bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2025–08–31
sixty papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. STAT3 sustains tumorigenicity following mutant KRAS ablation.
  2. Endocytosis is essential for cysteine-deprivation-induced ferroptosis.
  3. Signaling and actin waves at a glance.
  4. Multifaceted role of the vitamin B6 pathway in cancer: metabolism, immune interaction, and temporal and spatial regulation.
  5. Cell type-specific autophagy in human leukocytes: signatures of aging, sex, and nutrient restriction.
  6. Mechanical confinement governs phenotypic plasticity in melanoma.
  7. STN1 facilitates metastasis by promoting transcription of EMT-activator ZEB1 in pancreatic cancer.
  8. Deacetylation of ATG16L1 is required for LC3-associated lysosomal microautophagy.
  9. Deciphering Spatiotemporal Control of Ferroptosis in HCC: A Bifunctional Probe for Lipid Droplet Viscosity Dynamics and Interorganelle Communication.
  10. Quantitative imaging of lipid transport in mammalian cells.
  11. Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy.
  12. LYVAC/PDZD8 is a lysosomal vacuolator.
  13. A regulator of amino acid sensing links lipid peroxidation and lipid droplet-dependent antioxidant response.
  14. Bayesian reconstruction of rapidly scanned mid-infrared optoacoustic signals enables fast, label-free chemical microscopy.
  15. Integrative genomic identification of therapeutic targets for pancreatic cancer.
  16. Physical Activity, Exerkines, and Their Role in Cancer Cachexia.
  17. Glutaminase inhibition ameliorates cancer-associated fibroblast lipid support of pancreatic cancer cell growth.
  18. Unveiling CTRB2, RSPO3, KLOTB, and ROR1 as obesity-pancreatic disease association proteins: a comprehensive Mendelian randomization study.
  19. Targeting cancer-associated fibroblast-driven LIF/LIFR axis improves the therapeutic efficacy of gemcitabine and nab-paclitaxel in pancreatic cancer.
  20. Cells prioritize the regulation of cell mass density.
  21. The impact of eligibility criteria on KRASG12C inhibitor trials in patients with NSCLC.
  22. Nanoscale engagement of programmed death ligand 1 (PD-L1) in membrane lipid raft domains of cancer cells.
  23. Lipid accumulation in nitrogen and phosphorus-limited yeast is caused by less growth-related dilution.
  24. Self-generated chemotaxis of mixed cell populations.
  25. Molecular mechanism of ultrafast transport by plasma membrane Ca2+-ATPases.
  26. Polarization-Sensitive Holotomography for Multidimensional Label-Free Imaging and Characterization of Lipid Droplets in Cancer Cells.
  27. Micropost Arrays to Model ECM Fiber Obstacles During Cell Migration in Confinement.
  28. α-Ketoglutarate dictates AMPK protein synthesis for energy sensing in human cancers.
  29. The role of phosphatidylcholine metabolism in tumors.
  30. Accelerated maturation of branched organoids confined in collagen droplets.
  31. PRISM: a Python package for interactive and integrated analysis of multiplexed tissue microarrays.
  32. Cell mechanics, environmental geometry, and cell polarity control cell-cell collision outcomes.
  33. Cysteine metabolism at the crossroads of ferroptosis and cancer therapy.
  34. ERG-driven prostate cancer initiation is cell-context dependent and requires KMT2A and DOT1L.
  35. PARP7 is a proteotoxic stress sensor that labels proteins for degradation.
  36. Loss of NOTCH2 creates a TRIM28-dependent vulnerability in small cell lung cancer.
  37. PRMT1 (protein arginine methyltransferase 1) is essential for neuromuscular junction and mitochondrial homeostasis via mitophagy regulation.
  38. Preclinical Fluorescence-Guided Imaging Leveraging Surrounding Sentinel Tumor Microenvironment Identifies High-Risk Premalignant Pancreatic Lesions.
  39. Phosphate Improves Mitochondrial Function and Reduces Pancreatitis in Hypertriglyceridemia.
  40. A closer look at how cells sense dietary nutrients.
  41. Cryo-light microscopy with angstrom precision deciphers structural conformations of PIEZO1 in its native state.
  42. Ruxolitinib alleviated muscle atrophy in cancer cachexia by inhibiting IL-6/JAK/STAT3 signaling pathway in mice.
  43. Tamoxifen induces PI3K activation in uterine cancer.
  44. Cancer Cachexia Rehabilitation in a Novel Outpatient Clinical Program.
  45. Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer.
  46. DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations.
  47. CHIP protects lysosomes from CLN4 mutant-induced membrane damage.
  48. Identification of organelle-specific autophagy regulators from tandem CRISPR screens.
  49. Heterogeneity as a feature: unraveling chromatin's role in nuclear mechanics.
  50. Gut microbial diversity is preserved through localised chemo-immunotherapy delivery in a KPC mouse model of pancreatic cancer.
  51. inTRACKtive: a web-based tool for interactive cell tracking visualization.
  52. Elemental mass spectrometry imaging of biomolecules using metal-conjugated probes.
  53. Multiparametric cellular and spatial organization in cancer tissue lesions with a streamlined pipeline.
  54. Genome-wide CRISPR screens identify critical targets to enhance CAR-NK cell antitumor potency.
  55. Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells.
  56. Spatial isotope deep tracing deciphers inter-tissue metabolic crosstalk.
  57. Liver CYP4A autophagic lysosomal degradation: A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site.
  58. ACAA1 knockout increases the survival rate of KPC mice by activating autophagy.
  59. IL6 genetic perturbation mimicking IL-6 inhibition is associated with lower cardiometabolic risk.
  60. A platform for multisite immune profiling of premetastatic pancreatic cancer at single-cell resolution.
  1. EMBO Rep. 2025 Aug 26.
    STAT3 sustains tumorigenicity following mutant KRAS ablation.
    Stephen D'Amico, Varvara Kirillov, Jingxuan Liu, Zhijuan Qiu, Xinyuan Lei, Hong Qin, Brian S Sheridan, Nancy C Reich.
      Oncogenic KRAS mutations underlie some of the deadliest human cancers. Genetic or pharmacological KRAS inactivation produces mixed outcomes and frequent relapse. Mechanisms of tumor resistance to KRAS inhibition remain poorly understood. We present evidence that STAT3 supports tumor growth following KRAS depletion. Using a conceptual framework of pancreatic ductal adenocarcinoma, we show that cancer cells that survive CRISPR-mediated ablation of mutant KRAS are dependent on STAT3 function to maintain tumorigenicity. Mechanistically, the combined loss of mutant KRAS and STAT3 disrupts a core transcriptional program of cancer cells critical to oncogenic competence. This in turn impairs tumor growth in mice and enhances immune rejection, leading to tumor clearance. We propose that the STAT3 transcriptional program operating in cancer cells enforces their malignant identity, rather than providing classical features of transformation, and shapes cancer persistence following KRAS inactivation. Our findings establish STAT3 as a critical enforcer of oncogenic identity in KRAS-ablated tumors, revealing a key vulnerability.
    Keywords:  KRAS; Oncogene Dependence; Pancreatic Cancer; STAT3
    DOI:  https://doi.org/10.1038/s44319-025-00563-w
  2. Mol Cell. 2025 Aug 19. pii: S1097-2765(25)00656-2. [Epub ahead of print]
    Endocytosis is essential for cysteine-deprivation-induced ferroptosis.
    Xuesong Liu, Zechuan Zhao, Zhixuan Bian, Fahad A Benthani, Yingying Hu, Deguang Liang, Xuejun Jiang.
      Ferroptosis is a form of cell death caused by iron-dependent phospholipid peroxidation and subsequent membrane rupture. Autophagic degradation of the iron-storage protein ferritin promotes ferroptosis by increasing cytosolic bioactive iron, presumably explaining how lysosomal inhibitors suppress ferroptosis. Surprisingly, we found that lysosomal inhibitors suppress cysteine-deprivation-induced (CDI) ferroptosis, even in autophagy-defective cells, and subsequently discovered that clathrin-mediated endocytosis (CME) of transferrin is essential for CDI ferroptosis. Blocking lysosomal proteolytic activity failed to inhibit ferroptosis, whereas disrupting endosomal acidification and eliminating the endocytic protein AP2M1 both impeded ferroptosis. Conversely, replenishing cellular iron with ferric ammonium citrate, but not with transferrin, restored CDI ferroptosis in endocytosis-deficient cells. Unexpectedly, abolishing endosomal acidification, CME, and the associated increase in cellular labile iron could not prevent ferroptosis triggered by direct inhibition of the ferroptosis-suppressing enzyme glutathione peroxidase-4 (GPX4). Together, this study reveals the essential role of endocytosis, specifically for CDI ferroptosis.
    Keywords:  AP2M1; GPX4; autophagy; cysteine deprivation; endocytosis; endosome; ferroptosis; iron; lysosome; transferrin
    DOI:  https://doi.org/10.1016/j.molcel.2025.08.006
  3. J Cell Sci. 2025 Aug 15. pii: jcs263634. [Epub ahead of print]138(16):
    Signaling and actin waves at a glance.
    Tatsat Banerjee, Yu Deng, Dhiman Sankar Pal, Huiwang Zhan, Pablo A Iglesias, Peter N Devreotes.
      Waves of signaling and cytoskeletal components, which can be easily seen propagating on the ventral surface of a cell, are a systemic feature of biochemical networks that define the spatiotemporal dynamics of diverse cell physiological processes. In this Cell Science at a Glance article and the accompanying poster, we summarize the origin, mathematical basis, and function of signaling and actin waves from systems biology and biophysics perspectives, focusing on cell migration and polarity. We describe how waves control membrane protrusion morphologies, how different proteins and lipids are organized within the waves by distinct mechanisms, and how excitable network-based mathematical models can explain wave patterns and predict cell behavior. We further delineate how specific components interact biochemically to generate these dynamic patterns. Finally, we provide a set of generalizable underlying biophysical principles to describe the exquisite subcellular organization of signaling and cytoskeletal events, membrane symmetry breaking, protein compartmentalization and wave propagation.
    Keywords:  Biophysical organization; Cell migration; Chemotaxis; Cortical waves; Pattern formation; Signal transduction
    DOI:  https://doi.org/10.1242/jcs.263634
  4. Genes Dev. 2025 Aug 22.
    Multifaceted role of the vitamin B6 pathway in cancer: metabolism, immune interaction, and temporal and spatial regulation.
    Sushanta Kumar Mishra, Bo Li, Ana S H Costa, Linda Van Aelst, Lingbo Zhang.
      Vitamin B6 is a metabolic cofactor that underpins critical regulatory pathways, including amino acid flux, one-carbon pathways, redox homeostasis, and neurotransmitter biosynthesis. Emerging evidence suggests that vitamin B6 deficiency or its metabolic dysregulation perturbs these core metabolic pathways, driving oncogenic programs in both solid tumors and hematologic malignancies. Moreover, vitamin B6-dependent processes can modulate several tumorigenic processes, such as proliferation, oncogenic signaling, immune regulation, and adaptive metabolic reprogramming. The tumor-specific spatiotemporal dynamics of vitamin B6 metabolism uncover context-dependent metabolic vulnerabilities that are tightly regulated by cellular state and tumor niche. This review addresses emerging mechanistic insights into the multifaceted functions of vitamin B6 in tumorigenesis. Furthermore, it proposes dynamic vitamin B6 metabolism as a promising therapeutic axis, offering novel opportunities for tumor-specific targeted intervention.
    Keywords:  cancer; immune regulation; metabolism; temporal and spatial specificity; vitamin B6
    DOI:  https://doi.org/10.1101/gad.352770.125
  5. Autophagy Rep. 2025 ;4(1): 2543560
    Cell type-specific autophagy in human leukocytes: signatures of aging, sex, and nutrient restriction.
    Linh Vp Dang, Timothy J Sargeant.
      Macroautophagy (referred to here as autophagy) is thought to play a critical role in aging and age-related disease, making it a priority for development of targeted human therapies. We developed a flow cytometry-based method to measure autophagic flux in 19 subpopulations from whole blood, using chloroquine (CQ) to inhibit lysosomal degradation, and the autophagy protein MAP1LC3B (microtubule associated protein 1 light chain 3 beta) isoform II/LC3B-II to measure autophagic flux (the acquisition and degradation of autophagic cargo over time). Autophagic flux varies by cell type and is higher in whole blood compared with RPMI culture media. Basal autophagic flux shows sex- and age-specific variations. Further, monocytes, but not T cells, respond robustly to amino acid starvation by increasing autophagy, with older individuals exhibiting stronger responses, particularly in non-classical monocytes. These findings underscore the importance of cell type-specific autophagy measurements to understand the effects of aging, sex and nutrition, to develop targeted interventions for age-related diseases.
    Keywords:  Aging; LC3B-II; PBMCs; autophagic flux; autophagy; nutrition; sex
    DOI:  https://doi.org/10.1080/27694127.2025.2543560
  6. Nature. 2025 Aug 27.
    Mechanical confinement governs phenotypic plasticity in melanoma.
    Miranda V Hunter, Eshita Joshi, Sydney Bowker, Emily Montal, Yilun Ma, Young Hun Kim, Zhifan Yang, Laura Tuffery, Zhuoning Li, Eric Rosiek, Alexander Browning, Reuben Moncada, Itai Yanai, Helen Byrne, Mara Monetti, Elisa de Stanchina, Pierre-Jacques Hamard, Richard P Koche, Richard M White.
      Phenotype switching is a form of cellular plasticity in which cancer cells reversibly move between two opposite extremes: proliferative versus invasive states1,2. Although it has long been hypothesized that such switching is triggered by external cues, the identity of these cues remains unclear. Here we demonstrate that mechanical confinement mediates phenotype switching through chromatin remodelling. Using a zebrafish model of melanoma coupled with human samples, we profiled tumour cells at the interface between the tumour and surrounding microenvironment. Morphological analysis of interface cells showed elliptical nuclei, suggestive of mechanical confinement by the adjacent tissue. Spatial and single-cell transcriptomics demonstrated that interface cells adopted a gene program of neuronal invasion, including the acquisition of an acetylated tubulin cage that protects the nucleus during migration. We identified the DNA-bending protein HMGB2 as a confinement-induced mediator of the neuronal state. HMGB2 is upregulated in confined cells, and quantitative modelling revealed that confinement prolongs the contact time between HMGB2 and chromatin, leading to changes in chromatin configuration that favour the neuronal phenotype. Genetic disruption of HMGB2 showed that it regulates the trade-off between proliferative and invasive states, in which confined HMGB2high tumour cells are less proliferative but more drug-resistant. Our results implicate the mechanical microenvironment as a mechanism that drives phenotype switching in melanoma.
    DOI:  https://doi.org/10.1038/s41586-025-09445-6
  7. Nat Commun. 2025 Aug 21. 16(1): 7815
    STN1 facilitates metastasis by promoting transcription of EMT-activator ZEB1 in pancreatic cancer.
    Di Dong, Zhe Zhou, Minglu Zhu, Zhiyuan Hou, Mo Chen, Jingjing Gong, Xuyang Zhao, Aohui Yan, Hui Liang, Yuxin Yin.
      Pancreatic ductal adenocarcinoma (PDAC) poses a serious clinical challenge, demanding further exploration of its pathogenesis and therapeutic targets for metastasis, the main cause of mortality. Here, we identify STN1, a CST complex member crucial for maintaining telomere lengths and genome stability, as a key factor in promoting PDAC metastasis. Elevated STN1 levels correlate with poor patient survival, with oncogenic protein HOXB7 as an upstream transcription factor regulating STN1. Utilizing multiple PDAC experimental models, we discover STN1's role in promoting metastasis by functioning as an upstream factor in epithelial-mesenchymal transition (EMT). Our mechanistic evidence suggests that during transcription, STN1 binds to structurally displaced single-stranded DNA flanking the R-loop, recruiting STAT3 to activate ZEB1 transcription independent of its known telomere maintenance function. Notably, STAT3 inhibitors show enhanced efficiency in restraining metastatic potential in STN1-overexpressed PDAC cells, offering a potential therapeutic avenue for targeting metastasis in STN1-overexpressed PDAC patients facing an unfavorable prognosis.
    DOI:  https://doi.org/10.1038/s41467-025-63083-0
  8. Autophagy. 2025 Aug 28. 1-15
    Deacetylation of ATG16L1 is required for LC3-associated lysosomal microautophagy.
    Qian Wang, Wei Wan, Hongtao Zhang, Tianhua Zhou, Han-Ming Shen, Pingtong Huang, Wei Liu.
      Microautophagy is a selective cellular process in which endolysosomes directly engulf cytoplasmic cargo through membrane invagination. The regulatory mechanisms governing microautophagy remain poorly understood. Here, we identified the deacetylation of ATG16L1 as a critical regulator of LC3-associated lysosomal microautophagy. We demonstrate that ATG16L1 acetylation is dynamically controlled by the acetyltransferase KAT2B and the deacetylase HDAC3. Under lysosomal osmotic stress or glucose deprivation, HDAC3-mediated deacetylation of ATG16L1 within its WD40 domain promotes its interaction with V-ATPase, facilitating ATG16L1 recruitment to lysosomal membranes. While dispensable for macroautophagy, this post-translational modification is essential for LC3 lipidation on lysosomes and enables lysosomal recovery, including the restoration of lysosomal size and degradative capacity following stress. Our results reveal a key role for ATG16L1 deacetylation in driving LC3-associated microautophagy to maintain lysosomal homeostasis.
    Keywords:  ATG16L1; Acetylation; LC3 lipidation; LC3-associated microautophagy; V-ATPase; lysosome
    DOI:  https://doi.org/10.1080/15548627.2025.2551669
  9. Anal Chem. 2025 Aug 25.
    Deciphering Spatiotemporal Control of Ferroptosis in HCC: A Bifunctional Probe for Lipid Droplet Viscosity Dynamics and Interorganelle Communication.
    Tian Cheng, Chaomin Gao, Xueying Zheng, Cuimin Feng, Shuhong Huang, Junling Yin.
      Although lipid droplets (LDs) are established as metabolic regulators of iron-dependent ferroptosis in hepatocellular carcinoma (HCC), their biophysical remodeling and spatiotemporal interactions with other organelles during this cell death process have been incompletely characterized. In this study, we developed ZYB, a bifunctional molecular probe that combines lipophilicity-guided organelle targeting with viscosity-dependent fluorescence activation while exhibiting ideal spectral orthogonality to commercial fluorescent markers. Using ZYB, we detected elevated LD viscosity during erastin-induced ferroptosis and reduced viscosity upon ferrostatin-1-mediated inhibition. Time-lapse imaging of ZYB-labeled LDs revealed significant alterations in diameter, number, morphology, and spatial dynamics as ferroptosis progressed. Capitalizing on ZYB's spectral properties (Ex/Em ∼350/500 nm) alongside organelle-specific dyes (lysosome red tracker: ∼577/590 nm; mitochondria red tracker: ∼579/599 nm), we uncovered a highly dynamic interorganelle communication network involving sequential contact and separation events between LDs and mitochondria, LDs and lysosomes, and neighboring LDs. Beyond providing a powerful LD-imaging tool, this work deciphers the role of organelle communication networks in ferroptosis, offering a mechanistic foundation for targeting HCC vulnerabilities.
    DOI:  https://doi.org/10.1021/acs.analchem.5c03877
  10. Nature. 2025 Aug 20.
    Quantitative imaging of lipid transport in mammalian cells.
    Juan M Iglesias-Artola, Kristin Böhlig, Kai Schuhmann, Katelyn C Cook, H Mathilda Lennartz, Milena Schuhmacher, Pavel Barahtjan, Cristina Jiménez López, Radek Šachl, Vannuruswamy Garikapati, Karina Pombo-Garcia, Annett Lohmann, Petra Riegerová, Martin Hof, Björn Drobot, Andrej Shevchenko, Alf Honigmann, André Nadler.
      Eukaryotic cells produce over 1,000 different lipid species that tune organelle membrane properties, control signalling and store energy1,2. How lipid species are selectively sorted between organelles to maintain specific membrane identities is largely unclear, owing to the difficulty of imaging lipid transport in cells3. Here we measured the retrograde transport and metabolism of individual lipid species in mammalian cells using time-resolved fluorescence imaging of bifunctional lipid probes in combination with ultra-high-resolution mass spectrometry and mathematical modelling. Quantification of lipid flux between organelles revealed that directional, non-vesicular lipid transport is responsible for fast, species-selective lipid sorting, in contrast to the slow, unspecific vesicular membrane trafficking. Using genetic perturbations, we found that coupling between energy-dependent lipid flipping and non-vesicular transport is a mechanism for directional lipid transport. Comparison of metabolic conversion and transport rates showed that non-vesicular transport dominates the organelle distribution of lipids, while species-specific phospholipid metabolism controls neutral lipid accumulation. Our results provide the first quantitative map of retrograde lipid flux in cells4. We anticipate that our pipeline for mapping of lipid flux through physical and chemical space in cells will boost our understanding of lipids in cell biology and disease.
    DOI:  https://doi.org/10.1038/s41586-025-09432-x
  11. Nature. 2025 Aug 20.
    Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy.
    Erez N Baruch, Frederico O Gleber-Netto, Priyadharsini Nagarajan, Xiayu Rao, Shamima Akhter, Tuany Eichwald, Tongxin Xie, Mohammad Balood, Adebayo Adewale, Shorook Naara, Hinduja N Sathishkumar, Shajedul Islam, William McCarthy, Brandi J Mattson, Renata Ferrarotto, Michael K Wong, Michael A Davies, Sonali Jindal, Sreyashi Basu, Karine Roversi, Amin Reza Nikpoor, Maryam Ahmadi, Ali Ahmadi, Catherine Harwood, Irene Leigh, Dennis Gong, Paulino Tallón de Lara, Derrick L Tao, Tara M Davidson, Nadim J Ajami, Andrew Futreal, Kunal Rai, Veena Kochat, Micah Castillo, Preethi Gunaratne, Ryan P Goepfert, Sharia D Hernandez, Nikhil I Khushalani, Jing Wang, Stephanie S Watowich, George A Calin, Michael R Migden, Mona Yuan, Naijiang Liu, Yi Ye, William L Hwang, Paola D Vermeer, Nisha J D'Silva, Yuri L Bunimovich, Dan Yaniv, Jared K Burks, Javier Gomez, Patrick M Dougherty, Kenneth Y Tsai, James P Allison, Padmanee Sharma, Jennifer A Wargo, Jeffrey N Myers, Sebastien Talbot, Neil D Gross, Moran Amit.
      Perineural invasion (PNI) is a well-established factor of poor prognosis in multiple cancer types1, yet its mechanism remains unclear. Here we provide clinical and mechanistic insights into the role of PNI and cancer-induced nerve injury (CINI) in resistance to anti-PD-1 therapy. Our study demonstrates that PNI and CINI of tumour-associated nerves are associated with poor response to anti-PD-1 therapy among patients with cutaneous squamous cell carcinoma, melanoma and gastric cancer. Electron microscopy and electrical conduction analyses reveal that cancer cells degrade the nerve fibre myelin sheets. The injured neurons respond by autonomously initiating IL-6- and type I interferon-mediated inflammation to promote nerve healing and regeneration. As the tumour grows, the CINI burden increases, and its associated inflammation becomes chronic and skews the general immune tone within the tumour microenvironment into a suppressive and exhaustive state. The CINI-driven anti-PD-1 resistance can be reversed by targeting multiple steps in the CINI signalling process: denervating the tumour, conditional knockout of the transcription factor mediating the injury signal within neurons (Atf3), knockout of interferon-α receptor signalling (Ifnar1-/-) or by combining anti-PD-1 and anti-IL-6-receptor blockade. Our findings demonstrate the direct immunoregulatory roles of CINI and its therapeutic potential.
    DOI:  https://doi.org/10.1038/s41586-025-09370-8
  12. Science. 2025 Aug 21. 389(6762): eadz0972
    LYVAC/PDZD8 is a lysosomal vacuolator.
    Haoxiang Yang, Jinrui Xun, Yajuan Li, Awishi Mondal, Bo Lv, Simon C Watkins, Lingyan Shi, Jay Xiaojun Tan.
      Lysosomal vacuolation is commonly found in many pathophysiological conditions, but its molecular mechanisms and functions remain largely unknown. Here, we show that the endoplasmic reticulum (ER)-anchored lipid transfer protein PDZ domain-containing 8 (PDZD8), which we propose to be renamed as lysosomal vacuolator (LYVAC), is a general mediator of lysosomal vacuolation. Using human cell lines, we found that diverse lysosomal vacuolation inducers converged on lysosomal osmotic stress, triggering LYVAC recruitment through multivalent interactions. Stress-induced lysosomal lipid signaling contributed to both the recruitment and activation of LYVAC. By directly sensing lysosomal phosphatidylserine and cholesterol, the lipid transfer domain of LYVAC mediated directional ER-to-lysosome lipid movement, leading to osmotic membrane expansion of lysosomes. These findings uncover an essential mechanism for lysosomal vacuolation with broad implications in pathophysiology.
    DOI:  https://doi.org/10.1126/science.adz0972
  13. Mol Cell. 2025 Aug 19. pii: S1097-2765(25)00659-8. [Epub ahead of print]
    A regulator of amino acid sensing links lipid peroxidation and lipid droplet-dependent antioxidant response.
    Jinhua Li, Yansong Zhang, Jingyu Peng, Wei Yang, Yanzhe Pan, Ying Xu, Jiayi Yao, Siyuan Lin, Yizhi Li, Xinran Gu, Wei Dong, Xiang Yu, Ming Ge, Min Liu, Alan Jian Zhu.
      Recent studies highlight the antioxidant role of lipid droplets (LDs) in shielding unsaturated lipids from peroxidation. While LDs accumulate during oxidative stress, the underlying mechanism remains unclear. Our previous research revealed that intracellular amino acids directly bind to and activate the E3 ubiquitin ligase Ubr1 to degrade Plin2, an LD protein inhibiting lipolysis. Here, we unexpectedly find that Ubr1's ability to bind to amino acids is inhibited during oxidative stress. Mechanistically, oxidative stress-induced lipid peroxidation blocks the activity of Hsc70-4, an ATPase that maintains the amino-acid-binding ability of Ubr1. 4-hydroxynonenal, a reactive product of lipid peroxidation, covalently modifies and inactivates Hsc70-4, leading to Ubr1 inactivation, Plin2 stabilization, and LD accumulation. Increased LDs minimize lipid peroxidation, thus protecting cells from oxidative damage and cell death. Together, we identify a regulator of amino acid sensing with redox-dependent activity, bridging the gap in understanding how lipid peroxidation stimulates LD-dependent antioxidant responses.
    Keywords:  4-hydroxynonenal; HSPA8; Hsc70-4; Plin2; Ubr1; amino acid sensing; antioxidant response; lipid droplet; lipid peroxidation
    DOI:  https://doi.org/10.1016/j.molcel.2025.08.009
  14. Sci Adv. 2025 Aug 22. 11(34): eadu7319
    Bayesian reconstruction of rapidly scanned mid-infrared optoacoustic signals enables fast, label-free chemical microscopy.
    Constantin Berger, Myeongseop Kim, Lukas Scheel-Platz, Andreas Eigenberger, Lukas Prantl, Panhang Liu, Vipul Gujrati, Vasilis Ntziachristos, Dominik Jüstel, Miguel A Pleitez.
      Hyperspectral optoacoustic microscopy (OAM) enables obtaining images with label-free biomolecular contrast, offering excellent perspectives as a diagnostic tool to assess freshly excised and unprocessed biological samples. However, time-consuming raster scanning image formation currently limits the translation potential of OAM into the clinical setting, for instance, in intraoperative histopathological assessments, where micrographs of excised tissue need to be taken within a few minutes for fast clinical decision-making. Here, we present a non-data-driven computational framework tailored to enable fast OAM by rapid data acquisition and model-based image reconstruction, termed Bayesian raster-computed optoacoustic microscopy (BayROM). Unlike data-driven approaches, BayROM does not require training datasets, but instead, it uses probabilistic model-based reconstruction to facilitate fast high-resolution imaging. We show that BayROM enables acquiring micrographs 10 times faster on average than conventional raster scanning microscopy and provides sufficient image quality to facilitate the intraoperative histological assessment of processed fat grafts for autologous fat transfer.
    DOI:  https://doi.org/10.1126/sciadv.adu7319
  15. Cell Rep. 2025 Aug 21. pii: S2211-1247(25)00962-3. [Epub ahead of print]44(9): 116191
    Integrative genomic identification of therapeutic targets for pancreatic cancer.
    Jimmy A Guo, Dennis Gong, Kyle Evans, Kazuki Takahashi, Ananya D Jambhale, Carina Shiau, Patrick Yu, Steven Wang, Wenbo W Wu, Seema Chugh, Kevin S Kapner, Julien Dilly, Daniel Zhao, Peter Chen, Eric L Smith, Joseph D Mancias, Francisca Vazquez, Harshabad Singh, William L Hwang, Andrew J Aguirre.
      Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease, and new therapeutic strategies are urgently needed. Here, we conduct an integrative, genome-scale examination of genetic dependencies and cell surface targets using CRISPR-Cas screening and multi-omic data, including single-nucleus and spatial transcriptomic data from patient tumors. We systematically identify clinically tractable and biomarker-linked PDAC dependencies, including CDS2 as a synthetic lethal target in cancer cells expressing signatures of epithelial-to-mesenchymal transition. We examine biomarkers and co-dependencies of the KRAS oncogene, defining gene expression signatures of sensitivity and resistance associated with response to pharmacological inhibition of KRAS. mRNA and protein profiling reveal cell surface protein-encoding genes with robust expression in patient tumors and minimal expression in non-malignant tissues. Furthermore, we define intratumoral and interpatient heterogeneity of target gene expression and identify orthogonal targets that suggest combinatorial strategies. Collectively, this work identifies multiple targets that may inform therapeutic strategies for patients with PDAC.
    Keywords:  CDS2; CP: Cancer; CP: Genomics; biomarkers; cancer dependency map; multi-omics; pancreatic cancer; therapeutic targets
    DOI:  https://doi.org/10.1016/j.celrep.2025.116191
  16. Int J Mol Sci. 2025 Aug 19. pii: 8011. [Epub ahead of print]26(16):
    Physical Activity, Exerkines, and Their Role in Cancer Cachexia.
    Jan Bilski, Aleksandra Szlachcic, Agata Ptak-Belowska, Tomasz Brzozowski.
      Cancer-associated cachexia is a multifaceted wasting syndrome characterized by progressive loss of skeletal muscle mass, systemic inflammation, and metabolic dysfunction and is particularly prevalent in gastrointestinal cancers. Physical activity has emerged as a promising non-pharmacological intervention capable of attenuating key drivers of cachexia. Exercise modulates inflammatory signaling (e.g., IL-6/STAT3 and TNF-α/NF-κB), enhances anabolic pathways (e.g., IGF-1/Akt/mTOR), and preserves lean body mass and functional capacity. Exercise-induced signaling molecules, known as exerkines, are key mediators of these benefits, which are released during physical activity and act in an autocrine, paracrine, and endocrine manner. However, many of these molecules also exhibit context-dependent effects. While they exert protective, anti-inflammatory, or anabolic actions when transiently elevated after exercise, the same molecules may contribute to cachexia pathogenesis when chronically secreted by tumors or in systemic disease states. The biological effects of a given factor depend on its origin, timing, concentration, and physiological milieu. This review presents recent evidence from clinical and experimental studies to elucidate how physical activity and exerkines may be harnessed to mitigate cancer cachexia, with particular emphasis on gastrointestinal malignancies and their unique metabolic challenges.
    Keywords:  cancer cachexia; context-dependent signaling; exerkines; gastrointestinal cancers; metabolic dysfunction; physical activity; skeletal muscle; systemic inflammation
    DOI:  https://doi.org/10.3390/ijms26168011
  17. Cancer Metab. 2025 Aug 20. 13(1): 38
    Glutaminase inhibition ameliorates cancer-associated fibroblast lipid support of pancreatic cancer cell growth.
    Xu Han, Laura C Kim, Nicholas P Lesner, Xuanyan Cai, Tran Ngoc Van Le, M Celeste Simon.
       BACKGROUND: Lipid homeostasis is critical for pancreatic adenocarcinoma (PDAC) cell survival under hypoxic and nutrient-deprived conditions. Hypoxia inhibits unsaturated lipid biosynthesis, compelling cancer cells to depend on exogenous unsaturated lipids to counteract saturated lipid-induced toxicity. Our previous work revealed that cancer-associated fibroblasts (CAFs) secrete unsaturated lipids, primarily lysophosphatidylcholines (LPCs), to alleviate lipotoxic stress in PDAC cells. Here, we conducted a drug screen to identify compounds that bypass the rescue effect of exogenous LPCs on cancer cell survival under stress.
    METHODS: We employed high-throughput screening of a bioactive chemical library with 3,336 compounds, including FDA-approved drugs and drug-like molecules against defined molecular targets. Two assays were performed: a cytotoxicity assay to exclude indiscriminately toxic compounds at 1 μM and an LPC crosstalk inhibition assay to identify compounds that selectively reduce cancer cell viability in the presence of LPCs under stress conditions.
    RESULTS: CB-839, a glutaminase inhibitor, was identified as the most effective compound, selectively inhibiting the LPC-mediated rescue of PDAC cell viability effect without intrinsic cytotoxicity. Mechanistic studies revealed that CB-839 induces cell death by activating the pro-apoptotic ATF4/CHOP pathway, reducing antioxidant production, and increasing reactive oxygen species (ROS). While CB-839 showed limited efficacy against PDAC tumor cells alone in vivo, it modestly inhibited tumor growth in a PDAC-CAF co-implanted subcutaneous mouse model, highlighting its potential to disrupt CAF-mediated nutrient support. Additionally, glutamine antagonists showed more potent tumor-suppressive effects than CB-839.
    CONCLUSION: Our findings emphasize the importance of glutamine metabolism inhibition in suppressing tumor growth and disrupting CAF-mediated crosstalk. We further underscore the potential of glutamine antagonist prodrugs as a strategy to target metabolic vulnerabilities in PDAC.
    DOI:  https://doi.org/10.1186/s40170-025-00389-z
  18. Gastroenterol Rep (Oxf). 2025 ;13 goaf057
    Unveiling CTRB2, RSPO3, KLOTB, and ROR1 as obesity-pancreatic disease association proteins: a comprehensive Mendelian randomization study.
    Chunhua Zhou, Xixian Ruan, Tianyi Che, Yao Zhang, Shuai Yuan, Xue Li, Jie Zheng, Xiaocang Cao, Jie Chen, Xiaoyan Wang, Duowu Zou.
       Background: Obesity is recognized as a prominent contributing factor for pancreatic diseases; however, the mechanisms remain elusive. We aimed to identify the mediating role of circulating proteins in these associations.
    Methods: A two-step Mendelian randomization (MR) was conducted to investigate associations between nine obesity indicators, thousands of circulating proteins, with three pancreatic diseases (acute pancreatitis, chronic pancreatitis, and pancreatic carcinoma). Colocalization analyses were performed to validate these associations. Protein mediating networks among obesity indicators and pancreatic diseases were investigated by mediation analysis.
    Results: Genetically predicted circulating levels of 4, 2, and 2 proteins were associated with acute pancreatitis, chronic pancreatitis, and pancreatic carcinoma, respectively. In mediation analysis, decreased chymotrypsin B2 (CTRB2) levels mediated 1.03% (95% CI [confidence interval] 0.02%-2.03%) of the effects of body mass index on acute pancreatitis. Increased R-spondin 3 (RSPO3) levels mediated the effects of body mass index (2.95%, 95% CI 0.18%-5.73%), body fat percentage (4.53%, 95% CI 1.11%-7.96%), waist-hip ratio (8.48%, 95% CI 3.11%-13.86%), and visceral adipose tissue (3.93%, 95% CI 0.64%-7.22%) on acute pancreatitis. We also found increased klotho beta (KLOTB) levels mediated the effects of waist-hip ratio (7.01%, 95% CI 3.30%-10.71%) and visceral adipose tissue (8.98%, 95% CI 4.55%-13.41%) on chronic pancreatitis, and decreased receptor tyrosine kinase-like orphan receptor 1 (ROR1) levels mediated the effects of body mass index (10.39%, 95% CI 3.36%-17.42%) and visceral adipose tissue (6.29%, 95% CI 1.00%-11.58%) on pancreatic carcinoma.
    Conclusions: The MR suggests that circulating CTRB2, RSPO3, KLOTB, and ROR1 proteins may mediate associations between obesity and pancreatic diseases.
    Keywords:  Mendelian randomization; colocalization; obesity; pancreatic diseases; proteomics
    DOI:  https://doi.org/10.1093/gastro/goaf057
  19. NPJ Precis Oncol. 2025 Aug 22. 9(1): 296
    Targeting cancer-associated fibroblast-driven LIF/LIFR axis improves the therapeutic efficacy of gemcitabine and nab-paclitaxel in pancreatic cancer.
    Rakesh Bhatia, Imran Khan, Xiaoqi Li, Shailendra Gautam, Parthasarathy Seshacharyulu, Zahraa Wajih Alsafwani, Namita Bhyravbhatla, Moorthy P Ponnusamy, Maneesh Jain, Mokenge Malafa, Santhamma Bindu, Ahmed Gulzar, Hareesh Nair, Surinder K Batra, Sushil Kumar.
      Pancreatic ductal adenocarcinoma (PDAC) is inherently therapy resistant due to cancer cell-stroma crosstalk across several signaling pathways. Among these, the LIF/LIFR axis has been implicated in cancer cell and cancer-associated fibroblast (CAF) crosstalk. We evaluated the efficacy of EC359, a competitive inhibitor of LIFR, in combination with gemcitabine. EC359 reduced tumor burden by 90% compared to controls and by 55% compared to gemcitabine alone in cancer cell and CAFs co-implannation model. The RNA-seq analysis revealed a significant alteration in extracellular matrix components, stemness, microtubule assembly, and immune response, suggesting simultaneous targeting of cancer cell-intrinsic and stroma-mediated mechanisms by EC359. In autochthonous murine model of PDAC, EC359 enhanced the therapeutic efficacy of gemcitabine and nab-paclitaxel, accompanied by an increase in dendritic cells but a reduction in T-regulatory cells. Thus, EC359 reduces PDAC cell stemness, stabilizes microtubule assembly, and reduces the immunosuppressive microenvironment to improve the efficacy of standard-of-care in PDAC.
    DOI:  https://doi.org/10.1038/s41698-025-01046-w
  20. Sci Adv. 2025 Aug 29. 11(35): eadv9759
    Cells prioritize the regulation of cell mass density.
    Jinyu Fu, Qin Ni, Yufei Wu, Anoushka Gupta, Zhuoxu Ge, Hongru Yang, Yasin Afrida, Ishan Barman, Sean X Sun.
      A cell's global physical state is characterized by its volume and dry mass. The ratio of cell mass to volume defines the cell mass density (CMD), which is also a measure of macromolecular crowding and concentrations of all proteins. Using the fluorescence eXclusion method (FXm) and quantitative phase microscopy (QPM), we investigate CMD dynamics following sudden changes in media osmolarity. We find that while cell volume and mass exhibit complex behavior after osmotic shock, CMD follows a straightforward monotonic recovery over 48 hours. This recovery is cell cycle independent and depends on coordinated adjustment of protein synthesis and volume growth rates. Unexpectedly, the protein synthesis rate decreases when CMD increases. We observe that nucleoplasm-cytoplasm transport is CMD dependent, which contributes to negative regulatory feedback on CMD. The Na+/H+ exchanger helps regulate CMD by affecting both protein synthesis and volume change. Together, we reveal that cells have a robust control system that actively regulates CMD during environmental change.
    DOI:  https://doi.org/10.1126/sciadv.adv9759
  21. J Natl Cancer Inst. 2025 Aug 22. pii: djaf236. [Epub ahead of print]
    The impact of eligibility criteria on KRASG12C inhibitor trials in patients with NSCLC.
    Margaux Wooster, Michael May, Prashasti Agrawal, Jonathan Lee, Benjamin May, Xin Ma, Stephanie Bogdan, Catherine A Shu, Brian S Henick, Anjali Saqi, Mahesh Mansukhani, Gregory Riely, Dawn L Hershman, Christine Garcia, Kathryn C Arbour, Benjamin O Herzberg.
       BACKGROUND: 20% of cancer patients are estimated to be ineligible for phase III trials due to restrictive eligibility criteria. In response, several groups, including the FDA, have advocated for more inclusive study designs. We examined KRAS G12C inhibitor trials to determine if inclusivity has shifted in the development of molecularly-targeted therapies.
    METHODS: We evaluated Phase I-III studies of KRAS G12C inhibitors in non-small cell lung cancer (NSCLC) by applying criteria from 15 US trials to a multi-institutional real-world cohort of patients with metastatic NSCLC and universal KRAS testing (N = 2383). Eligibility analysis, multivariate logistic regression for ineligibility, and a Cox proportional hazards model were used on patient with KRAS G12C-mutated NSCLC (N = 185) to compare trial enrollment and overall survival under various eligibility modifications.
    RESULTS: 60-70% of patients with metastatic KRAS G12C-mutated NSCLC were ineligible for any KRAS inhibitor clinical trial, including studies aiming to establish first-line standard of care. Eligibility criteria remained unchanged from Phase I to Phase III. Performance status, renal function, and active brain metastases were the main causes of trial ineligibility. Liberalizing criteria for renal function and brain metastases increased enrollment by 25% without affecting overall survival (p = .49), whereas allowing worse performance status reduced study effect sizes (p = .001 in second line and p = .04 in first line).
    CONCLUSIONS: Most patients with metastatic KRAS G12C-mutated NSCLC are excluded from trials. There is significant potential to refine trial entry criteria to better balance generalizability, safety, speed, and success.
    Keywords:  Lung cancer; clinical trials; eligibility
    DOI:  https://doi.org/10.1093/jnci/djaf236
  22. FEBS J. 2025 Aug 22.
    Nanoscale engagement of programmed death ligand 1 (PD-L1) in membrane lipid raft domains of cancer cells.
    Simone Civita, Martina Ruglioni, Matteo Mariangeli, Serena Barachini, Tiziano Salvadori, Sofia Cristiani, Vittoria Carnicelli, Iacopo Petrini, Irene Nepita, Marco Castello, Alberto Diaspro, Stefano Fogli, Paolo Bianchini, Barbara Storti, Ranieri Bizzarri, Romano Danesi.
      Several tumors have evolved the ability to evade the immune system by expressing programmed death ligand 1 (PD-L1; also known as programmed cell death 1 ligand 1) on the membrane of neoplastic cells. PD-L1 binds the receptor programmed cell death protein 1 (PD-1) on T cells, deactivating the immune response. Accordingly, PD-L1 has recently become a crucial target for cancer therapy. Yet, the molecular organization of PD-L1 on the membrane is still rather obscure. Here, we investigated the plasma membrane organization of PD-L1 by a multiscale fluorescence imaging toolbox reaching the nanoscale by super-resolution microscopy. Our results indicate that a major fraction of PD-L1 is largely engaged in membrane nanodomains of 25 nm mean radius, which in turn organize in an irregular mesoscopic lattice with mean interdomain distance of about 180 nm. The significant colocalization of PD-L1 with lipid raft markers, which we assessed from 200 to 250 nm down to < 10 nm, supports a raft-driven organization of PD-L1, which may follow its extended palmitoylation upon expression. This pattern was also demonstrated in living cells by visualizing PD-L1 diffusion at different spatial scales. The raft-orchestrated multiscale PD-L1 organization on the cell membrane may afford novel targets for improved immuno-oncology strategies.
    Keywords:  PD‐L1; STED; STORM; confined diffusion; lipid rafts
    DOI:  https://doi.org/10.1111/febs.70238
  23. Metab Eng. 2025 Aug 22. pii: S1096-7176(25)00129-6. [Epub ahead of print]
    Lipid accumulation in nitrogen and phosphorus-limited yeast is caused by less growth-related dilution.
    Xi Li, Daniel R Weilandt, Felix C Keber, Arjuna M Subramanian, Shayne R Loynes, Christopher V Rao, Yihui Shen, Martin Wühr, Joshua D Rabinowitz.
      Oleaginous yeasts are used commercially to produce oleochemicals and hold potential also for biodiesel production. In response to nitrogen or phosphorous limitation, oleaginous yeasts accumulate lipids in the form of triacylglycerols. Previous work has investigated potential mechanisms by which nutrient limitation induces lipid biosynthesis without verifying whether lipid biosynthesis flux is actually enhanced. Here we show, using 13C-glucose tracing, that in nitrogen or phosphorous limitation, lipid accumulation occurs without consistent increases in biosynthetic flux. Instead, the main driver of increased lipid pools is decreased growth-related dilution. This conclusion holds across two divergent oleaginous yeasts: Rhodotorula toruloides and Yarrowia lipolytica. Quantitative proteomics shows a substantial proteome reallocation in response to nitrogen and phosphorous limitation, with ribosomal proteins strongly downregulated, while lipid enzymes are preserved but not consistently upregulated in absolute quantity. Thus, nutrient limitation, rather than triggering greatly enhanced lipid synthesis, results in roughly sustained lipid enzyme levels and biosynthetic flux. Due to slower lipid dilution by cell division, this suffices to drive marked lipid accumulation.
    Keywords:  biodiesel; de novo lipogenesis; isotope tracing; kinetic flux profiling; oleaginous yeast
    DOI:  https://doi.org/10.1016/j.ymben.2025.08.010
  24. Proc Natl Acad Sci U S A. 2025 Aug 26. 122(34): e2504064122
    Self-generated chemotaxis of mixed cell populations.
    Mehmet Can Uçar, Zane Alsberga, Jonna Alanko, Michael Sixt, Edouard Hannezo.
      Cell and tissue movement in development, cancer invasion, and immune response relies on chemical or mechanical guidance cues. In many systems, this behavior is locally directed by self-generated signaling gradients rather than long-range, prepatterned cues. However, how heterogeneous mixtures of cells interact nonreciprocally and navigate through self-generated gradients remains largely unexplored. Here, we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous cell populations. We find that the relative chemotactic sensitivities of different cell populations control their long-time coupling and comigration dynamics, with boundary conditions such as external cell and attractant reservoirs substantially influencing the migration patterns. Our model predicts an optimal parameter regime that enables robust and colocalized migration. We test our theoretical predictions with in vitro experiments demonstrating the comigration of distinct immune cell populations, and quantitatively reproduce observed migration patterns under wild-type and perturbed conditions. Interestingly, immune cell comigration occurs close to the predicted optimal regime. Finally, we incorporate mechanical interactions into our framework, revealing a nontrivial interplay between chemotactic and mechanical nonreciprocity in driving collective migration. Together, our findings suggest that self-generated chemotaxis is a robust strategy for the navigation of mixed cell populations.
    Keywords:  Keller–Segel model; cell migration; chemotaxis; nonreciprocity; traveling waves
    DOI:  https://doi.org/10.1073/pnas.2504064122
  25. Nature. 2025 Aug 20.
    Molecular mechanism of ultrafast transport by plasma membrane Ca2+-ATPases.
    Deivanayagabarathy Vinayagam, Oleg Sitsel, Uwe Schulte, Cristina E Constantin, Wout Oosterheert, Daniel Prumbaum, Gerd Zolles, Bernd Fakler, Stefan Raunser.
      Tight control of intracellular Ca2+ levels is fundamental as they are used to control numerous signal transduction pathways1. Plasma membrane Ca2+-ATPases (PMCAs) have a crucial role in this process by extruding Ca2+ against a steep concentration gradient from the cytosol to the extracellular space2. Although new details of PMCA biology are constantly being uncovered, the structural basis of the most distinguishing features of these pumps, namely, transport rates in the kilohertz range and regulation of activity by the plasma membrane phospholipid PtdIns(4,5)P2, has so far remained elusive. Here we present the structures of mouse PMCA2 in the presence and absence of its accessory subunit neuroplastin in eight different stages of its transport cycle. Combined with whole-cell recordings that accurately track PMCA-mediated Ca2+ extrusion in intact cells, these structures enable us to establish the first comprehensive transport model for a PMCA, reveal the role of disease-causing mutations and uncover the structural underpinnings of regulatory PMCA-phospholipid interaction. The transport cycle-dependent dynamics of PtdIns(4,5)P2 are fundamental for its role as a 'latch' promoting the fast release of Ca2+ and opening a passageway for counter-ions. These actions are required for maintaining the ultra-fast transport cycle. Moreover, we identify the PtdIns(4,5)P2-binding site as an unanticipated target for drug-mediated manipulation of intracellular Ca2+ levels. Our work provides detailed structural insights into the uniquely fast operation of native PMCA-type Ca2+ pumps and its control by membrane lipids and drugs.
    DOI:  https://doi.org/10.1038/s41586-025-09402-3
  26. Adv Sci (Weinh). 2025 Aug 21. e09420
    Polarization-Sensitive Holotomography for Multidimensional Label-Free Imaging and Characterization of Lipid Droplets in Cancer Cells.
    Hossein Khadem, Maria Mangini, Maria Antonietta Ferrara, Anna Chiara DeLuca, Giuseppe Coppola.
      Lipid droplets (LDs) are key markers of cellular metabolism, often altered in cancer. While holotomography enables 3D, label-free imaging of LDs via refractive index, it relies on complex thresholding and lacks biochemical specificity. Here, polarization-sensitive holotomography (PS-HT), which leverages the intrinsic birefringence of LDs for high-contrast, selective identification with a fixed near-zero threshold is presented. Using prostate cell models (healthy PNT2 and cancer PC3), PS-HT is validated against fluorescence microscopy and holotomography, showing that it enables accurate quantification of birefringence, LD volume, dry mass, molecular organization, and spatial distribution. Cancer cells show significantly higher birefringence after glucose treatment, reflecting enhanced lipid accumulation. PS-HT, combined with principal component analysis, achieves near-perfect classification of cancer versus healthy cells, establishing it as a robust, label-free tool for studying lipid metabolism and cancer diagnostics.
    Keywords:  birefringence imaging; cancer cell metabolism; lipid droplets; polarization‐sensitive holotomography; quantitative phase imaging
    DOI:  https://doi.org/10.1002/advs.202509420
  27. Methods Mol Biol. 2025 ;2958 159-167
    Micropost Arrays to Model ECM Fiber Obstacles During Cell Migration in Confinement.
    Aditya Katiyar, Richard B Dickinson, Tanmay P Lele.
      Micropost arrays are a valuable platform for studying cell migration in controlled microenvironments. These arrays enable researchers to mimic how migrating cells deform their nuclei in reaction to physical constraints presented by extracellular matrix (ECM) fibers during processes such as wound healing and cancer metastasis. By tuning micropost patterns and sizes, researchers can not only explore the impact of confining spaces created by such patterns on cell migration, signaling, and nuclear deformation but also simultaneously quantify cell-generated forces and forces of nuclear deformation. This paper outlines methods to design and fabricate ECM fiber mimicking micropost arrays for use in fundamental studies of confining cell migration.
    Keywords:  Confining cell migration; Microfabrication; Nuclear mechanics
    DOI:  https://doi.org/10.1007/978-1-0716-4714-1_11
  28. Nat Chem Biol. 2025 Aug 22.
    α-Ketoglutarate dictates AMPK protein synthesis for energy sensing in human cancers.
    Wen Mi, Yun Xue, Haohang Yan, Yurou Zhang, Xinlei Cai, Shuyuan Zhang, Ruiping He, Liucheng Li, Lingzhi Zhu, Xinyi Xia, Yifan Liang, Chongwen Cao, Yi Xu, Junfeng Bi, Guanlin Wang, Li Chen, Dan Ye, Fei Li, Ruobing Ren, Pingyu Liu, Hongbin Ji, Fuming Li.
      The energy sensor AMP-activated protein kinase (AMPK) promotes tumor cell survival under stress but how to prevent AMPK activation to blunt tumor progression remains unclear. Here we show that the metabolite α-ketoglutarate (α-KG) dictates AMPK translation through a TET-YBX1 axis, which can be exploited to sensitize human cancer cells to energy stress. α-KG-deficient cells fail to activate AMPK under glucose starvation, which elicits cytosolic NADPH depletion and disulfidptosis. Mechanistically, α-KG insufficiency inhibits TET-dependent transcription of YBX1, an RNA-binding protein required for human-specific AMPK protein synthesis. Similarly, α-KG competitors including succinate and itaconate inhibit the YBX1-AMPK axis and sensitize cancer cells to glucose deprivation. Lastly, cotargeting oncogenic YBX1 and GLUT1 creates synthetic lethality and blunts tumor growth in vivo. Together, our findings link α-KG to energy sensing through AMPK translation and propose that targeting α-KG-YBX1-dependent AMPK translation can sensitize human cancer cells to energy stress for treatment.
    DOI:  https://doi.org/10.1038/s41589-025-02013-z
  29. Med Oncol. 2025 Aug 27. 42(10): 450
    The role of phosphatidylcholine metabolism in tumors.
    Lulu Li, Yongxiu Huang, Yaoqi Gui, Wenqiong Xiang, Min Yang, Yu Hou, Meixi Peng.
      Phosphatidylcholine (PC), a core component of eukaryotic cell membranes essential for maintaining membrane integrity, has emerged as a critical regulator in oncogenic metabolic reprogramming. Accumulating evidence reveals that dysregulated PC metabolism constitutes a central mechanism driving malignant tumor progression. This review systematically delineates the biosynthetic pathways (Kennedy pathway, PEMT pathway, Lands cycle) and catabolic processes (phospholipase-mediated hydrolysis via PLA2, PC-PLC, and PLD) governing PC homeostasis. We highlight how PC metabolic networks orchestrate pro-tumorigenic effects via multifaceted mechanisms, such as enhancing membrane biosynthesis to support rapid tumor proliferation, activating some proliferative signaling cascades coupled with apoptosis suppression, remodeling the immunosuppressive microenvironment, et al. Notably, small-molecule inhibitors targeting key PC metabolic enzymes (e.g., RSM-932A, FIPI) demonstrate promising anti-tumor efficacy in preclinical models, though therapeutic outcomes are constrained by metabolic plasticity and tumor heterogeneity. By integrating recent advances in lipidomics and spatial metabolomics, this synthesis not only deciphers the evolutionary logic underlying PC-driven oncogenesis but also proposes innovative therapeutic strategies combining metabolic inhibitors with immune checkpoint modulators. Our analysis provides a conceptual framework for targeting phospholipid vulnerabilities in cancer, paving the way for precision oncology applications.
    Keywords:  Metabolic reprogramming; Phosphatidylcholine metabolism; Tumor; Tumor microenvironment
    DOI:  https://doi.org/10.1007/s12032-025-03017-4
  30. Lab Chip. 2025 Aug 20.
    Accelerated maturation of branched organoids confined in collagen droplets.
    Iris Ruider, Anna Pastucha, Marion K Raich, Wentao Xu, Yan Liu, Maximilian Reichert, David Weitz, Andreas R Bausch.
      Droplet-based organoid culture offers several advantages over conventional bulk organoid culture, such as improved yield, reproducibility, and throughput. However, organoids grown in droplets typically display only a spherical geometry and lack the intricate structural complexity found in native tissue. By incorporating singularised pancreatic ductal adenocarcinoma cells into collagen droplets, we achieve the growth of branched structures, indicating a more complex interaction with the surrounding hydrogel. A comparison of organoid growth in droplets of different diameters showed that while geometrical confinement improves organoid homogeneity, it also impairs the formation of more complex organoid morphologies. Thus, only in 750 μm diameter collagen droplets did we achieve the consistent growth of highly branched structures with a morphology closely resembling the structural complexity achieved in traditional bulk organoid culture. Moreover, our analysis of organoid morphology and transcriptomic data suggests an accelerated maturation of organoids cultured in collagen droplets, highlighting a shift in developmental timing compared to traditional systems.
    DOI:  https://doi.org/10.1039/d5lc00287g
  31. NAR Genom Bioinform. 2025 Sep;7(3): lqaf114
    PRISM: a Python package for interactive and integrated analysis of multiplexed tissue microarrays.
    Rafael Tubelleza, Aaron Kilgallon, Chin Wee Tan, James Monkman, John F Fraser, Arutha Kulasinghe.
      Tissue microarrays (TMAs) enable researchers to analyse hundreds of tissue samples simultaneously by embedding multiple samples into single arrays, enabling conservation of valuable tissue samples and experimental reagents. Moreover, profiling TMAs allows efficient screening of tissue samples for translational and clinical applications. Multiplexed imaging technologies allow for spatial profiling of proteins at single-cell resolution, providing insights into tumour microenvironments and disease mechanisms. High-plex spatial single-cell protein profiling is a powerful tool for biomarker discovery and translational cancer research; however, there remain limited options for end-to-end computational analysis of this type of data. Here, we introduce PRISM, a Python package for interactive, end-to-end analyses of TMAs with a focus on translational and clinical research using multiplexed proteomic data. PRISM leverages the SpatialData framework to standardize data storage and ensure interoperability with single-cell and spatial analysis tools. It consists of two main components: TMA Image Analysis for marker-based tissue masking, TMA dearraying, cell segmentation, and single-cell feature extraction; and AnnData Analysis for quality control, clustering, iterative cell-type annotation, and spatial analysis. Integrated as a plugin within napari, PRISM provides an intuitive and purely interactive graphical interface for real time and human-in-the-loop analyses. PRISM supports efficient multi-resolution image processing and accelerates bioinformatics workflows using efficient scalable data structures, parallelization and GPU acceleration. By combining modular flexibility, computational efficiency, and a completely interactive interface, PRISM simplifies the translation of raw multiplexed images to actionable clinical insights, empowering researchers to explore and interact effectively with spatial omics data.
    DOI:  https://doi.org/10.1093/nargab/lqaf114
  32. Soft Matter. 2025 Aug 27.
    Cell mechanics, environmental geometry, and cell polarity control cell-cell collision outcomes.
    Yongtian Luo, Amrinder S Nain, Brian A Camley.
      Interactions between crawling cells, which are essential for many biological processes, can be quantified by measuring cell-cell collisions. Conventionally, experiments of cell-cell collisions are conducted on two-dimensional flat substrates, where colliding cells repolarize and move away upon contact with one another in "contact inhibition of locomotion" (CIL). Inspired by recent experiments that show cells on suspended nanofibers have qualitatively different CIL behaviors than those on flat substrates, we develop a phase field model of cell motility and two-cell collisions in fiber geometries. Our model includes cell-cell and cell-fiber adhesion, and a simple positive feedback mechanism of cell polarity. We focus on cell collisions on two parallel fibers, finding that larger cell deformability (lower membrane tension), larger positive feedback of polarization, and larger fiber spacing promote more occurrences of cells walking past one another. We can capture this behavior using a simple linear stability analysis on the cell-cell interface upon collision.
    DOI:  https://doi.org/10.1039/d5sm00359h
  33. Crit Rev Oncol Hematol. 2025 Aug 18. pii: S1040-8428(25)00294-X. [Epub ahead of print]215 104906
    Cysteine metabolism at the crossroads of ferroptosis and cancer therapy.
    Jaewang Lee, Jong-Lyel Roh.
      Cysteine metabolism plays a pivotal role in ferroptosis regulation by modulating antioxidant defense, lipid peroxidation, and iron homeostasis. Cancer cells exploit cysteine availability to evade ferroptotic cell death, contributing to tumor progression and therapy resistance. Despite growing interest in ferroptosis as a therapeutic vulnerability, a comprehensive understanding of cysteine metabolism in this process remains essential. This review explores key sources of intracellular cysteine, its roles in ferroptosis suppression, and therapeutic strategies targeting cysteine metabolism in cancer. We discuss systemic cysteine depletion, xCT inhibition, suppression of H2S biosynthesis, and GPX4-targeted therapies, along with promising drug combinations. While preclinical studies highlight the efficacy of these approaches, in vivo validation and clinical translation remain limited. Advancing cysteine-targeting therapies require further mechanistic insights, biomarker identification, and optimized delivery strategies. A deeper understanding of cysteine metabolism may pave the way for ferroptosis-based cancer treatments with improved precision and efficacy.
    Keywords:  Cancer therapy; Cyst(e)inases; Cysteine metabolism; Ferroptosis; XCT targeting
    DOI:  https://doi.org/10.1016/j.critrevonc.2025.104906
  34. Nat Genet. 2025 Aug 26.
    ERG-driven prostate cancer initiation is cell-context dependent and requires KMT2A and DOT1L.
    Weiran Feng, Erik Ladewig, Matthew Lange, Nazifa Salsabeel, Huiyong Zhao, Young Sun Lee, Anuradha Gopalan, Hanzhi Luo, Wenfei Kang, Ning Fan, Eric Rosiek, Elisa de Stanchina, Yu Chen, Brett S Carver, Christina S Leslie, Charles L Sawyers.
      Despite the high prevalence of ERG transcription factor translocations in prostate cancer, the mechanism of tumorigenicity remains poorly understood. Using lineage tracing, we find the tumor-initiating activity of ERG resides in a subpopulation of murine basal cells that coexpress luminal genes (BasalLum) and not in the larger population of ERG+ luminal cells. Upon ERG activation, BasalLum cells give rise to highly proliferative intermediate (IM) cells with stem-like features that coexpress basal, luminal, hillock and club marker genes, before transitioning to Krt8+ luminal cells. Transcriptomic analysis of ERG+ human prostate cancers confirms the presence of rare ERG+ BasalLum cells, as well as IM cells whose presence is associated with a worse prognosis. Single-cell analysis revealed a chromatin state in ERG+ IM cells enriched for STAT3 transcription factor binding sites and elevated expression of the KMT2A/MLL1 and DOT1L, all three of which are essential for ERG-driven tumorigenicity in vivo. In addition to providing translational opportunities, this work illustrates how single-cell approaches combined with lineage tracing can identify cancer vulnerabilities not evident from bulk analysis.
    DOI:  https://doi.org/10.1038/s41588-025-02289-w
  35. EMBO J. 2025 Aug 20.
    PARP7 is a proteotoxic stress sensor that labels proteins for degradation.
    Nonso J Ikenga, Jörg Vervoorts, Bernhard Lüscher, Roko Žaja, Karla L H Feijs-Žaja.
      ADP-ribosylation is a post-translational modification that plays a critical role in cellular stress responses. We have observed that during proteotoxic stress, cellular ADP-ribosylation increases, with ADP-ribosylated proteins accumulating in cytoplasmic foci containing ubiquitin and p62. During prolonged stress, these ADP-ribosylated proteins are transported to aggresomes and subsequently degraded via autophagy. In the absence of ubiquitination, ADP-ribosylated proteins become more prevalent and less soluble, indicating that ubiquitination is indispensable for this process. Upon inhibition of PARP7, accumulation of mono(ADP-ribosyl)ated proteins in response to proteotoxic stress is impeded. PARP7 turnover is very high under normal conditions; however, the protein becomes stabilised following proteotoxic stress and thereby forms an ideal proteotoxic stress sensor. Our findings imply that, contrary to the current paradigm, not all ADP-ribosylation may occur on specific sites to regulate specific protein characteristics. Instead, it may be rather promiscuous to enable efficient protein degradation or segregation to prevent irreversible damage caused by defective proteins.
    Keywords:  ADP-ribosylation; Macrodomain; PARP; Protein Degradation; Ubiquitination
    DOI:  https://doi.org/10.1038/s44318-025-00545-7
  36. Dev Cell. 2025 Aug 25. pii: S1534-5807(25)00499-X. [Epub ahead of print]
    Loss of NOTCH2 creates a TRIM28-dependent vulnerability in small cell lung cancer.
    Deli Hong, Ying Lyu, Richa Nayak, Justin S Becker, Matthew A Booker, Keita Masuzawa, Zoe Devos, Tianchu Wang, Shin Saito, Qi Liu, Yixiang Li, Zhaorong Li, Eric H Knelson, Tran Thai, Leslie Duplaquet, Yasmin N Laimon, Gabriel Roberti De Oliveira, Sabina Signoretti, John G Doench, David A Barbie, Michael Y Tolystorukov, Jun Qi, Bradley E Bernstein, Yejing Ge, Matthew G Oser.
      Small cell lung cancer (SCLC) is a highly aggressive malignancy that lacks effective targeted therapies, in part due to frequent loss-of-function mutations in tumor suppressors and the absence of recurrent oncogenic drivers. Approximately 15% of SCLCs harbor inactivating mutations in NOTCH1 or NOTCH2, and most neuroendocrine-high SCLCs exhibit low NOTCH activity. Using CRISPR-Cas9 screening in primary cell lines derived from NOTCH1/2-isogenic SCLC genetically engineered mouse models, we identified TRIM28 as a synthetic lethal dependency in NOTCH2-inactivated SCLCs. Loss of TRIM28 in this context robustly induced expression of endogenous retroviruses (ERVs), activated viral sensing pathways, and triggered a type I interferon response. Mechanistically, NOTCH2 inactivation increased reliance on TRIM28-mediated ERV silencing, creating a hyperdependence on TRIM28 via the STING-MAVS-TBK1 axis. Notably, TRIM28 was essential for tumor growth only in the setting of NOTCH2 loss. These findings identify TRIM28 as a potential therapeutic target in NOTCH2-deficient or low-NOTCH2-expressing SCLC.
    Keywords:  CRISPR-Cas9 screening; NOTCH2; TRIM28; endogenous retroviruses; small cell lung cancer; synthetic lethality; viral sensing
    DOI:  https://doi.org/10.1016/j.devcel.2025.07.023
  37. Autophagy. 2025 Sep 01. 1-18
    PRMT1 (protein arginine methyltransferase 1) is essential for neuromuscular junction and mitochondrial homeostasis via mitophagy regulation.
    Ju-Hyeon Bae, Chang-Lim You, Yideul Jeong, June Kim, Jinwoo Lee, Hyeon-Ju Jeong, Hyebeen Kim, Tuan Anh Vuong, Youngdae Gwon, Gyu-Un Bae, Jong-Sun Kang.
      The neuromuscular junction (NMJ) is essential for transmitting neural stimulus to muscles, triggering muscle contraction. Mitochondria are enriched in NMJ to support the energy needs required for neuromuscular function and stability. Thus, maintaining mitochondrial homeostasis through the clearance of damaged mitochondria, a process known as mitophagy, is vital for preserving neuromuscular health. Here, we highlight the crucial role of muscle PRMT1 in maintaining NMJ and mitochondrial homeostasis via mitophagy regulation. PRMT1 is distinctively expressed in myofibers, accumulating in the postsynaptic area, with its levels upregulated in denervated muscles. PRMT1-ablated muscles displayed disrupted NMJs and an accumulation of abnormal mitochondria, accompanied by increased mitochondrial oxidative stress. Additionally, prmt1 depletion in muscles specifically impaired TBK1 (TANK binding kinase 1)-OPTN (optineurin)-mediated mitophagy. Overall, our findings suggest that PRMT1 plays a critical role in maintaining NMJ and mitochondrial health by regulating selective mitophagy through TBK1-OPTN.Abbreviations: ADMA: asymmetric arginine dimethylation; BTX: α-bungarotoxin; EDL: extensor digitorum longus; FDB: flexor digitorum brevis; GAS: gastrocnemius; NMJ: Neuromuscular junction; Mko: mice with muscle-specific prmt1 ablation; MTOR: mechanistic target of rapamycin kinase; OPTN: optineurin; PRMT1: protein arginine methyltransferase 1; SA: sodium arsenate; SNI: sciatic nerve crush injury; Sol: soleus; SQSTM1/p62: sequestosome 1; TBK1: TANK binding kinase 1; TOMM20: translocase of outer mitochondrial membrane 20; TA: tibialis anterior; VDAC1: voltage dependent anion channel 1.
    Keywords:  Mitophagy; PRMT1; TBK1; neuromuscular junction; skeletal muscle
    DOI:  https://doi.org/10.1080/15548627.2025.2551477
  38. Clin Cancer Res. 2025 Aug 25.
    Preclinical Fluorescence-Guided Imaging Leveraging Surrounding Sentinel Tumor Microenvironment Identifies High-Risk Premalignant Pancreatic Lesions.
    Shilpa Sharma, Xiaoxia Wen, Jianbo Wang, Beibei Huang, Denise Hernandez, Cong-Dat Pham, Zhiwen Liu, Susanne Je-Han Lin, Aiko Yamaguchi, Dimitra K Georgiou, Ryan P Coll, H Charles Manning.
       PURPOSE: With surgery being the only potential cure for pancreatic cancer, high-risk premalignant pancreatic lesions often go unnoticed by palpation or white light visualization, leading to recurrence. We asked whether near-infrared fluorescence imaging of tumor-associated inflammation could identify high-risk premalignant lesions, leveraging the tumor microenvironment (TME) as a sentinel of local disease and, thus, enhance surgery outcomes.
    EXPERIMENTAL DESIGN: Fluorescence-guided surgery was performed on genetically engineered mice (Ptf1a-Cre; LSL-KrasG12D/+; Smad4flox/flox [KSC]) at discrete stages of disease progression, histologically confirmed high-risk, premalignant lesions in postnatal mice to locally advanced pancreatic tumors in adults, using the imaging agent V-1520, a translocator protein (TSPO) ligand. Age-matched wild-type littermates were used as controls, while Ptf1a-Cre; LSL-KrasG12D/+(KC) mice modeled pancreatitis and precursors of low penetrance. Localization of V-1520 and tumor-associated macrophages amongst the TME was detected by immunofluorescence imaging.
    RESULTS: V-1520 exhibited robust accumulation in the pancreata of KSC mice from the early postnatal stage. Increased accumulation was observed in the pancreata of adolescent- and adult-aged mice with greater ductal lesion and stromal burden. Confocal microscopy of ex vivo pancreas specimens co-localized V-1520 accumulation primarily with CD68-expressing macrophage in KSC mice. Unlike the pancreata of KSC mice, accumulation of V-1520 did not exceed background levels in the pancreata of KC mice with pancreatitis.
    CONCLUSION: V-1520 exhibited differential accumulation in pancreatic cancer-associated inflammation compared to pancreatitis. Given the robust tracer uptake in tissues associated with early yet high-risk lesions, we envision V-1520 could enhance surgical resection and reduce the potential for recurrence from residual disease.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-25-1092
  39. FASEB J. 2025 Aug 31. 39(16): e70983
    Phosphate Improves Mitochondrial Function and Reduces Pancreatitis in Hypertriglyceridemia.
    Nidula Mullappilly, Sandip M Swain, Joelle M-J Romac, Husam Mikati, Rodger A Liddle.
      Hypertriglyceridemia-associated pancreatitis (HTGP) accounts for 9% to 10% of acute pancreatitis; however, the exact cause and associated factors advancing HTGP are unclear. Clinical studies have revealed that hypophosphatemia is a common factor in many patients with pancreatitis. Phosphate depletion occurs in metabolic disorders and can lead to dyslipidemia. To determine if phosphate status is critical in HTGP, we used an APOC3 transgenic mouse model of hypertriglyceridemia. We found that hypertriglyceridemic mice exhibit mild pancreatic injury with elevated intra-acinar nonendoplasmic reticulum (non-ER) organelle calcium levels, decreased mitochondrial function, and increased levels of pancreatic tissue myeloperoxidase and proinflammatory cytokines (TNF-α, IL-6, and IL-1β) compared to mice with normal serum triglycerides. Phosphate supplementation normalized the non-ER stored calcium levels, restored mitochondrial function, and attenuated fatty acid-induced sustained intracellular calcium elevation in acini, protecting the pancreas from hypertriglyceridemia-induced injury by reducing inflammation. Furthermore, phosphate supplementation reduced the severity of caerulein-induced pancreatic injury in mice on a low-phosphate diet under hypertriglyceridemic conditions. This study highlights an important role for phosphate in protecting the pancreas during hypertriglyceridemia by reversing the dysregulated calcium homeostasis in non-ER organelles, restoring mitochondrial function in acini, and reducing the severity of hypertriglyceridemia-associated pancreatitis.
    Keywords:  APOC3; ATP; hypertriglyceridemia; hypophosphatemia; mitochondria; pancreatitis
    DOI:  https://doi.org/10.1096/fj.202501155R
  40. Nature. 2025 Aug 27.
    A closer look at how cells sense dietary nutrients.
      
    Keywords:  Cell biology; Metabolism; Structural biology
    DOI:  https://doi.org/10.1038/d41586-025-02694-5
  41. Sci Adv. 2025 Aug 22. 11(34): eadw4402
    Cryo-light microscopy with angstrom precision deciphers structural conformations of PIEZO1 in its native state.
    Hisham Mazal, Franz-Ferdinand Wieser, Daniel Bollschweiler, Alexandra Schambony, Vahid Sandoghdar.
      Investigations based on cryo-electron microscopy (cryo-EM), atomic force microscopy, and super-resolution microscopy reveal a symmetric trimer with propeller-like blades for the mechanosensitive ion channel PIEZO. However, a conclusive understanding of its conformations in the cell membrane is lacking. Here, we implement a high-vacuum cryogenic shuttle to transfer shock-frozen cell membranes in and out of a cryostat designed for single-particle cryo-light microscopy (spCryo-LM). By localizing fluorescent labels placed at the extremities of the blades of the mouse PIEZO1 protein in unroofed cell membranes, we ascertain three configurations with radii of 6, 12, and 20 nanometers as projected onto the membrane plane. We elaborate on the correspondence of these data with previous reports in the literature. The combination of spCryo-LM with cryo-EM promises to provide quantitative insights into the structure and function of biomolecular complexes in their native environments without the need for chemical fixation or protein isolation, ushering in a new regime of correlative studies in structural biology.
    DOI:  https://doi.org/10.1126/sciadv.adw4402
  42. J Pharm Pharmacol. 2025 Aug 20. pii: rgaf073. [Epub ahead of print]
    Ruxolitinib alleviated muscle atrophy in cancer cachexia by inhibiting IL-6/JAK/STAT3 signaling pathway in mice.
    Cong Li, Xiaofan Gu, Zixia Zhu, Xiaojuan Pan, Meng Fan, Xuan Liu, Xiongwen Zhang.
       OBJECTIVES: Ruxolitinib (Rux), an oral Janus tyrosine Kinase (JAK) tyrosine kinase inhibitor, has demonstrated anti-inflammatory properties and the ability to mitigate denervation-induced skeletal muscle atrophy. Here, we checked the potential efficacy of Rux on cancer cachexia and tried to clarified its mechanisms.
    METHODS: The in vitro cell models of C26 or LLC CM-induced C2C12 myotubes were used to check the influence of Rux on myotube atrophy. C26 tumour-bearing mice (male BALB/c mice) were applied as the animal model to examine the effects of Rux in attenuating cachexia symptoms. Western blot analysis was utilized to investigate the potential mechanisms of Rux.
    KEY FINDINGS: Rux significantly attenuated C2C12 myotube atrophy in vitro. Rux suppressed the interleukin-6 secretion by inhibiting STAT3 activation in tumour cells and macrophages. The administration of Rux prevented body weight loss and muscle wasting in C26 tumour-bearing mice without affecting tumour growth. At the end of the experiment, mice in the Rux treatment group exhibited a 6.7% increase in body weight compared to the C26 model group. Furthermore, Rux enhanced in gastrocnemius myofibres cross-sectional area and grip strength.
    CONCLUSIONS: Rux ameliorates cancer cachexia muscle atrophy by inhibiting STAT3/Atrogin-1 signaling. Rux may represent a promising therapeutic candidate for the treatment of cancer cachexia.
    Keywords:  IL-6/JAK/STAT3; Rux; cancer cachexia; macrophages; muscle atrophy; systemic inflammatory response
    DOI:  https://doi.org/10.1093/jpp/rgaf073
  43. Nat Genet. 2025 Aug 22.
    Tamoxifen induces PI3K activation in uterine cancer.
    Kirsten Kübler, Agostina Nardone, Shankara Anand, Daniel Gurevich, Jianjiong Gao, Marjolein Droog, Francisco Hermida-Prado, Tara Akhshi, Ariel Feiglin, Avery S Feit, Gabriella Cohen Feit, Gwen Dackus, Matthew Pun, Yanan Kuang, Justin Cha, Mendy Miller, Sebastian Gregoricchio, Mirthe Lanfermeijer, Sten Cornelissen, William J Gibson, Cloud P Paweletz, Eliezer M Van Allen, Flora E van Leeuwen, Petra M Nederlof, Quang-Dé Nguyen, Marian J E Mourits, Milan Radovich, Ignaty Leshchiner, Chip Stewart, Ursula A Matulonis, Wilbert Zwart, Yosef E Maruvka, Gad Getz, Rinath Jeselsohn.
      Mutagenic processes and clonal selection contribute to the development of therapy-associated secondary neoplasms, a known complication of cancer treatment. The association between tamoxifen therapy and secondary uterine cancers is uncommon but well established; however, the genetic mechanisms underlying tamoxifen-driven tumorigenesis remain unclear. We find that oncogenic PIK3CA mutations, common in spontaneously arising estrogen-associated de novo uterine cancer, are significantly less frequent in tamoxifen-associated tumors. In vivo, tamoxifen-induced estrogen receptor stimulation activates phosphoinositide 3-kinase (PI3K) signaling in normal mouse uterine tissue, potentially eliminating the selective benefit of PI3K-activating mutations in tamoxifen-associated uterine cancer. Together, we present a unique pathway of therapy-associated carcinogenesis in which tamoxifen-induced activation of the PI3K pathway acts as a non-genetic driver event, contributing to the multistep model of uterine carcinogenesis. While this PI3K mechanism is specific to tamoxifen-associated uterine cancer, the concept of treatment-induced signaling events may have broader applicability to other routes of tumorigenesis.
    DOI:  https://doi.org/10.1038/s41588-025-02308-w
  44. Am J Phys Med Rehabil. 2025 Jul 16.
    Cancer Cachexia Rehabilitation in a Novel Outpatient Clinical Program.
    Kelly Dong, Kathryn Abplanalp, Ishan Roy.
       ABSTRACT: Cancer cachexia is a tumor-induced muscle wasting syndrome that has a debilitating impact on patient functional status, quality of life, and cancer prognosis. This brief report summarizes a retrospective cohort study that aims to describe the oncological histories, functional co-impairments, therapy referral patterns, and physical therapy (PT) outcomes of 163 patients who were evaluated at a novel physiatry-led outpatient cancer cachexia clinic (2021-2023). 49% of the cohort that met Fearon consensus criteria for cachexia demonstrated increased odds of experiencing multiple impairments [OR = 7.4, p < 0.0001], specifically gluteal weakness [OR = 2.6, p = 0.0078], and 4 times the odds of receiving a walking program intervention [OR = 4.1, p = 0.0004]. PT was prescribed for 71% of the cohort, with no significant difference between cachexia and non-cachexia groups in PT order frequency [OR = 0.9, p = 0.7307] or PT initiation [OR = 0.8, p = 0.5419]. However, cachexia patients trended toward lower odds of meeting PT long-term goals or having these goals reassessed [OR = 0.2, p = 0.0032]. This study highlights cachexia prevalence, rehabilitation challenges, and the need for standardized, evidence-based treatment protocols. Gluteal weakness assessment may improve referrals to cachexia rehabilitation.
    Keywords:  Cachexia Rehabilitation; Cancer Cachexia; Cancer Rehabilitation; Functional Impairment; Gluteal Weakness; Oncology; Physical Therapy
    DOI:  https://doi.org/10.1097/PHM.0000000000002817
  45. Sci Adv. 2025 Aug 22. 11(34): eadt1798
    Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer.
    Otto Kauko, Mikko Turunen, Päivi Pihlajamaa, Antti Häkkinen, Rayner M L Queiroz, Mirva Pääkkönen, Sami Ventelä, Massimiliano Gaetani, Susanna L Lundström, Antonio Murgia, Biswajyoti Sahu, Johannes Routila, Gong-Hong Wei, Heikki Irjala, Julian L Griffin, Kathryn S Lilley, Teemu Kivioja, Sampsa Hautaniemi, Jussi Taipale.
      Mutations in numerous genes contribute to human cancer, with different oncogenic lesions prevalent in different cancer types. However, the malignant phenotype is simple, characterized by unrestricted cell growth, invasion, and often metastasis. One possible hypothesis explaining this dichotomy is that cancer genes regulate common targets, which then function as master regulators of essential cancer phenotypes. To identify mechanisms that drive the most fundamental feature shared by all tumors-unrestricted cell proliferation-we used a multiomic approach, which identified translation and ribosome biogenesis as common targets of major oncogenic pathways across cancer types. Proteomic analysis of tumors and functional studies of cell cultures established nucleolar and coiled-body phosphoprotein 1 as a key node, whose convergent regulation, both transcriptionally and posttranslationally, is critical for tumor cell proliferation. Our results indicate that lineage-specific oncogenic pathways regulate the same set of targets for growth control, revealing key downstream nodes that could be targeted for therapy or chemoprevention.
    DOI:  https://doi.org/10.1126/sciadv.adt1798
  46. Nat Methods. 2025 Aug 26.
    DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations.
    Bo Wen, Chenwei Wang, Kai Li, Ping Han, Matthew V Holt, Sara R Savage, Jonathan T Lei, Yongchao Dou, Zhiao Shi, Yi Li, Bing Zhang.
      Post-translational modifications (PTMs) are critical regulators of protein function, and their disruption is a key mechanism by which missense variants contribute to disease. Accurate PTM site prediction using deep learning can help identify PTM-altering variants, but progress has been limited by the lack of large, high-quality training datasets. Here, we introduce PTMAtlas, a curated compendium of 397,524 PTM sites generated through systematic reprocessing of 241 public mass-spectrometry datasets, and DeepMVP, a deep learning framework trained on PTMAtlas to predict PTM sites for phosphorylation, acetylation, methylation, sumoylation, ubiquitination and N-glycosylation. DeepMVP substantially outperforms existing tools across all six PTM types. Its application to predicting PTM-altering missense variants shows strong concordance with experimental results, validated using literature-curated variants and cancer proteogenomic datasets. Together, PTMAtlas and DeepMVP provide a robust platform for PTM research and a scalable framework for assessing the functional consequences of coding variants through the lens of PTMs.
    DOI:  https://doi.org/10.1038/s41592-025-02797-x
  47. Nat Cell Biol. 2025 Aug 25.
    CHIP protects lysosomes from CLN4 mutant-induced membrane damage.
    Juhyung Lee, Natalie Chin, Jizhong Zou, Wan Nur Atiqah Binti Mazli, Michal Jarnik, Layla Saidi, Yue Xu, Eutteum Jeong, Jessica Suh, John Replogle, Michael E Ward, Juan S Bonifacino, Wei Zheng, Ling Hao, Yihong Ye.
      Understanding how cells mitigate lysosomal damage is critical for unravelling pathogenic mechanisms of lysosome-related diseases. Here we generate and characterize induced pluripotent stem cell (iPSC)-derived neurons (i3Neuron) bearing ceroid lipofuscinosis neuronal 4 (CLN4)-linked DNAJC5 mutations, which revealed extensive lysosomal abnormality in mutant neurons. In vitro membrane-damaging experiments establish lysosomal damages caused by lysosome-associated CLN4 mutant aggregates, as a critical pathogenic linchpin in CLN4-associated neurodegeneration. Intriguingly, in non-neuronal cells, a ubiquitin-dependent microautophagy mechanism downregulates CLN4 aggregates to counteract CLN4-associated lysotoxicity. Genome-wide CRISPR screens identify the ubiquitin ligase carboxyl terminus of Hsc70-interacting protein (CHIP) as a central microautophagy regulator that confers ubiquitin-dependent lysosome protection. Importantly, CHIP's lysosome protection function is transferrable: ectopic CHIP improves lysosomal function in CLN4 i3Neurons and effectively alleviates lipofuscin accumulation and cell death in a Drosophila CLN4 disease model. Our study establishes CHIP-mediated microautophagy as a key organelle guardian that preserves lysosome integrity, offering new insights into therapeutic development for lysosome-related neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41556-025-01738-2
  48. J Cell Biol. 2025 Oct 06. pii: e202405138. [Epub ahead of print]224(10):
    Identification of organelle-specific autophagy regulators from tandem CRISPR screens.
    Truc T Losier, Karyn E King, Maxime W C Rousseaux, Ryan C Russell.
      Autophagy is a conserved degradative process that promotes cellular homeostasis under stress conditions. Under nutrient starvation, autophagy is nonselective, promoting indiscriminate breakdown of cytosolic components. Conversely, selective autophagy is responsible for the specific turnover of damaged organelles. We hypothesized that selective autophagy may be regulated by signaling pathways distinct from those controlling starvation-induced autophagy, thereby promoting organelle turnover. To address this question, we conducted kinome-wide CRISPR screens to identify distinct signaling pathways responsible for the regulation of basal autophagy, starvation-induced autophagy, and two types of selective autophagy, ER-phagy and pexophagy. These parallel screens identified both known and novel autophagy regulators, some common to all conditions and others specific to selective autophagy. More specifically, CDK11A and NME3 were further characterized to be selective ER-phagy regulators. Meanwhile, PAN3 and CDC42BPG were identified as an activator and inhibitor of pexophagy, respectively. Collectively, these datasets provide the first comparative description of the kinase signaling that defines the regulation of selective autophagy and bulk autophagy.
    DOI:  https://doi.org/10.1083/jcb.202405138
  49. Nucleus. 2025 Dec;16(1): 2545037
    Heterogeneity as a feature: unraveling chromatin's role in nuclear mechanics.
    Wessel S Rodenburg, Amy R Strom, Jorine M Eeftens.
      Mechanical forces are a ubiquitous feature of the cellular environment. These forces propagate to the nucleus, where the mechanical response is critical for cellular function and survival. In addition to the nuclear lamina and cytoskeletal connections, chromatin is a key structural and mechanoresponsive element which not only contributes to bulk stiffness but also dynamically adapts its organization in response to mechanical stress. Crucially, chromatin is not a uniform material - its organization and mechanical properties vary across time, cell state, and even within individual nuclei. This heterogeneity underpins compartmentalization, gene regulation, and potentially, disease states when disrupted. In this review, we summarize recent experimental advances that have illuminated chromatin's role in nuclear mechanics, emphasizing the importance of heterogeneity. We argue that an integrated, multiscale, and quantitative framework is essential for dissecting chromatin's mechanical contributions. By doing so, the field will be better positioned to link nuclear mechanics to functional biological outcomes.
    Keywords:  Chromatin; genome organization; heterogeneity; multiscale quantification; nuclear mechanics
    DOI:  https://doi.org/10.1080/19491034.2025.2545037
  50. J Control Release. 2025 Aug 19. pii: S0168-3659(25)00754-0. [Epub ahead of print]386 114143
    Gut microbial diversity is preserved through localised chemo-immunotherapy delivery in a KPC mouse model of pancreatic cancer.
    Elahe Minaei, Paul Joyce, Samantha J Wade, Christopher Brownlee, Chelsea Penney, Marie Ranson, Morteza Aghmesheh, Ronald Sluyter, Kara L Vine-Perrow.
      Systemic chemotherapy and immunotherapy can disrupt gut microbial homeostasis, contributing to inflammation, treatment-related toxicity, and diminished anti-tumour immunity in pancreatic ductal adenocarcinoma (PDAC). Here, we evaluated whether localised delivery of chemo-immunotherapy via biodegradable implants could mitigate these adverse effects and preserve gut microbiota integrity. Using a syngeneic KPC mouse model of PDAC, we compared systemic versus implant-based delivery of gemcitabine/nab-paclitaxel and anti-CD40/anti-PD1 antibodies. 16S rRNA sequencing of faecal samples revealed that systemic chemo-immunotherapy significantly reduced alpha diversity, depleted immunoregulatory species (e.g. Akkermansia muciniphila, Bifidobacterium longum), and enriched pathobionts (Escherichia coli, Clostridium septicum), accompanied by elevated intestinal pro-inflammatory cytokines. In contrast, localised delivery preserved microbial diversity, maintained beneficial taxa and suppressed inflammatory cytokine levels. Further, high-dose localised chemotherapy promoted M1 macrophage polarisation while preserving microbiota more effectively than even low-dose systemic regimens. This is the first study to demonstrate that spatial control of drug exposure via localised delivery can protect the gut microbiome and modulate systemic immunity in PDAC. These findings subsequently provide proof-of-concept that implant-based approaches can enhance tolerability and efficacy of chemo-immunotherapy by minimising microbiome disruption.
    Keywords:  Chemotherapy; Gut microbiome; Immunotherapy; Localised drug delivery; Pancreatic cancer
    DOI:  https://doi.org/10.1016/j.jconrel.2025.114143
  51. Nat Methods. 2025 Aug 25.
    inTRACKtive: a web-based tool for interactive cell tracking visualization.
    Teun A P M Huijben, Ashley G Anderson, Andrew Sweet, Erin Hoops, Connor Larsen, Kyle Awayan, Jordão Bragantini, Merlin Lange, Chi-Li Chiu, Loïc A Royer.
      
    DOI:  https://doi.org/10.1038/s41592-025-02777-1
  52. Nat Rev Chem. 2025 Aug 20.
    Elemental mass spectrometry imaging of biomolecules using metal-conjugated probes.
    Anthony Thai, Thomas E Lockwood, Ioannis Kohilas, Rosemary J Bergin, Andrew M McDonagh, David P Bishop.
      In situ imaging of proteins, RNA, immune cells and other biomolecules is necessary to determine their function, interactions and roles in disease pathology. Increasingly, this is achieved via metal-conjugated probes in conjunction with elemental mass spectrometry imaging (MSI). This targeted technique is capable of simultaneously imaging up to 40 analytes, in comparison to the traditional bioimaging techniques that use fluorescent or chromogenic reagents that are typically restricted to less than four analytes without complex sample handling and analysis workflows. These analyses, however, are not straightforward, with a number of factors that require optimization. They require the use of probes specific to the target biomolecules, which are conjugated with analytes detectable by elemental MSI. Here, we summarize the MSI technology, the types of biological probes used for identification, and the forms of metal analytes used. We provide examples of their application including understanding cancer cell heterogeneity to direct clinical trials, which may impact clinical diagnostics and personalized medicine. We conclude with future perspectives on the potential of the technique and what is required to meet it.
    DOI:  https://doi.org/10.1038/s41570-025-00749-9
  53. Nat Biomed Eng. 2025 Aug 25.
    Multiparametric cellular and spatial organization in cancer tissue lesions with a streamlined pipeline.
    Mark Buckup, Igor Figueiredo, Giorgio Ioannou, Sinem Ozbey, Rafael Cabal, Alexandra Tabachnikova, Leanna Troncoso, Jessica Le Berichel, Zhen Zhao, Stephen C Ward, Clotilde Hennequin, Guray Akturk, Steve Hamel, Maria Isabel Fiel, Rachel Brody, Myron Schwartz, Thomas U Marron, Seunghee Kim-Schulze, Vladimir Roudko, Edgar Gonzalez-Kozlova, Pauline Hamon, Miriam Merad, Sacha Gnjatic.
      Multiplex immunostaining analysis remains fragmented, underperforming and labour intensive despite tissue proteomic methodologies achieving ever-increasing marker complexity. Here we propose an open-source, user-guided automated pipeline that streamlines start-to-finish, single-cell resolution analysis of whole-slide tissue, named multiplex-imaging analysis, registration, quantification and overlaying (MARQO). MARQO integrates elastic image registration, iterative nuclear segmentation, unsupervised clustering with mini-batch k-means and user-guided cell classification through a graphical interface. We compare and validate MARQO using multiplexed immunohistochemical consecutive staining on a single slide using human tumour and adjacent normal tissue samples. Performance is compared with manually curated pathologist determinations and quantification of multiple markers. We optimize MARQO to analyse diverse tissue sizes from whole tissue, biopsy, and tissue microarray and staining approaches, such as singleplex immunohistochemistry and 20-colour multiplex immunofluorescence, to determine marker co-expression patterns in multiple human solid cancer types. Lastly, we validate CD8+ T cell enrichment in hepatocellular carcinoma responders to neoadjuvant cemiplimab in a phase 2 clinical trial, further showing the ability of MARQO to identify spatially resolved in situ mechanisms by providing multiplex whole-slide single-cell resolution data.
    DOI:  https://doi.org/10.1038/s41551-025-01475-9
  54. Cancer Cell. 2025 Aug 18. pii: S1535-6108(25)00327-7. [Epub ahead of print]
    Genome-wide CRISPR screens identify critical targets to enhance CAR-NK cell antitumor potency.
    Alexander Biederstädt, Rafet Basar, Jeong-Min Park, Nadima Uprety, Rejeena Shrestha, Francia Reyes Silva, Merve Dede, John Watts, Sunil Acharya, Donghai Xiong, Bin Liu, May Daher, Hind Rafei, Pinaki Banerjee, Ping Li, Sanjida Islam, Huihui Fan, Mayra Shanley, Jingling Jin, Bijender Kumar, Vernikka Woods, Paul Lin, Silvia Tiberti, Ana Karen Nunez Cortes, Xin Ru Jiang, Inci Biederstädt, Patrick Zhang, Ye Li, Seema Rawal, Enli Liu, Luis Muniz-Feliciano, Gary M Deyter, Elizabeth J Shpall, Natalie Wall Fowlkes, Ken Chen, Katayoun Rezvani.
      Adoptive cell therapy using engineered natural killer (NK) cells is a promising approach for cancer treatment, with targeted gene editing offering the potential to further enhance their therapeutic efficacy. However, the spectrum of actionable genetic targets to overcome tumor and microenvironment-mediated immunosuppression remains largely unexplored. We performed multiple genome-wide CRISPR screens in primary human NK cells and identified critical checkpoints regulating resistance to immunosuppressive pressures. Ablation of MED12, ARIH2, and CCNC significantly improved NK cell antitumor activity against multiple treatment-refractory human cancers in vitro and in vivo. CRISPR editing augmented both innate and CAR-mediated NK cell function, associated with enhanced metabolic fitness, increased secretion of proinflammatory cytokines, and expansion of cytotoxic NK cell subsets. Through high-content genome-wide CRISPR screening in NK cells, this study reveals critical regulators of NK cell function and provides a valuable resource for engineering next-generation NK cell therapies with improved efficacy against cancer.
    Keywords:  CAR-NK cell therapy; adoptive cell therapy; functional perturbomics; genome-wide CRISPR screens; metabolic reprogramming; multiplexed cellular engineering; natural killer cells; precision gene editing; solid tumors; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.ccell.2025.07.021
  55. Nat Commun. 2025 Aug 27. 16(1): 8008
    Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells.
    Alexander Kowar, Jonas P Becker, Rossella Del Pizzo, Zhiwei Tang, Julien Champagne, Kathrin Wellach, Kiana Samimi, Ariel Galindo-Albarrán, Pierre-René Körner, Jasmine Montenegro Navarro, Andrés Elía, Fiona Megan Tilghman, Hanan Sakeer, Marco Antonio Mendoza-Parra, Angelika B Riemer, Reuven Agami, Fabricio Loayza-Puch.
      Mitosis is a critical phase of the cell cycle and a vulnerable point where cancer cells can be disrupted, causing cell death and inhibiting tumor growth. Challenges such as drug resistance persist in clinical applications. During mitosis, mRNA translation is generally downregulated, while non-canonical translation of specific transcripts continues. Here, we show that mitotic cancer cells redistribute ribosomes toward the 5' untranslated region (5' UTR) and beginning of the coding sequence (CDS), enhancing translation of thousands of upstream open reading frames (uORFs) and upstream overlapping open reading frames (uoORFs). This mitotic induction of uORF/uoORF enriches human leukocyte antigen (HLA) presentation of non-canonical peptides on the surface of cancer cells after mitotic inhibitor treatment. Functional assays indicate these epitopes provoke cancer-cell killing by T cells. Our findings highlight the therapeutic potential of targeting uORF/uoORF-derived epitopes with mitotic inhibitors to enhance immune recognition and tumor cell elimination.
    DOI:  https://doi.org/10.1038/s41467-025-63405-2
  56. Nat Commun. 2025 Aug 26. 16(1): 7934
    Spatial isotope deep tracing deciphers inter-tissue metabolic crosstalk.
    Xinzhu Li, Ying Zhu, Ting Li, Xinyi Tu, Shiyu Zhu, Lingzhi Wang, Fei Li, Chenglong Sun, Xin Li, Haiyi Zhao, Tang Tang, Qingce Zang, Ruiping Zhang, Zeper Abliz.
      Organs collaborate to maintain metabolic homeostasis in mammals. Spatial metabolomics makes strides in profiling the metabolic landscape, yet can not directly inspect the metabolic crosstalk between tissues. Here, we introduce an approach to comprehensively trace the metabolic fate of 13C-nutrients within the body and present a robust computational tool, MSITracer, to deep-probe metabolic activity in a spatial manner. By discerning spatial distribution differences between isotopically labeled metabolites from ambient mass spectrometry imaging-based isotope tracing data, this approach empowers us to characterize fatty acid metabolic crosstalk between the liver and heart, as well as glutamine metabolic exchange across the kidney, liver, and brain. Moreover, we disclose that tumor burden significantly influences the host's hexosamine biosynthesis pathway, and that the glucose-derived glutamine released from the lung as a potential source for tumor glutamate synthesis. The developed approach facilitates the systematic characterization of metabolic activity in situ and the interpretation of tissue metabolic communications in living organisms.
    DOI:  https://doi.org/10.1038/s41467-025-63243-2
  57. Mol Pharmacol. 2025 Jul 11. pii: S0026-895X(25)15321-2. [Epub ahead of print]107(9): 100061
    Liver CYP4A autophagic lysosomal degradation: A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site.
    Liang He, Doyoung Kwon, Michael J Trnka, Yi Liu, Jade Yang, Kathy H Li, Rheem A Totah, Eric F Johnson, Alma L Burlingame, Maria Almira Correia.
      The hepatic P450 hemoproteins CYPs 4A are typical N-terminally anchored type I endoplasmic reticulum (ER) proteins, inducible by many hypolipidemic drugs and peroxisome proliferators. They are engaged in the ω-/ω-1-oxidation of various fatty acids including arachidonic acid, prostaglandins, and leukotrienes and in the biotransformation of some therapeutic drugs. Because the proteolytic turnover of the mammalian liver CYPs 4A remains obscure, we have characterized it. We report that of these proteins, human CYP4A11 and mouse Cyp4a12a are preferential targets of the ER-lysosome-associated degradation. Consequently, these proteins are stabilized 2- to 3-fold both as 1%Triton X100-soluble and insoluble species in mouse hepatocytes and HepG2 cells deficient in the autophagic initiation ATG5 gene. Despite exhibiting surface microtubule-associated protein light chain 3-interacting regions that could target them directly to the autophagosome, they nevertheless interact intimately with the autophagic receptor SQSTM1/p62. Through structural deletion analyses and site-directed mutagenesis, we have identified the CYP4A-interacting p62 subdomain to lie between residues 170 and 233, which include its Traf6-binding and LIM-binding subdomains. Mice carrying a liver-specific genetic deletion of p62 residues 69-251 (p62Mut) that includes the CYP4A-interacting subdomain also exhibit Cyp4a-protein stabilization as 1% Triton X100-soluble and insoluble species. Consistently, p62Mut mouse liver microsomes exhibit 1.5- to 2-fold enhanced ω- and ω-1-arachidonic acid hydroxylation to its physiologically active metabolites 19 and 20-HETEs relative to the corresponding wild-type mouse liver microsomes. Collectively, our findings suggest that disruption of CYP4A ER-lysosome-associated degradation results in functionally active P450 protein stabilization and consequent proinflammatory metabolite generation along with insoluble CYP4A aggregates, which may contribute to pathological aggregates, ie, Mallory-Denk bodies/inclusions, hallmarks of many liver diseases. SIGNIFICANCE STATEMENT: Human CYP4A11 and mouse Cyp4a12a, liver P450 enzymes engaged in ω-/ω-1-oxidation of arachidonic acid, prostaglandins, and leukotrienes, are documented to physiologically turn over via endoplasmic reticulum-lysosome-associated autophagic degradation, which involves their intimate association with the autophagic receptor SQSTM1/p62. Genetic endoplasmic reticulum-lysosome-associated autophagic degradation disruption or deletion of their hepatic p62-interaction subdomain in mice results in Cyp4a-protein stabilization as functionally active solubilizable species with consequently enhanced proinflammatory 20-HETE arachidonate metabolite generation and insoluble Cyp4a aggregates, potential contributors to pathologic liver inclusions.
    Keywords:  Autophagic lysosomal degradation (ALD); Chemical crosslinking mass spectrometry (XLMS); Cytochromes P450; ER-lysosomal-associated degradation (ERLAD); Endoplasmic reticulum (ER)-associated degradation (ERAD); Sequestosome 1 (SQSTM-1/p62)
    DOI:  https://doi.org/10.1016/j.molpha.2025.100061
  58. Mol Metab. 2025 Aug 21. pii: S2212-8778(25)00144-9. [Epub ahead of print]100 102237
    ACAA1 knockout increases the survival rate of KPC mice by activating autophagy.
    Ho Lee, Mingyu Kang, Sung Hoon Sim, Joon Hee Kang, Wonyoung Choi, Jung Won Chun, Woosol Hong, Chaeyoung Kim, Woojin Ham, Jeong Hwan Park, Eun-Byeol Koh, Yoon Jeon, Sang Myung Woo, Soo-Youl Kim.
       OBJECTIVES: We found that the levels of the peroxisomal fatty acid oxidation (FAO) marker in pancreatic ductal adenocarcinoma (PDAC) patients were higher than those in healthy individuals, based on tissue microarray analysis. This study investigates FAO in preclinical in vitro and in vivo models.
    METHODS: To examine the role of FAO in the peroxisome, we created acetyl-coenzyme A acyltransferase (ACAA1) knockout mice, crossed them with KPC mice, and monitored their survival rates. Additionally, we tested a mouse xenograft model with ACAA1 knockdown in human PDAC cells.
    RESULTS: In normal cells, ACAA1 knockdown did not affect oxygen consumption. In contrast, in PDAC cells, ACAA1 knockdown reduced the oxygen consumption rate by up to 60% and decreased ATP production by up to 70%. This suggests that peroxisomes in PDAC supply various acyl-carnitines for FAO in mitochondria. In PDAC cells, ACAA1 knockdown lowered ATP levels, resulting in mTOR inactivation and autophagy induction. Additionally, ACAA1 knockdown significantly increased LC3-II levels, leading to growth retardation in mouse xenograft models. Acaa1a+/- mice showed a median survival increase of 3 weeks after crossing Acaa1a+/- with KPC mice (KrasG12D/+; Trp53R172H/+;Pdx1-Cre, a genetically engineered mice model for PDAC).
    CONCLUSIONS: ACAA1 knockdown inhibited tumor growth by triggering autophagy, which supported the survival of KPC mice. The most important benefit of targeting ACAA1 is that it blocks tumor growth specifically in cancer cells without harming normal cell energy metabolism.
    Keywords:  ACAA1; Autophagy; Fatty acid oxidation; Pancreatic cancer; Peroxisome
    DOI:  https://doi.org/10.1016/j.molmet.2025.102237
  59. Nat Cardiovasc Res. 2025 Aug 26.
    IL6 genetic perturbation mimicking IL-6 inhibition is associated with lower cardiometabolic risk.
    Lanyue Zhang, Murad Omarov, Lingling Xu, Emil deGoma, Pradeep Natarajan, Marios K Georgakis.
      Human genetics supports a causal involvement of IL-6 signaling in atherosclerotic cardiovascular disease, prompting the clinical development of anti-IL-6 therapies. Genetic evidence has historically focused on IL6R missense variants, but emerging cardiovascular treatments target IL-6, not its receptor, questioning the translatability of genetic findings. Here we develop a genetic instrument for IL-6 signaling downregulation comprising IL6 locus variants that mimic the effects of the anti-IL-6 antibody ziltivekimab and use it to predict the effects of IL-6 inhibition on cardiometabolic and safety endpoints. Similar to IL6R, we found that genetically downregulated IL-6 signaling via IL6 perturbation is associated with lower lifetime risks of coronary artery disease, peripheral artery disease and ischemic atherosclerotic stroke in individuals of European and East Asian ancestry. Unlike IL6R missense variants linked to bacterial infections, the IL6 instrument was associated with lower risk of pneumonia hospitalization. Our data suggest that IL-6 inhibition can reduce cardiovascular risk without major unexpected safety concerns.
    DOI:  https://doi.org/10.1038/s44161-025-00700-7
  60. Cancer Immunol Immunother. 2025 Aug 23. 74(9): 291
    A platform for multisite immune profiling of premetastatic pancreatic cancer at single-cell resolution.
    Elishama N Kanu, Ashley A Fletcher, Jiayin Bao, Ethan S Agritelley, Julia Button, Austin M Eckhoff, Karrie Comatas, Tao Wang, Bin-Jin Hwang, Michael E Lidsky, Sabino Zani, Dan G Blazer, Peter J Allen, Zhicheng Ji, Frank J Lowery, Sri Krishna, Nicholas D Klemen, Daniel P Nussbaum, Erika J Crosby.
       BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is characterized by exceedingly high rates of metastatic progression, with the liver representing the most common site of distant spread. Here, we established a platform for multisite immune profiling of human PDAC encompassing the tumor, peripheral circulation, and premetastatic liver, to more comprehensively study how various immune subsets might contribute to patient outcomes.
    METHODS: Tumor, liver, and blood samples were obtained from patients undergoing resection for non-metastatic PDAC. Derived immune cells underwent paired single-cell RNA and TCR sequencing. Immune composition, cell-type functional profiles, and T cell clonal expansion patterns were evaluated across tissue sites.
    RESULTS: In total, 106,539 immune cells were sequenced, of which 85,748 met criteria for analysis. We identified 32 cell populations, of which seven demonstrated significant enrichment within a particular tissue, highlighting that this workflow possesses the granularity needed for identifying potential future biomarkers. Functional profiling revealed tissue-specific differences in cell phenotypes. This included terminally differentiated exhausted CD8 T cells within the tumor, highly active Tregs within the premetastatic liver and tumor, and M1 versus M2 polarization of liver and tumor macrophage populations, respectively. Within the tumor, expanded Treg clones were uniquely abundant, and while expanded clones could be tracked to the blood and premetastatic liver, many of these mapped back to known viral antigens. Leveraging previously validated gene sets, we show how these can be applied to predict the tumor reactivity of intratumoral T cells using transcriptional signatures. We demonstrated a high degree of concordance between multiple independent signatures and tracked high-priority TCRs within the blood and liver.
    CONCLUSION: This study demonstrates the feasibility of a platform, which has already been implemented into ongoing clinical protocols, for immune profiling of human PDAC across the sites most relevant to metastatic progression. Future applications of this work can monitor immune populations throughout metastatic progression to build a temporal database of immune phenotypes and track association with clinical outcomes.
    Keywords:  PDAC; Pre-metastatic liver; Single cell RNAseq; T cell clonality; TCR
    DOI:  https://doi.org/10.1007/s00262-025-04146-5
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