org/10.1016/j.bpj.2025.07.005
J Vis Exp. 2025 Jun 20.

In vitro Reconstitution of Cytoskeletal Networks inside Phase Separated Giant Unilamellar Vesicles (GUVs).

Nishu Kanwa, María Reverte-López, Petra Schwille.

Biomimetic lipid membranes in the form of giant unilamellar vesicles (GUVs) are commonly used to mimic cellular membrane behavior because of the ease of protein reconstitution inside GUVs, visualization, as well as understanding cellular membrane-protein dynamics. However, cell membranes comprise lipid rafts (or domains) arising from the presence of different lipids in the cellular membrane. Such increased complexity in model systems can be incorporated to result into phase separated GUVs, where lipid composition can be finely tuned. While encapsulation methods for the generation of homogeneous GUVs are widely known, methods to encapsulate proteins within phase separated GUVs are limited. Here, this protocol presents a simplified one-pot production of phase separated GUVs, comprised of liquid-disordered (Ld) and liquid ordered (Lo) domains, efficiently encapsulating different cytoskeletal proteins, i.e., FtsZ and actin, making the method a versatile tool for minimal cell production. Specifically, this approach uses an emulsion transfer protocol to produce GUVs with a high encapsulation efficiency. In this method, a lipid-monolayer is first generated by emulsifying a protein solution in a lipid/oil mixture, where lipids of varying phase transition temperatures are chosen to yield phase separation in the resultant GUVs. This emulsion is transferred gently on top of a lipid-in-oil solution in another tube, resulting in the formation of a water-oil interface. The solution is then centrifuged at elevated temperatures (ideally at 37 °C to retain protein activity), after which GUVs are collected for imaging. This method simplifies the in vitro reconstitution of cytoskeletal proteins within phase separated GUVs without using a cumbersome laboratory setup, and thus serves as a convenient method for studying the mechanics of cytoskeletal-membrane interactions in confinement.

DOI: https://doi.org/10.3791/68530
Nat Phys. 2025 Jan 08. pii: s41567-024-02716-5. [Epub ahead of print]

Dynamic forces shape the survival fate of eliminated cells.

Lakshmi Balasubramaniam, Siavash Monfared, Aleksandra Ardaševa, Carine Rosse, Andreas Schoenit, Tien Dang, Chrystelle Maric, Mathieu Hautefeuille, Leyla Kocgozlu, Ranjith Chilupuri, Sushil Dubey, Elisabetta Marangoni, Bryant L Doss, Philippe Chavrier, René-Marc Mège, Amin Doostmohammadi, Benoit Ladoux.

Tissues eliminate unfit, unwanted, or unnecessary cells through cell extrusion, and this can lead to the elimination of both apoptotic and live cells. However, the mechanical signatures that influence the fate of extruding cells remain unknown. Here we show that modified force-transmission across adherens junctions inhibits apoptotic cell eliminations. By combining cell experiments with varying levels of E-cadherin junctions and three-dimensional modelling of cell monolayers, we find that these changes not only affect the fate of the extruded cells but also shift extrusion from the apical to the basal side, leading to cell invasion into soft collagen gels. We generalize our findings using breast cancer patient-derived xenografts and cysts cultured in matrigel. Our results link intercellular force transmission regulated by cell-cell communication to cell extrusion mechanisms, with potential implications during morphogenesis and invasion of cancer cells.

DOI: https://doi.org/10.1038/s41567-024-02716-5
BMC Cancer. 2025 Jul 08. 25(1): 1154

Extracellular Vesicles in cancer: from isolation and characterization to metastasis, drug resistance, and clinical applications.

Ancuta Jurj, Doru Paul, George A Calin.

  Cancer progression, along with other hallmarks of cancer, is sustained through bidirectional cell-to-cell communication. This function is primarily facilitated by lipid-rich nanoparticles expelled into the extracellular matrix by stromal and/or malignant cells. These entities, known as extracellular vesicles, contain a vast repertoire of bioactive molecules and hold promise as potential biomarkers and nanovehicles for drug delivery. Intriguingly, the cellular and molecular mechanisms governing the functions of extracellular vesicles remain poorly understood. In the present manuscript, we highlight the intracellular and intercellular journey of extracellular vesicles, from their inception to the present day, their implications in various hallmarks of cancer, and their clinical applications.

Keywords:  Biomarkers; Cancer progression; Drug resistance; Extracellular vesicles

DOI:  https://doi.org/10.1186/s12885-025-14375-7
Discov Oncol. 2025 Jul 05. 16(1): 1266

Mendelian randomization analysis of immune cell populations, serum metabolites and hepatocellular carcinoma risk.

Wei Shen, Yuanying Zeng.

   BACKGROUND: Hepatocellular carcinoma (HCC) remains highly lethal globally, with complex pathogenic mechanisms. This study employs Mendelian randomization (MR) to investigate causal relationships between immune cells, serum metabolites, and HCC risk.
METHODS: A two-sample Mendelian randomization (2SMR) design was employed, based on large-scale genome-wide association studies (GWAS) databases, selecting single nucleotide polymorphisms (SNPs) strongly associated with immune cell features and plasma metabolites as genetic instrumental variables. The inverse variance weighted (IVW). method was primarily used for effect size estimation, with robustness verified through multiple sensitivity analysis methods including MR-Egger regression and weighted median method.
RESULTS: MR analysis revealed three immune cell subpopulations causally associated with HCC: CD127 on CD28 + CD4 + T cells (OR = 1.31, 95% CI: 1.15-1.49), unswitched memory B cell percentage (OR = 1.57, 95% CI: 1.23-2.01). Four causal serum metabolites were identified: 5-hydroxylysine (OR = 0.64), isobutyrylcarnitine (OR = 1.67), 1-stearoyl-GPC (OR = 0.27), and glycosyl-N-tricosanoyl-sphingadienine (OR = 0.32). For plasma metabolites, four metabolites were significantly associated with HCC risk: 5-hydroxylysine (OR = 0.64), isobutyrylcarnitine (OR = 1.67), 1-stearoyl-GPC (OR = 0.27), and glycosyl-N-tricosanoyl-sphingadienine (OR = 0.32).
CONCLUSION: This multi-omics approach provides evidence for causal relationships between specific immune populations, metabolites, and HCC risk, identifying potential biomarkers and therapeutic targets for HCC prevention and treatment.

Keywords:  Hepatocellular carcinoma; Immune cells; Mendelian randomization; Metabolites; Tumor microenvironment

DOI:  https://doi.org/10.1007/s12672-025-03037-6
Bioessays. 2025 Jul 06. e70038

Oxidative Phosphorylation in Uncoupled Mitochondria.

Henver S Brunetta, Marcelo A Mori, Alexander Bartelt.

  Mitochondrial membrane potential is highly dependent on coupled as well as uncoupled respiration. While brown adipose tissue (BAT) mediates non-shivering thermogenesis (NST), a highly adaptive bioenergetic process critical for energy metabolism, the relationship of coupled and uncoupled respiration in thermogenic adipocytes remains complicated. Uncoupling protein 1 (UCP1)-mediated proton leak is the primary driver of NST, but recent studies have shown that oxidative phosphorylation may be an underappreciated contributor to UCP1-dependent NST. Here, we highlight the role of ATP synthase for BAT thermogenesis and discuss the implications of fine-tuning adrenergic signaling in brown adipocytes by the protein inhibitory factor 1 (IF1). We conclude by hypothesizing future directions for mitochondrial research, such as investigating the potential role of IF1 for mitochondrial substrate preference, structural dynamics, as well as its role in cell fate decision and differentiation.

Keywords:  UCP1; adipocytes; bioenergetics; metabolism; mitochondria; obesity; thermogenesis

DOI:  https://doi.org/10.1002/bies.70038
Cells. 2025 Jun 20. pii: 943. [Epub ahead of print]14(13):

ECM Mechanics Control Jamming-to-Unjamming Transition of Cancer Cells.

Claudia Tanja Mierke.

  Cancer metastasis constitutes a multifactorial phenomenon that continues to confound therapeutic strategies. The biochemical signals governing motile phenotypes have been extensively characterized, but mechanobiological interactions have only recently been integrated into cancer cell motility models and remain less well elucidated. The identification of the biochemically and mechanically controlled epithelial-mesenchymal transition (EMT) of cancer cells, which occurs either completely or partially, has led to a major breakthrough and a universal phenomenon in cancers. In addition, a relatively new theory based on mechanobiological aspects called "jamming-to-unjamming transition" is being proposed to explain the transition of cancer cells to an invasive phenotype. The latter transition may help to better understand the different types of 3D migration and invasion of cancer cells. Similarly to EMT, the transition from jamming to unjamming seems to be controlled by molecular and physical factors, including cell mechanics and mechanical cues from the extracellular matrix (ECM) of the tumor microenvironment (TME). It is challenging to grasp the distinctions between the transition from jamming to unjamming and EMT, as they appear to be the same at first glance. However, upon closer examination, the two transitions are quite separate. Moreover, it is still unclear whether both transitions may act synergistically. This review highlights the most important breakthroughs in the transition from jamming to unjamming, with a focus on mechanobiology and extracellular environmental aspects, and it compares them with those of EMT. In addition, the impact of the TME, such as ECM scaffold and cancer-associated fibroblasts (CAFs) on the jamming-to-unjamming transition is discussed. Finally, the research frontiers and future directions in the field of mechanobiological research in cancer metastasis are outlined.

Keywords:  EMT; cell and tissue mechanics; extracellular matrix confinement; individual and collective migration and invasion; jamming-to-unjamming transition; mechanobiology; stiffness; viscoelasticity

DOI:  https://doi.org/10.3390/cells14130943
Adv Sci (Weinh). 2025 Jul 11. e00975

Advanced Microfluidics for Single Cell-Based Cancer Research.

Adriana Carneiro, Marta Aranda Palomer, Margarida Esteves, Carolina Rodrigues, José Maria Fernandes, Francisca Oliveira, Alexandra Teixeira, Carlos Honrado, Lorena Dieguez, Sara Abalde-Cela, Miguel Xavier.

  Cancer remains one of the leading causes of mortality worldwide, accounting for ≈10 million deaths annually. Critically, it is metastasis and not the primary tumour that causes most of these deaths. Understanding the mechanisms behind cancer dissemination and therapy resistance is thus a pressing challenge. Traditional bulk tissue analyses have failed to capture the full spectrum of intra-tumour heterogeneity and the dynamic interactions within the tumour microenvironment. Studying cancer at the single-cell level allows unravelling the roles of rare subpopulations, cell-cell interactions, and spatial dynamics that govern tumour evolution, metastasis, and immune evasion. This review explores how recent advances in microfluidic technologies are transforming ability to model and study cancer at the single-cell level. Cutting-edge platforms are highlighted, including droplet microfluidics, single cell-derived spheroids, and tumour-chips, that enable physiologically relevant 3D cancer models. By integrating immune components, biosensing, and patient-derived materials, these platforms hold promise for advancing drug screening, immunotherapy assessment, and personalised medicine. It is concluded by identifying key challenges and priorities for future work, which should focus on increasing model complexity, reproducibility, and integration of spatiotemporal multiomics to better dissect tumour heterogeneity and accelerate clinical translation.

Keywords:  3D models; microfluidics; multi‐omics; organ‐on‐chip; single‐cell technologies

DOI:  https://doi.org/10.1002/advs.202500975
Nat Chem Biol. 2025 Jul 10.

Molecular recording of cellular protein kinase activity with chemical labeling.

De-En Sun, Siu Wang Ng, Yu Zheng, Shu Xie, Niklas Schwan, Paula Breuer, Dirk C Hoffmann, Julius Michel, Daniel D Azorin, Kim E Boonekamp, Frank Winkler, Wolfgang Wick, Michael Boutros, Yulong Li, Kai Johnsson.

Protein kinases control most cellular processes and aberrant kinase activity is involved in numerous diseases. Here we introduce molecular recorders of kinase activities for later analysis to investigate the link between specific kinase activities and cellular phenotypes in heterogeneous cell populations and in vivo. Based on split-HaloTag and a phosphorylation-dependent molecular switch, our recorders become rapidly labeled in the presence of a specific kinase activity and a fluorescent HaloTag substrate. The kinase activity in a given cell controls the degree of fluorescent labeling, whereas the recording window is set by the presence of the fluorescent substrate. We designed specific recorders for four protein kinases, including protein kinase A. We apply our protein kinase A recorder to sort heterogeneous cell populations for subsequent transcriptome analysis, in genome-wide CRISPR screens to discover regulators of PKA activity and to track neuromodulation in freely moving mice.

DOI: https://doi.org/10.1038/s41589-025-01949-6
Cell Death Dis. 2025 Jul 09. 16(1): 504

Therapeutic targeting of FOSL1 and RELA-dependent transcriptional mechanisms to suppress pancreatic cancer metastasis.

Joana E Aggrey-Fynn, Meghana Manjunath, Ashish Rajput, Amro M Abdelrahman, Julia Thiel, Mark J Truty, Andrew Clark, Meng Dong, Steven A Johnsen.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer often diagnosed at an advanced stage, leading to a poor prognosis. The tumor microenvironment (TME) plays a crucial role in driving metastasis, with inflammatory signaling pathways contributing to tumor progression and therapy resistance. However, the combined effects of inflammatory and oncogenic signaling on the epigenetic regulation of PDAC metastasis are poorly understood. Here, we demonstrate that tumor necrosis factor-alpha (TNFα) and epidermal growth factor (EGF) signaling converge to regulate PDAC cell migration through the activation of NF-κB and AP-1 transcription factors. Using single-cell RNA sequencing, in vitro and in vivo models, we show that the simultaneous activation of these pathways with TNFα and EGF cooperatively induces the expression of genes associated with cell motility and migration. Consistently, combinatorial induced genes are co-regulated by the transcription factors FOSL1 and RELA. Remarkably, inhibition of NF-κB transcriptional activity with a glucocorticoid receptor (GR) mixed agonist significantly reduced PDAC cell migration by decreasing RNA polymerase II recruitment to target genes. These findings reveal a novel mechanism by which inflammatory and oncogenic pathways cooperate to drive PDAC metastasis and highlight the therapeutic potential of GR agonists in mitigating tumor cell migration. Our study offers promising avenues for developing mechanism-based therapeutic strategies in PDAC management.

DOI: https://doi.org/10.1038/s41419-025-07810-x
bioRxiv. 2025 Jul 02. pii: 2025.06.30.662349. [Epub ahead of print]

Polyamines buffer labile iron to suppress ferroptosis.

Pushkal Sharma, Heather R Keys, Sebastian Müller, Ivan S Pires, Ryan Mansell, Shinya Imada, Tenzin Kunchok, Millenia Waite, Christalyn Ausler, Bingbing Yuan, Amy Deik, Paula T Hammond, Raphaël Rodriguez, Whitney Henry, Ankur Jain.

Polyamines are essential and evolutionarily conserved metabolites present at millimolar concentrations in mammalian cells. Cells tightly regulate polyamine homeostasis through complex feedback mechanisms, yet the precise role necessitating this regulation remains unclear. Here, we show that polyamines function as endogenous buffers of redox-active iron, providing a molecular link between polyamine metabolism and ferroptosis. Using genome-wide CRISPR screens, we identified a synthetic lethal dependency between polyamine depletion and the key ferroptosis suppressor, GPX4. Mechanistically, we show that polyamine deficiency triggers a redistribution of cellular iron, increasing the labile iron pool and upregulating ferritin. To directly visualize this iron buffering in living cells, we developed a genetically encoded fluorescent reporter for redox-active iron. Live-cell analysis revealed a striking inverse correlation between intracellular polyamine levels and redox-active iron at single-cell resolution. These findings reposition polyamines as key regulators of iron homeostasis, with implications for ferroptosis-linked disease states and cellular redox balance.

DOI: https://doi.org/10.1101/2025.06.30.662349
Res Sq. 2025 Jun 30. pii: rs.3.rs-6431257. [Epub ahead of print]

KinoViz: A User-Friendly Web Application for High-Throughput Kinome Profiling Analysis and Visualization in Cancer Research.

Ehsan Saghapour, Joshua C Anderson, Jake Y Chen, Christopher D Willey.

Kinases, at the signaling level, dynamically mediate uncontrolled cellular growth, survival and other cancer supporting processes. This, paired with the inherent druggability of kinases, points to the importance of measuring kinase activity, and that of inhibitors against them, directly, and to analyze this accurately. High-throughput kinome profiling technologies, such as the PamStation®12, allow researchers to kinetically capture kinase activity, against a multitude of peptide targets simultaneously. Yet, the complex datasets produced often require advanced computational tools and bioinformatics expertise to properly analyze that are not intuitive or readily available. To address this gap, we developed KinoViz, a web-based application to simplify analysis and visualization of kinome array data. KinoViz offers a suite of interactive tools that enables users to upload raw peptide phosphorylation datasets and conduct in-depth analyses without the need for coding knowledge. Key features include modules for visualizing kinetic phosphorylation curves, identifying statistically significant peptide changes, exploring individual peptide profiles, and generating insightful visualizations such as heatmaps, network diagrams, and dimensionality reduction plots (PCA, UMAP). By making complex kinomic data more accessible and interpretable, KinoViz allows researchers to rapidly generate interactive visualizations and comparative analyses. We aim to expand KinoViz's analytical capabilities for more advanced use, including use in direct translational drug discovery.

DOI: https://doi.org/10.21203/rs.3.rs-6431257/v1
FEBS J. 2025 Jul 07.

A guide to characterizing the dynamic mitochondria-endoplasmic reticulum contact sites.

Antigoni Diokmetzidou, Luca Scorrano.

  Organelles were once regarded as discrete entities, but it is now established that they interact through specialized membrane contacts maintained by protein tethers and lipid interactions. Among these, mitochondria-endoplasmic reticulum contact sites (MERCS) emerged as hubs for calcium signaling, lipid metabolism, and mitochondrial dynamics. Here, we critically appraise current methodologies for MERC visualization and quantification, survey the molecular toolbox for their selective perturbation, and highlight common experimental pitfalls. We also discuss key conceptual issues-defining MERCs on structural and functional grounds, addressing redundancy among tethering factors, and distinguishing primary MERC-mediated effects from secondary cellular responses. Finally, we propose that an integrative strategy combining imaging, precise biochemical isolation, proteomics, and functional assays will be essential to resolve outstanding questions about MERC dynamics in physiology and pathology.

Keywords:  endoplasmic reticulum; imaging; membrane contact sites; mitochondria; mitochondria–ER contact sites

DOI:  https://doi.org/10.1111/febs.70184