bims-cagime 2025-04-06 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–04–06
38 papers selected by
Kıvanç Görgülü, Technical University of Munich

Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.
Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis.
Connections across the Cancer Continuum.
Essential Biology of Lipid Droplets.
The Stmn1-lineage contributes to acinar regeneration but not to neoplasia upon oncogenic Kras expression.
Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics.
Muscle wasting in cancer cachexia: Mechanisms and the role of exercise.
Signaling networks in cancer stromal senescent cells establish malignant microenvironment.
First responder to starvation: microreticulophagy clears aberrant membrane proteins in quick bites.
A non-fluorescent immunohistochemistry method for measuring autophagy flux using MAP1LC3/LC3 and SQSTM1 as core markers.
Homeostatic regulation of nucleoporins is a central driver of nuclear pore biogenesis.
Distinct roles of protrusions and collagen deformation in collective invasion of cancer cell types.
Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer.
Method for Imaging and Quantifying Molecular Tensions at Cell-Cell Junctions Using DNA-Based Fluorescent Probes.
Nuclear Galectin-1 promotes KRAS-dependent activation of pancreatic cancer stellate cells.
RAF1 kinase contributes to autophagic lysosome reformation.
Resilience and vulnerabilities of tumor cells under purine shortage stress.
Multiplexed cytometry for single cell chemical biology.
Leveraging real-world data to advance biomarker discovery and precision oncology.
Method for Mapping the Membrane Protein Nanoenvironments Using DNA Nanostructures (NanoDeep).
A closed-loop system for millisecond readout and control of membrane tension.
Antigenic cancer persister cells survive direct T cell attack.
Differentiation stage predicts radiosensitivity in mesenchymal-like pancreatic cancer.
The mechanobiology of biomolecular condensates.
Moonlighting functions of glucose metabolic enzymes and metabolites in cancer.
Dynamic Duos: Coacervate-Lipid Membrane Interactions in Regulating Membrane Transformation and Condensate Size.
Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement.
p62 sorts Lupus La and selected microRNAs into breast cancer-derived exosomes.
Metallic trace elements in pancreatic tissue are associated with higher risk of pancreatic adenocarcinoma - METAPANDA study.
Genetically encoded reporters of actin filament organization in living cells and tissues.
The need to implement FAIR principles in biomolecular simulations.
Regulation of cell migration by extracellular matrix mechanics at a glance.
Programmable macromolecule delivery via engineered trogocytosis.
Translation dysregulation in cancer as a source for targetable antigens.
Patterns of disease dissemination and survival in patients with synchronous and metachronous metastatic pancreatic adenocarcinoma: Nationwide population-based study.
Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome.
In vivo validation of the palmitoylation cycle as a therapeutic target in NRAS -mutant cancer.
Nestin Regulates Autophagy-Dependent Ferroptosis Mediated Skeletal Muscle Atrophy by Ubiquitinating MAP 1LC3B.

Cell. 2025 Mar 26. pii: S0092-8674(25)00270-3. [Epub ahead of print]

Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.

Milka Doktorova, Jessica L Symons, Xiaoxuan Zhang, Hong-Yin Wang, Jan Schlegel, Joseph H Lorent, Frederick A Heberle, Erdinc Sezgin, Edward Lyman, Kandice R Levental, Ilya Levental.

  Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PMs). Using lipidomics, we report that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared with exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization.

Keywords:  cholesterol; lipid asymmetry; lipid diffusion; membrane packing; membrane structure; peripheral protein; permeability; phospholipid; plasma membrane; protein-membrane interactions

DOI:  https://doi.org/10.1016/j.cell.2025.02.034
bioRxiv. 2025 Mar 13. pii: 2025.03.10.642426. [Epub ahead of print]

Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis.

Patrick B Jonker, Mumina Sadullozoda, Guillaume Cognet, Juan J Apiz Saab, Kelly H Sokol, Violet X Wu, Deepa Kumari, Colin Sheehan, Mete E Ozgurses, Darby Agovino, Grace Croley, Smit A Patel, Althea Bock-Hughes, Kay F Macleod, Hardik Shah, Jonathan L Coloff, Evan C Lien, Alexander Muir.

Nutrient limitation is a characteristic feature of poorly perfused tumors. In contrast to well-perfused tissues, nutrient deficits in tumors perturb cellular metabolic activity, which imposes metabolic constraints on cancer cells. The metabolic constraints created by the tumor microenvironment can lead to vulnerabilities in cancers. Identifying the metabolic constraints of the tumor microenvironment and the vulnerabilities that arise in cancers can provide new insight into tumor biology and identify promising antineoplastic targets. To identify how the microenvironment constrains the metabolism of pancreatic tumors, we challenged pancreatic cancer cells with microenvironmental nutrient levels and analyzed changes in cell metabolism. We found that arginine limitation in pancreatic tumors perturbs saturated and monounsaturated fatty acid synthesis by suppressing the lipogenic transcription factor SREBP1. Synthesis of these fatty acids is critical for maintaining a balance of saturated, monounsaturated, and polyunsaturated fatty acids in cellular membranes. As a consequence of microenvironmental constraints on fatty acid synthesis, pancreatic cancer cells and tumors are unable to maintain lipid homeostasis when exposed to polyunsaturated fatty acids, leading to cell death by ferroptosis. In sum, arginine restriction in the tumor microenvironment constrains lipid metabolism in pancreatic cancers, which renders these tumors vulnerable to polyunsaturated-enriched fat sources.

DOI: https://doi.org/10.1101/2025.03.10.642426
Cancer Discov. 2025 Apr 02. 15(4): 663

Connections across the Cancer Continuum.

Luis A Diaz, Lewis C Cantley.

DOI: https://doi.org/10.1158/2159-8290.CD-25-0210
Annu Rev Biochem. 2025 Apr 01.

Essential Biology of Lipid Droplets.

Robert V Farese, Tobias C Walther.

Lipid droplets (LDs), long overlooked as inert cellular storage organelles, are now recognized for their complex and rich biology as membraneless organelles integral to cell metabolism. Significant advances have revealed that LDs are crucial for cellular processes that include the storage and retrieval of lipids for metabolic energy and membrane synthesis and the detoxification of lipids by sequestering them in the organelle's core. Here, we review current key aspects of LD biology, emphasizing insights into fundamental mechanisms of their formation, the mechanisms of protein targeting, new insights into LD turnover, and how LDs integrate into cellular metabolism. Where possible, we describe how these processes are important in physiology and how alterations in LD biology can lead to metabolic disease. We highlight unresolved questions and key challenges to be addressed for further advancing our understanding of LD biology and its implications for health and disease.

DOI: https://doi.org/10.1146/annurev-biochem-091724-013733
bioRxiv. 2025 Mar 19. pii: 2025.03.18.643944. [Epub ahead of print]

The Stmn1-lineage contributes to acinar regeneration but not to neoplasia upon oncogenic Kras expression.

Shakti Dahiya, Jorge R Arbujas, Arian Hajihassani, Sara Amini, Michael Wageley, Klara Gurbuz, Zhibo Ma, Celina Copeland, Mohamed Saleh, George K Gittes, Bon-Kyoung Koo, Kathleen E DelGiorno, Farzad Esni.

BACKGROUND & AIMS: The exocrine pancreas has a limited regenerative capacity, but to what extent all acinar cells are involved in this process is unclear. Nevertheless, the heterogenous nature of acinar cells suggests that cells exhibiting higher plasticity might play a more prominent role in acinar regeneration. In that regard, Stmn1 -expressing acinar cells have been identified as potential facultative progenitor-like cells in the adult pancreas. Here, we studied Stmn1-progeny under physiological conditions, during regeneration, and in the context of Kras G12D expression.
METHODS: We followed the fate of Stmn1-progenies both under baseline conditions, following caerulein-induced acute or chronic pancreatitis, pancreatic duct ligation, and in the context of Kras G12D expression.
RESULTS: The Stmn1-lineage contributes to baseline acinar cell turnover under physiological conditions. Furthermore, these cells rapidly proliferate and repopulate the acinar compartment in response to acute injury in an ADM-independent manner. Moreover, acinar regeneration during chronic pancreatitis progression is in conjunction with a decline in the proliferative capacity of the Stmn1-lineage. Interestingly, newly generated acinar cells display increased susceptibility to additional injury during recurrent acute pancreatitis (RAP). Finally, given their inability to form ADMs, the Stmn1-lineage fails to form PanINs upon oncogenic Kras expression.
CONCLUSIONS: Our findings establish the Stmn1-lineage as a pivotal subpopulation for acinar tissue homeostasis and regeneration. The ability of these cells to restore acinar tissue in an ADM-independent manner distinguishes them as a critical regenerative population. This study presents a new paradigm for acinar regeneration and repair in the context of pancreatitis and neoplasia.

DOI: https://doi.org/10.1101/2025.03.18.643944
Cancer Cell. 2025 Mar 21. pii: S1535-6108(25)00083-2. [Epub ahead of print]

Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics.

Yunhe Liu, Ansam Sinjab, Jimin Min, Guangchun Han, Francesca Paradiso, Yuanyuan Zhang, Ruiping Wang, Guangsheng Pei, Yibo Dai, Yang Liu, Kyung Serk Cho, Enyu Dai, Akshay Basi, Jared K Burks, Kimal I Rajapakshe, Yanshuo Chu, Jiahui Jiang, Daiwei Zhang, Xinmiao Yan, Paola A Guerrero, Alejandra Serrano, Mingyao Li, Tae Hyun Hwang, Andrew Futreal, Jaffer A Ajani, Luisa M Solis Soto, Amir A Jazaeri, Humam Kadara, Anirban Maitra, Linghua Wang.

  Cancer-associated fibroblasts (CAFs) are a multifaceted cell population essential for shaping the tumor microenvironment (TME) and influencing therapy responses. Characterizing the spatial organization and interactions of CAFs within complex tissue environments provides critical insights into tumor biology and immunobiology. In this study, through integrative analyses of over 14 million cells from 10 cancer types across 7 spatial transcriptomics and proteomics platforms, we discover, validate, and characterize four distinct spatial CAF subtypes. These subtypes are conserved across cancer types and independent of spatial omics platforms. Notably, they exhibit distinct spatial organizational patterns, neighboring cell compositions, interaction networks, and transcriptomic profiles. Their abundance and composition vary across tissues, shaping TME characteristics, such as levels, distribution, and state composition of tumor-infiltrating immune cells, tumor immune phenotypes, and patient survival. This study enriches our understanding of CAF spatial heterogeneity in cancer and paves the way for novel approaches to target and modulate CAFs.

Keywords:  cancer-associated fibroblast; cell-cell communication; cellular neighborhood; lymphoid aggregate; pan-cancer; spatial multi-omics; spatial transcriptomics; tertiary lymphoid structure; tumor associated macrophage; tumor microenvironment

DOI:  https://doi.org/10.1016/j.ccell.2025.03.004
Exp Physiol. 2025 Mar 30.

Muscle wasting in cancer cachexia: Mechanisms and the role of exercise.

Zoe P Libramento, Louisa Tichy, Traci L Parry.

  Cancer cachexia (CC) is a multifactorial disease marked by a severe and progressive loss of lean muscle mass and characterized further by inflammation and a negative energy/protein balance, ultimately leading to muscle atrophy and loss of muscle tissue. As a result, patients experiencing cachexia have reduced muscle function and thus less independence and a lower quality of life. CC progresses through stages of increasing severity: pre-cachexia, cachexia and refractory cachexia. Two proposed underlying mechanisms that drive cancer-induced muscle wasting are the autophagy-lysosome and ubiquitin-proteasome systems. An increase in autophagic flux and proteolytic activity leads to atrophy of both cardiac and skeletal muscle, ultimately mediated by tumour or immune-secreted inflammatory cytokines. These pathways occur at a basal level to maintain cellular homeostasis; therefore, it is the overactivation of the pathways that leads to muscle atrophy. Recent evidence demonstrates the ability of aerobic and resistance training to restore these pathways to their basal levels. The mechanism is not yet understood, and more research is needed to determine exactly how exercise influences each pathway. However, exercise has great promise as a therapeutic strategy for CC because of the evidence for it preserving muscle mass and function, and attenuating protein degradative pathways. The extent to which exercise affects the ubiquitin-proteasome and autophagy-lysosome systems is determined by the frequency, intensity and duration of the exercise protocol. As such, an ideal exercise prescription is lacking for individuals with CC.

Keywords:  atrophy; cancer cachexia; exercise

DOI:  https://doi.org/10.1113/EP092544
Proc Natl Acad Sci U S A. 2025 Apr 08. 122(14): e2412818122

Signaling networks in cancer stromal senescent cells establish malignant microenvironment.

Yue Zhang, Teh-Wei Wang, Maho Tamatani, Xinyi Zeng, Lindo Nakamura, Satotaka Omori, Kiyoshi Yamaguchi, Seira Hatakeyama, Eigo Shimizu, Satoshi Yamazaki, Yoichi Furukawa, Seiya Imoto, Yoshikazu Johmura, Makoto Nakanishi.

  The tumor microenvironment (TME) encompasses various cell types, blood and lymphatic vessels, and noncellular constituents like extracellular matrix (ECM) and cytokines. These intricate interactions between cellular and noncellular components contribute to the development of a malignant TME, such as immunosuppressive, desmoplastic, angiogenic conditions, and the formation of a niche for cancer stem cells, but there is limited understanding of the specific subtypes of stromal cells involved in this process. Here, we utilized p16-CreERT2-tdTomato mouse models to investigate the signaling networks established by senescent cancer stromal cells, contributing to the development of a malignant TME. In pancreatic ductal adenocarcinoma (PDAC) allograft models, these senescent cells were found to promote cancer fibrosis, enhance angiogenesis, and suppress cancer immune surveillance. Notably, the selective elimination of senescent cancer stromal cells improves the malignant TME, subsequently reducing tumor progression in PDAC. This highlights the antitumor efficacy of senolytic treatment alone and its synergistic effect when combined with conventional chemotherapy. Taken together, our findings suggest that the signaling crosstalk among senescent cancer stromal cells plays a key role in the progression of PDAC and may be a promising therapeutic target.

Keywords:  cancer stromal cells; pancreatic cancer; senescence

DOI:  https://doi.org/10.1073/pnas.2412818122
Autophagy. 2025 Apr 02.

First responder to starvation: microreticulophagy clears aberrant membrane proteins in quick bites.

Yaneris Alvarado Cartagena, Valeriya Gyurkovska, Nava Segev.

  Cells can use two different pathways for recycling their non-essential components in the lysosome during nutritional stress: macroautophagy and microautophagy. While the well-established macroautophagy pathway requires de novo formation of the double-membrane autophagosome, microautophagy involves direct engulfment of cargo by the lysosomal membrane. Recently, using a yeast model, we identified a novel microreticulophagy pathway induced by nutritional stress that selectively clears aberrant membrane proteins that accumulate during normal growth. This effective clearance occurs rapidly and precedes the degradation of normal ER- or mitochondrial-membrane proteins by macroautophagy. We showed that the nutritional-stress induced selective microreticulophagy pathway requires the ubiquitin-ligase Rsp5, its adaptor Ssh4, and the ESCRT complex. Moreover, live-cell fluorescence microscopy with high temporal and special resolution demonstrated that individual microautophagy events occur within seconds. Thus, cells use the effective microreticulophagy pathway to dispose of misfolded or excess membrane proteins as a first response to starvation. If the stress persists, the more costly macroautophagy pathway is activated for degrading normal cellular components. These findings point to an intricate interplay between microautophagy and macroautophagy during nutritional stress, which optimizes stress responses and could have significant implications for understanding how cells maintain homeostasis or progress to disease states.

Keywords:  Aberrant membrane proteins; ER-phagy; ERAD; macroautophagy; microautophagy; nutritional stress

DOI:  https://doi.org/10.1080/15548627.2025.2487675
FEBS Open Bio. 2025 Apr 03.

A non-fluorescent immunohistochemistry method for measuring autophagy flux using MAP1LC3/LC3 and SQSTM1 as core markers.

Shahla Shojaei, Amir Barzegar Behrooz, Marco Cordani, Mahmoud Aghaei, Negar Azarpira, Daniel J Klionsky, Saeid Ghavami.

  Macroautophagy/autophagy is a crucial cellular process for degrading and recycling damaged proteins and organelles, playing a significant role in diseases such as cancer and neurodegeneration. Evaluating autophagy flux, which tracks autophagosome formation, maturation, and degradation, is essential for understanding disease mechanisms. Current fluorescence-based methods are resource-intensive, requiring advanced equipment and expertise, limiting their use in clinical laboratories. Here, we introduce a non-fluorescent immunohistochemistry (IHC) method using MAP1LC3/LC3 and SQSTM1 as core markers for autophagy flux assessment. LC3 levels reflect autophagosome formation, whereas SQSTM1 degradation and a decrease in the number of its puncta indicate active flux (i.e., lysosomal turnover). We optimized chromogenic detection using diaminobenzidine (DAB) staining and developed a scoring system based on puncta number and the percentage of stained cells. This accessible, cost-effective method enables reliable autophagy quantification using a standard light microscope, bridging the gap between experimental research and clinical diagnostics. Our protocol allows accurate autophagy evaluation in fixed tissues, offering practical applications in biomedical research and clinical pathology assessment.

Keywords:  autophagometer; autophagy flux measurement; cellular homeostasis analysis; chromogenic detection; cost‐effective autophagy assay; non‐fluorescent immunohistochemistry

DOI:  https://doi.org/10.1002/2211-5463.70014
Cell Rep. 2025 Mar 26. pii: S2211-1247(25)00239-6. [Epub ahead of print] 115468

Homeostatic regulation of nucleoporins is a central driver of nuclear pore biogenesis.

Stephen Sakuma, Marcela Raices, Ethan Y S Zhu, Dana Mamriev, Charles I Fisher, Susanne Heynen-Genel, Maximiliano A D'Angelo.

  Nuclear pore complexes (NPCs) are channels that control access to the genome. The number of NPCs that cells assemble varies between different cell types and in disease. However, the mechanisms regulating NPC formation in mammalian cells remain unclear. Using a genome-wide small interfering RNA (siRNA) screen, we identify translation-related factors, proteasome components, and the CCR4-NOT complex as top regulators of NPC assembly and numbers. While inhibition of ribosomal function and protein translation reduces NPC formation, blocking protein degradation or CCR4-NOT function increases NPC numbers. We demonstrate that CCR4-NOT inhibition raises global mRNA levels, increasing the pool of nucleoporin mRNAs available for translation. Upregulation of nucleoporin complexes in CCR4-NOT-inhibited cells allows for higher NPC formation, increasing total NPC numbers in normal and cancer cells. Our findings uncover that nucleoporin mRNA stability and protein homeostasis are major determinants of NPC formation and highlight a role for the CCR4-NOT complex in negatively regulating NPC assembly.

Keywords:  CCR4-CNOT; CP: Cell biology; CP: Molecular biology; degradation; nuclear pore complexes; nucleoporin; proteostasis; translation

DOI:  https://doi.org/10.1016/j.celrep.2025.115468
Biophys J. 2025 Mar 31. pii: S0006-3495(25)00206-1. [Epub ahead of print]

Distinct roles of protrusions and collagen deformation in collective invasion of cancer cell types.

Ye Lim Lee, Gregory D Longmore, Amit Pathak.

The breast tumor microenvironment is composed of heterogeneous cell populations, including normal epithelial cells, cancer-associated fibroblasts, and tumor cells that lead collective cell invasion. Both leader tumor cells and CAFs are known to play important roles in tumor invasion across the collagen-rich stromal boundary. However, their individual abilities to utilize their cell-intrinsic protrusions and perform force-based collagen remodeling to collectively invade remain unclear. To compare collective invasion phenotypes of leader-like tumor cells and CAFs, we embedded spheroids composed of 4T1 tumor cells or mouse tumor-derived CAF cell lines within 3D collagen gels and analyzed their invasion and collagen deformation. We found that 4T1s undergo greater invasion while generating lower collagen deformation compared to CAFs. Although force-driven collagen deformations are conventionally associated with higher cellular forces and invasion, here 4T1s specifically rely on actin-based protrusions, while CAFs rely on myosin-based contractility for collective invasion. In denser collagen, both cell types slowed their invasion, and selective pharmacological inhibitions show that Arp2/3 is required but myosin-II is dispensable for 4T1 invasion. Furthermore, depletion of CDH3 from 4T1s and DDR2 from CAFs reduces their ability to distinguish between collagen densities. For effective invasion, both cell types reorient and redistribute magnetically pre-aligned collagen fibers. With heterogenous cell populations of co-cultured CAFs and 4T1s, higher percentage of CAFs impeded invasion while increasing collagen fiber alignment. Overall, our findings demonstrate distinctive mechanisms of collective invasion adopted by 4T1 tumor cells and CAFs, one relying more on protrusions and the other on force-based collagen deformation. These results suggest that individually targeting cellular protrusions or contractility may not be universally applicable for all cell types or collagen densities, and a better cell type-dependent approach could enhance effectiveness of cancer therapies.

DOI: https://doi.org/10.1016/j.bpj.2025.03.032
bioRxiv. 2025 Mar 14. pii: 2025.03.12.642933. [Epub ahead of print]

Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer.

Dennis Gong, Rachel Liu, Yi Cui, Michael Rhodes, Jung Woo Bae, Joseph M Beechem, William L Hwang.

Analyses of patient-derived cell lines have greatly enhanced discovery of molecular biomarkers and therapeutic targets. However, characterization of cellular morphological properties is limited. We studied cell morphologies of human pancreatic adenocarcinoma (PDAC) cell lines and their associations with drug sensitivity, gene expression, and functional properties. By integrating live cell and spatial mRNA imaging, we identified KRAS inhibitor-induced morphological changes specific for drug-resistant cells that correlated with gene expression changes. We then categorized a large panel of patient-derived PDAC cell lines into morphological (e.g., polygonal, irregular, spheroid) and organizational (e.g., tightly aggregated, multilayered, dispersed) subtypes and found differences in gene expression, therapeutic targeting potential, and metastatic proclivity. In human PDAC tissues, we identified prognostic expression signatures associated with distinct cancer cell organization patterns. In summary, we highlight the potential of cell morphological information in rapid, cost-effective assays to aid precision oncology efforts leveraging patient-derived in vitro models and tissues.

DOI: https://doi.org/10.1101/2025.03.12.642933
Methods Mol Biol. 2025 ;2901 131-144

Method for Imaging and Quantifying Molecular Tensions at Cell-Cell Junctions Using DNA-Based Fluorescent Probes.

Priyanka Bhattacharyya, Qian Tian, Mingxu You.

  Mechanical forces play crucial roles in regulating cellular communications. It has been challenging to measure intercellular forces due to the lack of proper tools. We have recently developed lipid-modified DNA probes that can anchor on the cell membranes and detect intercellular tensions through targeting particular cell surface receptors of interest. Herein, we describe the methods to synthesize, characterize, and apply these DNA-based fluorescent probes for imaging and quantifying intercellular forces.

Keywords:  Cell membrane analysis; DNA probes; Fluorescence microscopy; Intercellular forces; Lipid-DNA conjugate

DOI:  https://doi.org/10.1007/978-1-0716-4394-5_10
Proc Natl Acad Sci U S A. 2025 Apr 08. 122(14): e2424051122

Nuclear Galectin-1 promotes KRAS-dependent activation of pancreatic cancer stellate cells.

Judith Vinaixa, Neus Martínez-Bosch, Joan Gibert, Noemí Manero-Rupérez, Patricia Santofimia-Castaño, Federico G Baudou, Renzo E Vera, David R Pease, Mar Iglesias, Sandhya Sen, Xiyin Wang, Luciana L Almada, David L Marks, Mireia Moreno, Juan L Iovanna, Gabriel A Rabinovich, Martin E Fernandez-Zapico, Pilar Navarro.

  Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers, primarily due to its complex tumor microenvironment (TME), which drives both disease progression and therapy resistance. Understanding the molecular mechanisms governing TME dynamics is essential for developing new treatment strategies for this devastating disease. In this study, we uncover an oncogenic role for Galectin-1 (Gal1), a glycan-binding protein abundantly expressed by activated pancreatic stellate cells (PSCs), a key component of the PDAC TME that orchestrates tumor progression. Our findings reveal that Gal1 expression is elevated in the nucleus of human PSCs in both tissue samples and cultured cell lines. Using chromatin immunoprecipitation followed by sequencing analysis (ChIP-seq), we identify Gal1 occupancy at the promoters of several cancer-associated genes, including KRAS, a pivotal oncogene involved in PDAC pathogenesis. We demonstrate that Gal1 binds to the KRAS promoter, sustaining KRAS expression in PSCs, which, in turn, maintains PSC activation and promotes the secretion of protumorigenic cytokines. Mechanistically, Gal1 is required to preserve histone H3 lysine 4 monomethylation levels and to recruit the histone methyltransferase MLL1 to target promoters. Collectively, our findings define a nuclear function of Gal1 in modulating the transcriptional landscape of cancer-associated genes in PSCs within the PDAC TME, mediated through an epigenetic mechanism. These insights enhance our understanding of PDAC pathology and open potential avenues for therapeutic interventions targeting intracellular Gal1.

Keywords:  Galectin-1; KRAS; inflammation; pancreatic ductal adenocarcinoma; pancreatic stellate cells

DOI:  https://doi.org/10.1073/pnas.2424051122
Cell Rep. 2025 Apr 03. pii: S2211-1247(25)00261-X. [Epub ahead of print]44(4): 115490

RAF1 kinase contributes to autophagic lysosome reformation.

Stefanie Toifl, Sebastian Didusch, Karin Ehrenreiter, Enrico Desideri, Coralie Dorard, Manuela Baccarini.

  Autophagic lysosome reformation (ALR) is crucial for lysosomal homeostasis and therefore for different autophagic processes. Despite recent advances, the signaling mechanisms regulating ALR are incompletely understood. We show that RAF1, a member of the RAS/RAF/MEK/ERK pathway initiated by growth factors, has an essential, kinase-dependent role in lysosomal biology. RAF1 ablation impairs autophagy, and a proxisome screen identifies several proteins involved in autophagic and lysosomal pathways in the RAF1 molecular space. Two of these, SPG11 and the lipid phosphatase MTMR4, are RAF1 substrates. RAF1 ablation causes the appearance of enlarged autolysosomes and alters the phosphoinositide composition of autolysosomes. RAF1 and MTMR4 colocalize on autolysosomes, and overexpression of a MTMR4 mutant mimicking phosphorylation of the RAF1-dependent site rescues the lysosomal phenotypes induced by RAF1 ablation. Our data identify an RAF1 function in lysosomal homeostasis and a substrate through which the kinase regulates phospholipid metabolism at the lysosome, ALR, and autophagy.

Keywords:  CP: Cell biology; RAF1 interactome; RAF1 substrates; autophagic lysosome reformation; autophagy; lysosomal homeostasis

DOI:  https://doi.org/10.1016/j.celrep.2025.115490
bioRxiv. 2025 Mar 20. pii: 2025.03.19.644180. [Epub ahead of print]

Resilience and vulnerabilities of tumor cells under purine shortage stress.

Jianpeng Yu, Chen Jin, Cheng Su, David Moon, Michael Sun, Hong Zhang, Xue Jiang, Fan Zhang, Nomi Tserentsoodol, Michelle L Bowie, Christopher J Pirozzi, Daniel J George, Robert Wild, Xia Gao, David M Ashley, Yiping He, Jiaoti Huang.

Purine metabolism is a promising therapeutic target in cancer; however how cancer cells respond to purine shortage,particularly their adaptation and vulnerabilities, remains unclear. Using the recently developed purine shortage-inducing prodrug DRP-104 and genetic approaches, we investigated these responses in prostate, lung and glioma cancer models. We demonstrate that when de novo purine biosynthesis is compromised, cancer cells employ microtubules to assemble purinosomes, multi-protein complexes of de novo purine biosynthesis enzymes that enhance purine biosynthesis efficiency. While this process enables tumor cells to adapt to purine shortage stress, it also renders them more susceptible to the microtubule-stabilizing chemotherapeutic drug Docetaxel. Furthermore, we show that although cancer cells primarily rely on de novo purine biosynthesis, they also exploit Methylthioadenosine Phosphorylase (MTAP)-mediated purine salvage as a crucial alternative source of purine supply, especially under purine shortage stress. In support of this finding, combining DRP-104 with an MTAP inhibitor significantly enhances tumor suppression in prostate cancer (PCa) models in vivo. Finally, despite the resilience of the purine supply machinery, purine shortage-stressed tumor cells exhibit increased DNA damage and activation of the cGAS-STING pathway, which may contribute to impaired immunoevasion and provide a molecular basis of the previously observed DRP-104-induced anti-tumor immunity. Together, these findings reveal purinosome assembly and purine salvage as key mechanisms of cancer cell adaptation and resilience to purine shortage while identifying microtubules, MTAP, and immunoevasion deficits as therapeutic vulnerabilities.

DOI: https://doi.org/10.1101/2025.03.19.644180
Methods Cell Biol. 2025 ;pii: S0091-679X(23)00081-X. [Epub ahead of print]195 143-172

Multiplexed cytometry for single cell chemical biology.

Henry A M Schares, Madeline J Hayes, Joseph A Balsamo, Hannah L Thirman, Brian O Bachmann, Jonathan M Irish.

  Flow cytometry has great potential for screening in translational research areas due to its deep quantification of cellular features, ability to collect millions of cells in minutes, and consistently expanding suite of validated antibodies that detect cell identity and functions. However, cytometry remains under-utilized in discovery chemical biology due to the differences in expertise between chemistry groups developing chemical libraries and cell biologists developing single cell assays. This chapter is designed to bridge this gap by providing a detailed protocol aimed at both chemistry and biology audiences with the goal of helping train novice researchers. Assay users select from three elements: a small molecule input, a target cell type, and a module of cytometry readouts. For each, we explore basic and advanced examples of inputs, including screening fractionated microbial extracts and pure compounds, and target cells, including primary human blood cells, mouse cells, and cancer cell lines. One such module of cytometry readouts focuses on cell function and measures DNA damage response (γH2AX), growth (phosphorylated S6), DNA content, apoptosis (cleaved Caspase3), cell cycle M phase (phosphorylated Histone H3), and viability (membrane permeabilization). The protocol can also be adapted to measure different functional readouts, such as cell identity or differentiation and contrasting cell injury mechanisms. The protocol is designed to be used in 96-well plate format with fluorescent cell barcoding and the debarcodeR algorithm. Ultimately, the goal is to encourage the next generation of chemical biologists to use functional cell-based cytometry assays in discovery and translational research.

Keywords:  Chemical biology; Compound screening; Flow cytometry; Fluorescent cell barcoding; Metabolomics; Natural product discovery; Single cell; Training protocol

DOI:  https://doi.org/10.1016/bs.mcb.2023.03.007
Cancer Cell. 2025 Mar 25. pii: S1535-6108(25)00113-8. [Epub ahead of print]

Leveraging real-world data to advance biomarker discovery and precision oncology.

Jiaqian Luo, David B Solit.

Precision oncology is predicated on the availability of robust biomarkers deployed at scale at the point of care. Although simple in conception, precision oncology often fails in practice because of the limitations of current diagnostic platforms, the emergence of drug resistance, and an incomplete understanding of cancer pathogenesis and the host immune response. Here, we discuss using real-world data, including exceptional responder analyses, to identify biomarkers of therapy response and strategies for overcoming barriers to the broader adoption of precision oncology paradigms.

DOI: https://doi.org/10.1016/j.ccell.2025.03.012
Methods Mol Biol. 2025 ;2901 145-158

Method for Mapping the Membrane Protein Nanoenvironments Using DNA Nanostructures (NanoDeep).

Elena Ambrosetti, Ana I Teixeira.

  The distribution of proteins at the plasma membrane is not uniform, but rather many proteins localize to dynamic nanodomains. To understand the functional importance of membrane protein nanodomains, it is necessary to be able to map their composition and spatial organization en masse in cell populations. Here, we present the protocol to implement a non-microscopy-based method called NanoDeep, which enables ensemble analysis of membrane protein nanodomains. NanoDeep utilizes DNA nanoassemblies to convert information about membrane protein organization into a DNA sequencing readout. By using NanoDeep, we have previously investigated the Her2 nanoenvironments, an important membrane receptor in cancer. NanoDeep has the potential to provide a new understanding of the effects of protein composition and spatial organization on the regulation of membrane protein function. In this chapter, we describe the NanoDeep protocol as applied to Her2 nanoenvironments.

Keywords:  DNA nanoassembly; Detection of protein clusters; Membrane proteins; Spatial distribution

DOI:  https://doi.org/10.1007/978-1-0716-4394-5_11
Biophys J. 2025 Mar 30. pii: S0006-3495(25)00199-7. [Epub ahead of print]

A closed-loop system for millisecond readout and control of membrane tension.

Michael Sindoni, Jörg Grandl.

Characterizing the function of force-gated ion channels is essential for understanding their molecular mechanisms and how they are affected by disease-causing mutations, lipids, or small molecules. Pressure-clamp electrophysiology is a method that is established and widely used to characterize the mechanical sensitivity of force-gated ion channels. However, the physical stimulus many force-gated ion channels sense is not pressure, but membrane tension. Here, we further develop the approach of combining patch-clamp electrophysiology with differential interference contrast microscopy into a system that controls membrane tension in real time. The system uses machine learning object detection for millisecond analysis of membrane curvature and control of pipette pressure to produce a closed-loop membrane tension clamp. The analysis of membrane tension is fully automated and includes propagation of experimental errors, thereby increasing throughput and reducing bias. A dynamic control program clamps membrane tension with at least 93% accuracy and 0.3 mN/m precision. Additionally, the absence of tension drift enables averaging open probabilities of ion channels with low expression and/or unitary conductance over long durations. Using this system, we apply a tension step protocol and show that TMEM63A responds to tension with a tension of half-maximal activation of T50 = 5.5±0.1 mN/m. Overall, this system allows for precise and efficient generation of tension-response relationships of force-gated ion channels.

DOI: https://doi.org/10.1016/j.bpj.2025.03.025
bioRxiv. 2025 Mar 17. pii: 2025.03.14.643359. [Epub ahead of print]

Antigenic cancer persister cells survive direct T cell attack.

Michael X Wang, Brandon E Mauch, August F Williams, Tania Barazande-Pour, Filipe Araujo Hoffmann, Sophie H Harris, Cooper P Lathrop, Claire E Turkal, Bryan S Yung, Michelle H Paw, David A G Gervasio, Tiffany Tran, Anna E Stuhlfire, Theresa Guo, Gregory A Daniels, Soo J Park, J Silvio Gutkind, Matthew J Hangauer.

Drug-tolerant persister cancer cells were first reported fifteen years ago as a quiescent, reversible cell state which tolerates unattenuated cytotoxic drug stress. It remains unknown whether a similar phenomenon contributes to immune evasion. Here we report a persister state which survives weeks of direct cytotoxic T lymphocyte (CTL) attack. In contrast to previously known immune evasion mechanisms that avoid immune attack, antigenic persister cells robustly activate CTLs which deliver Granzyme B, secrete IFNγ, and induce tryptophan starvation resulting in apoptosis initiation. Instead of dying, persister cells paradoxically leverage apoptotic caspase activity to avoid inflammatory death. Furthermore, persister cells acquire mutations and epigenetic changes which enable outgrowth of CTL-resistant cells. Persister cell features are enriched in inflamed tumors which regressed during immunotherapy in vivo and in surgically resected human melanoma tissue under immune stress ex vivo . These findings reveal a persister cell state which is a barrier to immune-mediated tumor clearance.
Graphical abstract:

DOI: https://doi.org/10.1101/2025.03.14.643359
Int J Radiat Oncol Biol Phys. 2025 Apr 01. pii: S0360-3016(25)00266-4. [Epub ahead of print]

Differentiation stage predicts radiosensitivity in mesenchymal-like pancreatic cancer.

Tingshi Su, Xinjian Yu, Mojtaba Hoseini-Ghahfarokhi, David B Flint, Scott J Bright, Joana Antunes, David K J Martinus, Mandira Manandhar, Mariam Ben Kacem, Poliana C Marinello, Eurico Pereira, Hua-Sheng Chiu, Uwe Titt, David R Grosshans, Jan Schuemann, Henning Willers, Harald Paganetti, Pavel Sumazin, Gabriel O Sawakuchi.

   PURPOSE: To derive a genomic classifier to predict radiosensitivity of pancreatic cancer cell lines and pancreatic cancer patients to allow genomic-guided radiotherapy.
METHODS AND MATERIALS: We collected a comprehensive dataset of full clonogenic cell survival curves of 45 pancreatic cancer cell lines irradiated with clinical photon and proton beams. We derived classifiers based on data from human embryonic and fetal pancreas single-cell RNA-sequencing (scRNA-seq) to distinguish between epithelial and mesenchymal cells and to predict pancreas cell-line differentiation stage. Independent testing was done with an embryonic mouse pancreas scRNA-seq dataset. We then used bulk RNA-seq profiles from the Cancer Cell Line Encyclopedia (CCLE) to classify our pancreatic cancer cell lines using our epithelial-mesenchymal and differentiation stage classifiers. We then correlated the differentiation stage classifier with the radiosensitivity of the pancreatic cancer cell lines as well as with pancreatic cancer patient data from The Cancer Genome Atlas.
RESULTS: We found wide variability in radiosensitivity to both photons and protons among pancreatic cancer cell lines. We showed that the differentiation stage is predictive of radiosensitivity of mesenchymal pancreatic cancer cell lines but not epithelial pancreatic cancer cell lines. We found that chromatin compaction is associated with the differentiation stage and showed that the less differentiated mesenchymal pancreatic cancer cell lines tend to be radioresistant and with more compact chromatin than the radiosensitive differentiated cell lines. Patients with more differentiated tumors exhibit better overall survival.
CONCLUSIONS: We found that mesenchymal-like undifferentiated pancreatic cancer cell lines are more radioresistant than mesenchymal-like differentiated ones and that pancreatic cancer patients with mesenchymal-like undifferentiated tumors treated with radiotherapy tend to have lower overall survival compared to patients with mesenchymal-like differentiated tumors. We show that it is feasibility to use the differentiation stage of mesenchymal pancreatic cancer cells to predict tumor specific radiosensitivity.

Keywords:  LET; chromatin compaction; genomic signature; mesenchymal; pancreatic cancer; precision radiation oncology; proton therapy; radiobiolgy; radiosensitivity

DOI:  https://doi.org/10.1016/j.ijrobp.2025.03.034
Biophys Rev (Melville). 2025 Mar;6(1): 011310

The mechanobiology of biomolecular condensates.

Neus Sanfeliu-Cerdán, Michael Krieg.

The central goal of mechanobiology is to understand how the mechanical forces and material properties of organelles, cells, and tissues influence biological processes and functions. Since the first description of biomolecular condensates, it was hypothesized that they obtain material properties that are tuned to their functions inside cells. Thus, they represent an intriguing playground for mechanobiology. The idea that biomolecular condensates exhibit diverse and adaptive material properties highlights the need to understand how different material states respond to external forces and whether these responses are linked to their physiological roles within the cell. For example, liquids buffer and dissipate, while solids store and transmit mechanical stress, and the relaxation time of a viscoelastic material can act as a mechanical frequency filter. Hence, a liquid-solid transition of a condensate in the force transmission pathway can determine how mechanical signals are transduced within and in-between cells, affecting differentiation, neuronal network dynamics, and behavior to external stimuli. Here, we first review our current understanding of the molecular drivers and how rigidity phase transitions are set forth in the complex cellular environment. We will then summarize the technical advancements that were necessary to obtain insights into the rich and fascinating mechanobiology of condensates, and finally, we will highlight recent examples of physiological liquid-solid transitions and their connection to specific cellular functions. Our goal is to provide a comprehensive summary of the field on how cells harness and regulate condensate mechanics to achieve specific functions.

DOI: https://doi.org/10.1063/5.0236610
Nat Rev Cancer. 2025 Apr 02.

Moonlighting functions of glucose metabolic enzymes and metabolites in cancer.

Dong Guo, Ying Meng, Gaoxiang Zhao, Qingang Wu, Zhimin Lu.

Glucose metabolic enzymes and their metabolites not only provide energy and building blocks for synthesizing macromolecules but also possess non-canonical or moonlighting functions in response to extracellular and intracellular signalling. These moonlighting functions modulate various cellular activities, including gene expression, cell cycle progression, DNA repair, autophagy, senescence and apoptosis, cell proliferation, remodelling of the tumour microenvironment and immune responses. These functions integrate glucose metabolism with other essential cellular activities, driving cancer progression. Targeting these moonlighting functions could open new therapeutic avenues and lead to cancer-specific treatments.

DOI: https://doi.org/10.1038/s41568-025-00800-3
Small. 2025 Mar 30. e2501470

Dynamic Duos: Coacervate-Lipid Membrane Interactions in Regulating Membrane Transformation and Condensate Size.

Karthika S Nair, Sreelakshmi Radhakrishnan, Harsha Bajaj.

  Biomolecular condensates interfacing with lipid membranes is crucial for several key cellular functions. However, the role of lipid membranes in regulating condensates in cells remains obscure. Here, in-depth interactions between condensates and lipid membranes are probed and unraveled by employing cell-mimetic systems like Giant unilamellar vesicles (GUVs). An unprecedented influence of the coacervate size and their electrostatic interaction with lipid membranes is revealed on the membrane properties and deformation. Importantly, these findings demonstrate that the large relative size of coacervates and minimal electrostatic interaction strength with membranes allow for budding transitions at the interface. Membranes act as nucleation site for coacervates when the charge-charge interaction is high, giving a wrinkled vesicle surface appearance. Molecular diffusion property of lipids, quantified using Fluorescence recovery after photobleaching (FRAP), is modulated at the coacervate-membrane interaction site restricting the coarsening of coacervates. Notably, these results reveal coacervate droplets are intertwined in between membrane folds and invaginations discerned using Transmission electron microscopy (TEM) and high-resolution imaging, which further controls the dimension of droplets resembling size distributions observed in cells. Finally, these findings provide mechanistic insights of lipid bilayers controlling condensate sizes that play a prominent role in comprehending nucleation and localization of cellular condensates.

Keywords:  condensate size regulation; condensates; electrostatic interaction; giant unilamellar vesicles; liquid‐liquid phase separation; membrane transformation

DOI:  https://doi.org/10.1002/smll.202501470
Nat Methods. 2025 Mar 31.

Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement.

Ino de Bruijn, Milen Nikolov, Clarisse Lau, Ashley Clayton, David L Gibbs, Elvira Mitraka, Dar'ya Pozhidayeva, Alex Lash, Selcuk Onur Sumer, Jennifer Altreuter, Kristen Anton, Mialy DeFelice, Xiang Li, Aaron Lisman, William J R Longabaugh, Jeremy Muhlich, Sandro Santagata, Subhiksha Nandakumar, Peter K Sorger, Christine Suver, Xengie Doan, Justin Guinney, Nikolaus Schultz, Adam J Taylor, Vésteinn Thorsson, Ethan Cerami, James A Eddy.

Data from the first phase of the Human Tumor Atlas Network (HTAN) are now available, comprising 8,425 biospecimens from 2,042 research participants profiled with more than 20 molecular assays. The data were generated to study the evolution from precancerous to advanced disease. The HTAN Data Coordinating Center (DCC) has enabled their dissemination and effective reuse. We describe the diverse datasets, how to access them, data standards, underlying infrastructure and governance approaches, and our methods to sustain community engagement. HTAN data can be accessed through the HTAN Portal, explored in visualization tools-including CellxGene, Minerva and cBioPortal-and analyzed in the cloud through the NCI Cancer Research Data Commons. Infrastructure was developed to enable data ingestion and dissemination through the Synapse platform. The HTAN DCC's flexible and modular approach to sharing complex cancer research data offers valuable insights to other data-coordination efforts and researchers looking to leverage HTAN data.

DOI: https://doi.org/10.1038/s41592-025-02643-0
bioRxiv. 2025 Mar 20. pii: 2025.03.20.644464. [Epub ahead of print]

p62 sorts Lupus La and selected microRNAs into breast cancer-derived exosomes.

Jordan Matthew Ngo, Justin Krish Williams, Morayma Mercedes Temoche-Diaz, Abinayaa Murugupandiyan, Randy Schekman.

Exosomes are multivesicular body-derived extracellular vesicles that are secreted by metazoan cells. Exosomes have utility as disease biomarkers, and exosome-mediated miRNA secretion has been proposed to facilitate tumor growth and metastasis. Previously, we demonstrated that the Lupus La protein (La) mediates the selective incorporation of miR-122 into metastatic breast cancer-derived exosomes; however, the mechanism by which La itself is sorted into exosomes remains unknown. Using unbiased proximity labeling proteomics, biochemical fractionation, superresolution microscopy and genetic tools, we establish that the selective autophagy receptor p62 sorts La and miR-122 into exosomes. We then performed small RNA sequencing and found that p62 depletion reduces the exosomal secretion of tumor suppressor miRNAs and results in their accumulation within cells. Our data indicate that p62 is a quality control factor that modulates the miRNA composition of exosomes. Cancer cells may exploit p62-dependent exosome cargo sorting to eliminate tumor suppressor miRNAs and thus to promote cell proliferation.

DOI: https://doi.org/10.1101/2025.03.20.644464
Pancreatology. 2025 Mar 20. pii: S1424-3903(25)00059-6. [Epub ahead of print]

Metallic trace elements in pancreatic tissue are associated with higher risk of pancreatic adenocarcinoma - METAPANDA study.

Mireille Simon, Aurore Meurat, Sophie Stanislas, Hervé Dréau, Geneviève Belleannée, Christophe Laurent, Jean-Frédéric Blanc, Sandra Mounicou.

   OBJECTIVES: Few recent studies have indicated the possible involvement of some metallic trace element (MTE), commonly known as heavy metals, in pancreatic ductal adenocarcinoma (PDAC). To evaluate the potential role of MTE in PDAC onset, we compared concentrations of 23 MTE in healthy pancreas tissue close to the tumor, from patients who underwent pancreatic surgery for PDAC in cases group and for neuroendocrine or other lesion for controls.
METHODS: Samples were taken from paraffin-embedded pancreatectomy blocks of 33 PDAC cases and 29 controls. Concentrations of 23 MTE were determined by inductively coupled plasma mass spectrometry (ICP-MS).
RESULTS: In multivariate analysis, associations were found between risk of PDAC and higher tissue concentration of antimony (OR 6.31, 95 % CI 2.06-29.03; p = 0.006), thallium (OR 3.23, 95 % CI 1.35-12.07; p = 0.033) arsenic (OR 2.96, 95 % CI 1.22-10.10; p = 0.04) and lead (OR 2.27, 95 % CI 1.13-5.77; p = 0.044).
CONCLUSIONS: This pilot study presents unpublished information about a large set of MTE in pancreatic tissues, confirming the possible involvement of arsenic and lead in PDAC onset and highlighting the potential role of antimony and thallium which have never been implicated before.

Keywords:  Antimony; Arsenic; Heavy metal; Pancreatic cancer; Thallium

DOI:  https://doi.org/10.1016/j.pan.2025.03.006
Cell. 2025 Apr 01. pii: S0092-8674(25)00276-4. [Epub ahead of print]

Genetically encoded reporters of actin filament organization in living cells and tissues.

Carla Silva Martins, François Iv, Shashi Kumar Suman, Thomas C Panagiotou, Clara Sidor, María Ruso-López, Camille N Plancke, Shizue Omi, Rebecca Pagès, Maxime Gomes, Alexander Llewellyn, Sourish Reddy Bandi, Laurie Ramond, Federica Arbizzani, Caio Vaz Rimoli, Frank Schnorrer, François Robin, Andrew Wilde, Loïc LeGoff, Jean-Denis Pedelacq, Antoine Jégou, Stéphanie Cabantous, Sergio A Rincon, Cristel Chandre, Sophie Brasselet, Manos Mavrakis.

  The cytoskeletal protein actin is crucial for cell shape and integrity throughout eukaryotes. Actin filaments perform essential biological functions, including muscle contraction, cell division, and tissue morphogenesis. These diverse activities are achieved through the ability of actin filaments to be arranged into precise architectures. Much progress has been made in defining the proteome of the actin cytoskeleton, but a detailed appreciation of the dynamic organizational state of the actin filaments themselves has been hindered by available tools. Fluorescence polarization microscopy is uniquely placed for measuring actin filament organization by exploiting the sensitivity of polarized light excitation to the orientation of fluorophores attached to actin filaments. By engineering fusions of five widely used actin localization reporters to fluorescent proteins with constrained mobility, we have succeeded in developing genetically encoded, green- and red-fluorescent-protein-based reporters for non-invasive, quantitative measurements of actin filament organization in living cells and tissues by fluorescence polarization microscopy.

Keywords:  GFP mobility; actin filaments; filament alignment; fluorescence polarization microscopy; molecular order; molecular organization; molecular orientation

DOI:  https://doi.org/10.1016/j.cell.2025.03.003
Nat Methods. 2025 Apr 02.

The need to implement FAIR principles in biomolecular simulations.

Rommie E Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C Biggin, Massimiliano Bonomi, Gregory R Bowman, Richard A Bryce, Giovanni Bussi, Paolo Carloni, David A Case, Andrea Cavalli, Chia-En A Chang, Thomas E Cheatham, Margaret S Cheung, Christophe Chipot, Lillian T Chong, Preeti Choudhary, G Andres Cisneros, Cecilia Clementi, Rosana Collepardo-Guevara, Peter Coveney, Roberto Covino, T Daniel Crawford, Matteo Dal Peraro, Bert L de Groot, Lucie Delemotte, Marco De Vivo, Jonathan W Essex, Franca Fraternali, Jiali Gao, Josep Ll Gelpí, Francesco L Gervasio, Fernando D González-Nilo, Helmut Grubmüller, Marina G Guenza, Horacio V Guzman, Sarah Harris, Teresa Head-Gordon, Rigoberto Hernandez, Adam Hospital, Niu Huang, Xuhui Huang, Gerhard Hummer, Javier Iglesias-Fernández, Jan H Jensen, Shantenu Jha, Wanting Jiao, William L Jorgensen, Shina C L Kamerlin, Syma Khalid, Charles Laughton, Michael Levitt, Vittorio Limongelli, Erik Lindahl, Kresten Lindorff-Larsen, Sharon Loverde, Magnus Lundborg, Yun L Luo, F Javier Luque, Charlotte I Lynch, Alexander D MacKerell, Alessandra Magistrato, Siewert J Marrink, Hugh Martin, J Andrew McCammon, Kenneth Merz, Vicent Moliner, Adrian J Mulholland, Sohail Murad, Athi N Naganathan, Shikha Nangia, Frank Noe, Agnes Noy, Julianna Oláh, Megan L O'Mara, Mary Jo Ondrechen, Jose N Onuchic, Alexey Onufriev, Sílvia Osuna, Giulia Palermo, Anna R Panchenko, Sergio Pantano, Carol Parish, Michele Parrinello, Alberto Perez, Tomas Perez-Acle, Juan R Perilla, B Montgomery Pettitt, Adriana Pietropaolo, Jean-Philip Piquemal, Adolfo B Poma, Matej Praprotnik, Maria J Ramos, Pengyu Ren, Nathalie Reuter, Adrian Roitberg, Edina Rosta, Carme Rovira, Benoit Roux, Ursula Rothlisberger, Karissa Y Sanbonmatsu, Tamar Schlick, Alexey K Shaytan, Carlos Simmerling, Jeremy C Smith, Yuji Sugita, Katarzyna Świderek, Makoto Taiji, Peng Tao, D Peter Tieleman, Irina G Tikhonova, Julian Tirado-Rives, Iñaki Tuñón, Marc W van der Kamp, David van der Spoel, Sameer Velankar, Gregory A Voth, Rebecca Wade, Ariel Warshel, Valerie Vaissier Welborn, Stacey D Wetmore, Travis J Wheeler, Chung F Wong, Lee-Wei Yang, Martin Zacharias, Modesto Orozco.

DOI: https://doi.org/10.1038/s41592-025-02635-0
J Cell Sci. 2025 Apr 01. pii: jcs263574. [Epub ahead of print]138(7):

Regulation of cell migration by extracellular matrix mechanics at a glance.

Cole Allan, Ovijit Chaudhuri.

  Cell migration occurs throughout development, tissue homeostasis and regeneration, as well as in diseases such as cancer. Cells migrate along two-dimensional (2D) surfaces or interfaces, within microtracks, or in confining three-dimensional (3D) extracellular matrices. Although the basic mechanisms of 2D migration are known, recent studies have elucidated unexpected migration behaviors associated with more complex substrates and have provided insights into their underlying molecular mechanisms. Studies using engineered biomaterials for 3D culture and microfabricated channels to replicate cell confinement observed in vivo have revealed distinct modes of migration. Across these contexts, the mechanical features of the surrounding microenvironment have emerged as major regulators of migration. In this Cell Science at a Glance article and the accompanying poster, we describe physiological contexts wherein 2D and 3D cell migration are essential, report how mechanical properties of the microenvironment regulate individual and collective cell migration, and review the mechanisms mediating these diverse modes of cell migration.

Keywords:  3D migration; Cell migration; Extracellular matrix; Mechanotransduction

DOI:  https://doi.org/10.1242/jcs.263574
bioRxiv. 2025 Mar 14. pii: 2025.03.12.642522. [Epub ahead of print]

Programmable macromolecule delivery via engineered trogocytosis.

Xinyi Chen, Yinglin Situ, Yuexuan Yang, Maylin Lum Fu, Luna Lyu, Lei Stanley Qi.

Trogocytosis, the transfer of plasma membrane fragments during cell-cell contact, offers potential for macromolecular delivery but is limited by uncertain fate of trogocytosed molecules, constraints to membrane cargo, and unclear generalizability. Here, we demonstrate that donor cells engineered with designed receptors specific to intrinsic ligands can transfer proteins to recipient cells through direct contact. We identified key principles for enhancing contact-mediated transfer and subsequent functionalization of transferred macromolecules, including receptor design, pH-responsive membrane fusion, inducible cargo localization, release, and subcellular translocation. Exploiting these findings, we developed TRANSFER, a versatile delivery system that integrates logic gate-based control to sense multiple ligand inputs and deliver diverse functional cargos for genome editing and targeted cell ablation across cell types. The study establishes trogocytosis as a novel, programmable framework for cell-based macromolecular delivery.

DOI: https://doi.org/10.1101/2025.03.12.642522
Cancer Cell. 2025 Mar 21. pii: S1535-6108(25)00082-0. [Epub ahead of print]

Translation dysregulation in cancer as a source for targetable antigens.

Chen Weller, Osnat Bartok, Christopher S McGinnis, Heyilimu Palashati, Tian-Gen Chang, Dmitry Malko, Merav D Shmueli, Asuteka Nagao, Deborah Hayoun, Ayaka Murayama, Yuriko Sakaguchi, Panagiotis Poulis, Aseel Khatib, Bracha Erlanger Avigdor, Sagi Gordon, Sapir Cohen Shvefel, Marie J Zemanek, Morten M Nielsen, Sigalit Boura-Halfon, Shira Sagie, Nofar Gumpert, Weiwen Yang, Dmitry Alexeev, Pelgia Kyriakidou, Winnie Yao, Mirie Zerbib, Polina Greenberg, Gil Benedek, Kevin Litchfield, Ekaterina Petrovich-Kopitman, Adi Nagler, Roni Oren, Shifra Ben-Dor, Yishai Levin, Yitzhak Pilpel, Marina Rodnina, Jürgen Cox, Yifat Merbl, Ansuman T Satpathy, Yaron Carmi, Florian Erhard, Tsutomu Suzuki, Allen R Buskirk, Johanna Olweus, Eytan Ruppin, Andreas Schlosser, Yardena Samuels.

  Aberrant peptides presented by major histocompatibility complex (MHC) molecules are targets for tumor eradication, as these peptides can be recognized as foreign by T cells. Protein synthesis in malignant cells is dysregulated, which may result in the generation and presentation of aberrant peptides that can be exploited for T cell-based therapies. To investigate the role of translational dysregulation in immunological tumor control, we disrupt translation fidelity by deleting tRNA wybutosine (yW)-synthesizing protein 2 (TYW2) in tumor cells and characterize the downstream impact on translation fidelity and immunogenicity using immunopeptidomics, genomics, and functional assays. These analyses reveal that TYW2 knockout (KO) cells generate immunogenic out-of-frame peptides. Furthermore, Tyw2 loss increases tumor immunogenicity and leads to anti-programmed cell death 1 (PD-1) checkpoint blockade sensitivity in vivo. Importantly, reduced TYW2 expression is associated with increased response to checkpoint blockade in patients. Together, we demonstrate that defects in translation fidelity drive tumor immunogenicity and may be leveraged for cancer immunotherapy.

Keywords:  cancer immunopeptidome; immune checkpoint blockade; neoantigens; non-canonical peptides; translation fidelity

DOI:  https://doi.org/10.1016/j.ccell.2025.03.003
Eur J Cancer. 2025 Mar 23. pii: S0959-8049(25)00166-2. [Epub ahead of print]220 115385

Patterns of disease dissemination and survival in patients with synchronous and metachronous metastatic pancreatic adenocarcinoma: Nationwide population-based study.

Dutch Pancreatic Cancer Group

   AIM: Despite advances in understanding pancreatic adenocarcinoma, evidence on its metastatic patterns and impact on patient survival remains limited. This study aims to identify patterns of disease dissemination in synchronous versus metachronous metastatic pancreatic adenocarcinoma (mPAC) and their association with overall survival (OS).
METHODS: Patients diagnosed with synchronous- or metachronous-mPAC were selected from the Netherlands Cancer Registry (2015-2021). Patient, tumor, and treatment characteristics were compared using Chi-squared tests. Survival data, calculated from detection of metastatic disease (OS-M), were analyzed using Kaplan-Meier and Log-rank tests.
RESULTS: Overall, 10,788 patients with synchronous- and 508 with metachronous-mPAC were included. Median time to first metastasis in metachronous-mPAC was 13.2 months (IQR 9-23), varying significantly by metastatic site (liver-only 11.5; lung-only 28.0 months). Compared to synchronous-mPAC, patients with metachronous-mPAC had less liver metastases (48 % versus 75 %, p < 0.001), but more lung (29 % versus 21 %, p < 0.001) and peritoneal (35 % versus 25 %, p < 0.001) metastases. Synchronous metastases to liver-only, lung-only, lymph node-only, or multiple sites at first diagnosis had a median OS-M that was (nearly) half compared to metachronous metastases to the same sites. Bone-only or peritoneum-only metastases in synchronous-mPAC showed a median OS-M comparable to metachronous-mPAC.
CONCLUSION: This nationwide population-based study reveals that metachronous-mPAC less commonly presents with liver metastases and more often metastasizes to lung, peritoneum or other atypical sites compared to synchronous-mPAC. These distinct metastatic patterns and their differences in survival may help enhance the prognostic estimation for individual patients from the detection of metastatic disease and warrants further research into the biology underlying metastasis development.

Keywords:  Adenocarcinoma; Metastases; Pancreatic cancer; Survival

DOI:  https://doi.org/10.1016/j.ejca.2025.115385
Chem Rev. 2025 Apr 03.

Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome.

Kevin K Leung, Kaitlin Schaefer, Zhi Lin, Zi Yao, James A Wells.

The cell surface proteome, or surfaceome, is the hub for cells to interact and communicate with the outside world. Many disease-associated changes are hard-wired within the surfaceome, yet approved drugs target less than 50 cell surface proteins. In the past decade, the proteomics community has made significant strides in developing new technologies tailored for studying the surfaceome in all its complexity. In this review, we first dive into the unique characteristics and functions of the surfaceome, emphasizing the necessity for specialized labeling, enrichment, and proteomic approaches. An overview of surfaceomics methods is provided, detailing techniques to measure changes in protein expression and how this leads to novel target discovery. Next, we highlight advances in proximity labeling proteomics (PLP), showcasing how various enzymatic and photoaffinity proximity labeling techniques can map protein-protein interactions and membrane protein complexes on the cell surface. We then review the role of extracellular post-translational modifications, focusing on cell surface glycosylation, proteolytic remodeling, and the secretome. Finally, we discuss methods for identifying tumor-specific peptide MHC complexes and how they have shaped therapeutic development. This emerging field of neo-protein epitopes is constantly evolving, where targets are identified at the proteome level and encompass defined disease-associated PTMs, complexes, and dysregulated cellular and tissue locations. Given the functional importance of the surfaceome for biology and therapy, we view surfaceomics as a critical piece of this quest for neo-epitope target discovery.

DOI: https://doi.org/10.1021/acs.chemrev.4c00554
bioRxiv. 2025 Mar 21. pii: 2025.03.20.644389. [Epub ahead of print]

In vivo validation of the palmitoylation cycle as a therapeutic target in NRAS -mutant cancer.

Matthew Decker, Benjamin J Huang, Timothy Ware, Christopher Boone, Michelle Tang, Julia Ybarra, Aishwarya C Ballapuram, Katrine A Taran, Pan-Yu Chen, Marcos Amendáriz, Camille J Leung, Max Harris, Karensa Tjoa, Henry Hongo, Sydney Abelson, Jose Rivera, Nhi Ngo, Dylan M Herbst, Radu M Suciu, Carlos Guijas, Kimia Sedighi, Taylor Andalis, Elysia Roche, Boer Xie, Yunlong Liu, Catherine C Smith, Elliot Stieglitz, Micah J Niphakis, Benjamin F Cravatt, Kevin Shannon.

Normal and oncogenic Ras proteins are functionally dependent on one or more lipid modifications 1,2 . Whereas K-Ras4b farnesylation is sufficient for stable association with the plasma membrane, farnesylated H-Ras, K-Ras4a, and N-Ras traffic to the Golgi where they must undergo palmitoylation before regulated translocation to cell membranes. N-Ras palmitoylation by the DHHC family of palmitoyl acyl transferases (PATs) and depalmitoylation by ABHD17 serine hydrolases is a dynamic process that is essential for the growth of acute myeloid leukemias (AMLs) harboring oncogenic NRAS mutations 3-6 . Here, we have tested whether co-targeting ABHD17 enzymes and Ras signal output would cooperatively inhibit the proliferation and survival of NRAS -mutant AMLs while sparing normal tissues that retain K-Ras4b function. We show that ABD778, a potent and selective ABHD17 inhibitor with in vivo activity, selectively reduces the growth of NRAS -mutant AML cells in vitro and is synergistic with the allosteric MEK inhibitor PD0325901 (PD901) 7,8 . Similarly, ABD778 and PD901 significantly extended the survival of recipient mice transplanted with three independent primary mouse AMLs harboring an oncogenic Nras G12D driver mutation. Resistant leukemias that emerged during continuous drug treatment acquired by-pass mutations that confer adaptive drug resistance and increase mitogen activated protein kinase (MAPK) signal output. ABD778 augmented the anti-leukemia activity of the pan-PI3 kinase inhibitor pictilisib 9 , the K/N-Ras G12C inhibitor sotorasib 10 , and the FLT3 inhibitor gilteritinib 11 . Co-treatment with ABD778 and gilteritinib restored drug sensitivity in a patient-derived xenograft model of adaptive resistance to FLT3 inhibition. These data validate the palmitoylation cycle as a promising therapeutic target in AML and support exploring it in other NRAS -mutant cancers.

DOI: https://doi.org/10.1101/2025.03.20.644389
J Cachexia Sarcopenia Muscle. 2025 Apr;16(2): e13779

Nestin Regulates Autophagy-Dependent Ferroptosis Mediated Skeletal Muscle Atrophy by Ubiquitinating MAP 1LC3B.

Shunshun Han, Xiyu Zhao, Chunlin Yu, Can Cui, Yao Zhang, Qing Zhu, Mohan Qiu, Chaowu Yang, Huadong Yin.

   BACKGROUND: Programmed cell death plays a critical role in skeletal muscle atrophy. Ferroptosis, an iron-dependent form of programmed cell death driven by lipid peroxidation, has been implicated in various diseases, but its role in skeletal muscle atrophy remains unclear.
METHODS: Ferroptosis in skeletal muscle atrophy was investigated using two models: dexamethasone (Dex)-induced atrophy (n = 6 independent cell cultures per group) and simulated microgravity (n = 6 mice per group). Conditional Nestin knockout (KO) mice were generated using CRISPR/Cas9 (n = 6-8 mice per group), with wild-type (WT) controls (n = 6-8). Phenotypic analyses included histopathology (HE staining), functional assessments (muscle strength, weight analysis, treadmill), and dystrophy evaluation (dystrophin staining). Molecular analyses involved flow cytometry, ELISA, transmission electron microscopy, PI staining, and IP/MS to delineate Nestin-regulated ferroptosis pathways in skeletal muscle atrophy.
RESULTS: Ferroptosis was significantly activated in both atrophy models, with a 2.5-fold increase in lipid peroxidation (p < 0.01), a 2-fold accumulation of Fe2+ (p < 0.01) and a 50% reduction in Nestin expression (p < 0.001). Nestin KO mice exhibited exacerbated muscle atrophy, showing a 40% decrease in muscle weight (p < 0.01) and a 30% reduction in muscle strength (p < 0.05) compared to WT mice. Nestin overexpression mitigated Dex-induced ferroptosis, reducing lipid peroxidation by 40%, decreasing Fe2+ accumulation by 50% (p < 0.01), and improving muscle function by 30% (p < 0.05). Mechanistically, Nestin interacted with MAP 1LC3B (LC3B) to catalyse LC3B polyubiquitination at lysine-51, reducing LC3B availability for autophagy and inhibiting autophagy flux by 60% (p < 0.01), leading to a 50% reduction in ferroptosis (p < 0.001).
CONCLUSIONS: Our study identifies Nestin as a critical regulator of ferroptosis-autophagy crosstalk in skeletal muscle atrophy. Targeting Nestin-LC3B ubiquitination may offer novel therapeutic strategies for preventing muscle wasting in diseases such as cachexia and sarcopenia.

Keywords:  MAP 1LC3B; autophagy; ferroptosis; nestin; skeletal muscle atrophy

DOI:  https://doi.org/10.1002/jcsm.13779