bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2026–10–18
thirty-six papers selected by
Kıvanç Görgülü, Technical University of Munich



  1. Arch Med Sci. 2026 ;22(4): 2231-2249
      Ferroptosis is a programmed cell death characterized by excessive, iron-dependent accumulation of membrane lipid peroxides due to insufficient glutathione-dependent antioxidant defense. It is influenced by the metabolism of amino acids, lipids, and iron, and occurs in conditions of decreased glutathione peroxidase 4 (GPX4) activity. The increased polyunsaturated fatty acid (PUFA) content in membrane phospholipids is associated with cellular hypersusceptibility to ferroptosis. In contrast, incorporation of monounsaturated fatty acids may protect cells against ferroptotic cell death. Cellular sensitivity to ferroptosis is additionally influenced by glutamine catabolism and the xc-system-mediated import of cystine, which modulate glutathione production, and by elevated iron levels, which lead to the buildup of reactive oxygen species (ROS) that attack membrane-localized PUFAs. This review focuses on recent findings of perturbed metabolic processes in cancer that create a high iron demand and an altered lipid composition, thereby predisposing cells to ferroptosis. We analyze the therapeutic potential of pharmacological agents that can selectively trigger ferroptosis in tumor cells.
    Keywords:  GPX4; cancer therapeutics; ferroptosis; glutathione metabolism; iron metabolism; lipid metabolism; redox homeostasis
    DOI:  https://doi.org/10.5114/aoms/225096
  2. Nat Med. 2026 Oct 12.
      Cancer cachexia is a wasting syndrome with outsized impact on morbidity and mortality, yet its drivers and systemic consequences remain poorly defined. In this study, we repurposed longitudinal clinicogenomic data from 52,236 patients with cancer profiled by MSK-IMPACT (2010-2024) at Memorial Sloan Kettering Cancer Center to define episode-resolved trajectories of consensus-defined cachectic weight loss and linked these events to outcomes, serology and tumor genotypes. Cachectic episodes clustered near periods of disease progression and were associated with inferior outcomes in nearly all cancer types. Across diverse malignancies, cachectic weight loss episodes exhibited a consistent serologic signature characterized by lower albumin and hemoglobin and higher levels of liver enzymes. Numerous somatic tumor genotypes, including TP53 mutation across several diseases, were also associated with more frequent onset of cachectic episodes. Motivated by these observations, we developed a multivariate model to predict impending risk of cachectic weight loss in patients with lung, colorectal and prostate cancer, validated in an independent, external cohort from Dana-Farber Cancer Institute (n = 5,785). Routine clinicogenomic data are, therefore, a scalable resource for discovery in cancer cachexia.
    DOI:  https://doi.org/10.1038/s41591-026-04689-9
  3. Cell. 2026 Oct 15. pii: S0092-8674(26)01141-4. [Epub ahead of print]
      Ferroptosis is implicated as a vulnerability in multiple cancers, yet approaches for effectively inducing ferroptosis in vivo are limited. Bypassing conventional strategies targeting the antiferroptotic glutathione peroxidase 4 (GPX4) and ferroptosis suppressor protein 1 (FSP1) proteins, we designed metabolic initiators of lipid peroxidation (MILPOs) and developed the compounds WMK-1/2, which contain tetraoxane radical-generating and mitochondria-targeting groups, as de novo ferroptosis inducers. WMK-1 localizes primarily to mitochondria, induces local lipid peroxidation, and impairs oxidative phosphorylation. WMK-1 induces a "mito-ferroptosis" sub-pathway that skips GPX4 inhibition as a prerequisite, can be rescued by lipophilic radical-trapping antioxidants, yet is minimally sensitive to acyl-coenzyme A synthetase long-chain family member 4 (ACSL4) perturbation and long-chain polyunsaturated fatty acid (PUFA) supplementation, and evades retinol-mediated protection. Instead, WMK-1-induced cell death requires labile Fe2+ and can be selectively suppressed by ɑ-lipoic acid, an endogenous, mitochondria-resident antioxidant. WMK-1/2 are bioavailable and exhibit significant efficacy in tumor suppression by eliciting ferroptosis in multiple cancer models and augmenting the antitumor effects of immune-checkpoint blockers. Our work provides a protein-targeting-independent metabolic ferroptosis induction strategy for potential cancer therapy.
    Keywords:  cancer and metastasis; ferroptosis induction; iron metabolism; metabolic initiator of lipid peroxidation; mito-ferroptosis; mitochondria; tetraoxanes
    DOI:  https://doi.org/10.1016/j.cell.2026.09.040
  4. Cell Rep. 2026 Oct 13. pii: S2211-1247(26)01158-7. [Epub ahead of print]45(10): 118079
      Reactive oxygen species (ROS) drive pro-tumorigenic signaling but also promote lipid peroxidation and ferroptosis, making ROS regulation critical during high oxidative stress stages of tumor progression, such as metastasis. Loss of the antioxidant TIGAR in pancreatic ductal adenocarcinoma (PDAC) cells raises ROS and enhances metastatic behavior but also sensitizes cells to ferroptosis. To understand how TIGAR-null cells survive to metastasize, we examine the role of macrophage infiltration, which is increased in TIGAR-null tumors. Co-culturing TIGAR-null PDAC cells with macrophages protects them from ferroptosis. The tumor cells induce macrophage IL-6 secretion, which leads to the activation of STAT3 and upregulation of the iron-sequestering protein ferritin (FTH1) in cancer cells. FTH1 depletion in TIGAR-null cells restores ferroptosis sensitivity and reduces lung metastasis. These results suggest that the outcome of increased ROS in tumors may depend on the activation of mechanisms that selectively prevent ferroptosis while preserving ROS-induced oncogenic signaling and metastasis-promoting pathways.
    Keywords:  CP: cancer; CP: immunology; PDAC; ferritin; ferroptosis; macrophages; metastasis; oxidative stress; pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.1016/j.celrep.2026.118079
  5. Cancer Cell. 2026 Oct 12. pii: S1535-6108(26)00428-9. [Epub ahead of print]44(10): 1921-1923
      In this issue of Cancer Cell, Shi et al. report encouraging early-phase results combining HRS-4642, an allele-specific KRAS G12D inhibitor, with the PD-L1 inhibitor adebrelimab in previously treated metastatic pancreatic cancer. The intravenous combination was safe and well tolerated, notably sparing patients the gastrointestinal toxicity common to oral KRAS inhibitors, and achieved a promising 43% response rate at the recommended dose.
    DOI:  https://doi.org/10.1016/j.ccell.2026.09.009
  6. ACS Chem Biol. 2026 Oct 15.
      Polyunsaturated fatty acids (PUFAs) are essential nutrients supporting numerous cellular processes in normal and neoplastic cells, yet PUFA-containing phospholipids predispose cells to ferroptosis. How cancer cells from various lineages or genetic backgrounds proliferate in the presence of PUFA remains poorly understood. Here, by systematically profiling various fatty acids using a barcoded and pooled cancer cell line library, we show that a subset of cell lines is sensitive to PUFA treatment at concentrations comparable to physiological levels. We demonstrate that PUFA treatment alone is sufficient to induce ferroptosis in these cell lines that are also vulnerable to GPX4 inhibition. By correlating patterns of PUFA sensitivity with cancer cell line features including basal mRNA transcript levels, we show that PUFA sensitivity is positively associated with fatty acid binding protein 1 (FABP1) expression. Additionally, by profiling a diverse collection of fatty acids and analogs, we find that ferroptosis in cancer cells can be effectively induced by conjugated linolenic acids, in addition to PUFAs containing 1,4-pentadiene groups. Genome-wide CRISPR modifier screens in the PUFA-sensitive ES2 cells reveal a pro-ferroptosis pathway defined by enzymes that convert PUFAs to membrane-associated phospholipids, and an anti-ferroptosis pathway that segregates PUFAs by delivering them to lipid droplets. Together, we present the first comprehensive data set of PUFA-induced ferroptosis sensitivity in a collection of 554 cell lines from 19 primary lineages and suggest a potential therapeutic avenue to induce tumor cell ferroptosis using dietary metabolites.
    DOI:  https://doi.org/10.1021/acschembio.6c00581
  7. J Exp Med. 2026 Nov 02. pii: e20261370. [Epub ahead of print]223(11):
      Scientific independence alone does not create a sustainable research program. Drawing on the 2026 Irving Cancer Immunology Symposium, we offer practical strategies for navigating uncertainty and limited resources to build a coherent research program and resilient team across funding systems.
    DOI:  https://doi.org/10.1084/jem.20261370
  8. Biochem Soc Trans. 2026 Oct 28. 54(10): 1487-1495
      Plasma membrane rupture (PMR) is a terminal event in many forms of lytic cell death, yet was long regarded as a passive consequence of osmotic swelling and mechanical membrane failure. The identification of ninjurin-1 (NINJ1) as a key mediator of PMR fundamentally changed this view by establishing that membrane permeabilisation and terminal membrane rupture are mechanistically distinct processes. Across different cell death modalities, NINJ1 promotes the transition from membrane damage to catastrophic cellular disintegration. Structural studies have revealed how NINJ1 is restrained by autoinhibition in healthy cells and assembles into higher-order membrane-remodelling complexes following activation. However, how NINJ1 is activated and how its assemblies cooperate with the physical state of the dying cell to produce membrane rupture remain incompletely understood. NINJ1-dependent PMR also determines the release of intracellular contents, linking cell death to inflammation, host defence, tissue homeostasis and disease. Emerging evidence suggests that NINJ1 integrates molecular, metabolic and biophysical signals and can function beyond canonical cell-death pathways. Here, we discuss the molecular mechanisms governing NINJ1-mediated PMR, how diverse cell death pathways converge on this process, and how terminal membrane rupture shapes inflammatory responses, host defence and tissue pathology. We further consider unresolved mechanisms of NINJ1 activation and the therapeutic potential of uncoupling cell death from inflammatory membrane rupture.
    Keywords:  NINJ1; cell death; inflammation; membrane rupture; ninjurin-1
    DOI:  https://doi.org/10.1042/BST20260842
  9. Cell. 2026 Oct 15. pii: S0092-8674(26)01142-6. [Epub ahead of print]
      Self-organization generates cellular patterns that guide morphogenesis, but how it regulates collective cell fate remains underexplored. We show that cellular self-organization constrains the propagation of ferroptosis, an iron-dependent form of oxidative cell death that can otherwise spread as unbounded trigger waves. The spatial patterning of cell density and alignment encodes transcriptional programs, priming cells toward ferroptosis-sensitive or -resistant fates. Low-density, misaligned regions with elevated YAP/TEAD1 activity are sensitive, whereas high-density, aligned regions with increased NRF2 expression form propagation-resistant boundaries. Cell elongation establishes a polarized distribution of oxidizable lipids, creating peroxidation hotspots at the cell poles that promote propagation along cell alignment. In silico and pharmacological perturbations reveal that pattern-dependent susceptibility and polarized lipid organization act together to constrain isotropic waves into spatially confined, anisotropic propagation. These findings identify self-organization as a systems-level mechanism governing collective homeostasis, providing a paradigm to explore how tissue-scale organization regulates cell death in development and disease.
    Keywords:  active nematics; cellular patterns; ferroptosis; self-organization; topological defects; trigger waves
    DOI:  https://doi.org/10.1016/j.cell.2026.09.039
  10. bioRxiv. 2026 Sep 29. pii: 2026.09.28.754674. [Epub ahead of print]
      Pancreatic ductal adenocarcinoma (PDAC) progression involves malignant cell state plasticity. Epigenetic changes underlie this plasticity, yet the PDAC cis -regulatory landscape remains understudied. To address this, we profiled 33 primary tumors and 7 metastases from 39 patients with single-cell ATAC-seq, paired with 10 single-cell RNA-seq profiles. We found that epigenetic GATA6 + / KRT17 + co-accessibility identifies a classical-basal subtype-intermediate progenitor state (SIP) associated with better clinical outcomes. SIP cells display limited epigenetic reprogramming from premalignant epithelium and retain gastric-intestinal differentiation reminiscent of neoplastic precursors. Lineages without GATA6 + / KRT17 + co-accessibility exhibit greater lineage and epithelial-mesenchymal plasticity. Classical PDACs that repress basal gene accessibility activate neural-like progenitor (NRP) and tuft lineage enhancers, whereas basal committed tumors display esophageal transdifferentiation. Compared to SIP, classical-NRP and basal committed tumors have poorer outcomes, and show distinct PD-1/PD-L1 immune proteomic phenotypes and prognostic myofibroblast epigenetic states, respectively. Our work reveals links between lineage reprogramming, EMT, and epigenetic progression in human PDAC.
    DOI:  https://doi.org/10.64898/2026.09.28.754674
  11. Proc Natl Acad Sci U S A. 2026 Oct 20. 123(42): e2624455123
      Cancer-associated fibroblasts (CAFs) are often found forming a peripheral stromal barrier around tumors. Here, this paradigm is challenged using microfabricated 3D cancer-CAF spheroid models combined with quantitative magnetic force tensiometry. A surface tension atlas is established for eight cancer cell lines, three CAF populations, and heterotypic tumor-CAF assemblies, spanning nearly two orders of magnitude. Surface tension is first shown to govern spheroid morphology and modulate drug response. Besides, CAFs consistently occupy the highest end of the surface tension hierarchy, predicting core rather than peripheral localization and directly challenging the shell paradigm. Yet confocal imaging reveals not only central accumulation but also complete CAF-tumor mixing, including in spheroids where cancer cells exhibit surface tensions nearly two orders of magnitude lower than CAFs. Surface tension alone therefore fails to predict CAF organization. Instead, the epithelial-to-mesenchymal transition (EMT) state of cancer cells emerges as a major determinant: epithelial-like tumors promote CAF core accumulation, whereas mesenchymal-like states favor persistent mixing. Peripheral CAF localization emerges only under restricted conditions combining high tumor cohesion and sequential stromal recruitment. Together, these results identify surface tension, EMT state, and assembly chronology as joint determinants of tumor-stroma architecture, revealing a context-dependent organization landscape rather than a universal CAF shell.
    Keywords:  cancer spheroids; cancer-associated fibroblasts; epithelial-mesenchymal transition; magnetic force tensiometry; surface tension
    DOI:  https://doi.org/10.1073/pnas.2624455123
  12. Lab Chip. 2026 Oct 13.
      Label-free tracking of adherent cell migration could enable important insights into biological processes such as tissue repair, inflammatory response, or cancer progression. Nevertheless, visualizing unlabeled animal cells using optical microscopy remains challenging due to low contrast as well as frequent changes in cell shape and number. A promising alternative uses electrical capacitance measurements, which are sensitive to cell adhesion to electrode surfaces. However, prior examples often utilized electrodes with areas larger than single cells, resulting in averaged readouts over multiple cells. Here, we demonstrate label-free, live-cell tracking using a capacitance sensor array with more than 1 million pixels on a 10 micron pitch across an area larger than 1 square centimeter. We show that single cell morphology can be clearly segmented and used to reconstruct migration and proliferation dynamics using optical flow. We further track the spreading of multicellular spheroids, revealing fast-moving peripheral regions led by a collective leader cell "front". Finally, we demonstrate label-free imaging of millimeter-scale honeycomb-shaped tissues without the multi-image stitching often required for conventional microscopy. We utilize mutual capacitance measurements with electrically-programmable electrode spacing to map topographical features of these engineered tissues. Overall, CMOS capacitance imaging arrays enable label-free imaging spanning from single cells to large tissues, in a portable and scalable format for settings where optical microscopy may be difficult to access.
    DOI:  https://doi.org/10.1039/d6lc00530f
  13. Nat Genet. 2026 Oct 13.
      Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer characterized by profound desmoplasia and cellular heterogeneity, which cannot be fully resolved using traditional bulk sequencing approaches. To understand how this heterogeneity contributes to PDAC biology, we analyzed a large cohort of primary tumors (n = 62) profiled using single-cell RNA sequencing (443,451 single cells), including a subset of 11 tumors with matched spatial transcriptomics (53,236 spots), to map clonal, transcriptional and spatial diversity. Moreover, our sample set includes a unique cohort of matched samples from six tumors collected before and after treatment with chemotherapy. Our analysis revealed notable intratumoral heterogeneity, with multiple genetically distinct neoplastic clones coexisting within individual tumors. We observed clone-specific ligand-receptor programs that are modulated by genomic dosage: amplifications of ligands or receptors enriched corresponding interactions, while deletions suppressed them, with genetically encoded differences supported by spatial transcriptomics and multiplex immunofluorescence. Phylogenetic integration identified focal 8q24 (MYC) amplification as recurrently associated with classical-to-basal transitions occurring within tumor lineages at a frequency above chance; these transitions were accompanied by coordinated depletion of immune-response programs. Functional perturbation experiments in murine and primary human models showed that MYC knockdown reactivates classical transcriptional programs and restores immune-response pathways, supporting a role for MYC in maintaining a basal, immune-depleted state. Spatial analyses further revealed dispersed clones enriched for epithelial-to-mesenchymal transition activity and immune suppression, correlating with metastatic potential and colonization of lymph node niches. These dispersed clones shifted toward a basal phenotype, contributing to disease progression. Our findings highlight the critical role of clonal diversity, transcriptional plasticity and tumor microenvironment interactions in shaping human PDAC biology. This work provides a detailed view of the molecular and spatial heterogeneity of PDAC and offers potential avenues for therapeutic intervention targeting clonal evolution and the mechanisms driving metastasis.
    DOI:  https://doi.org/10.1038/s41588-026-02779-5
  14. Oxid Med Cell Longev. 2026 ;2026(1): e9604592
       BACKGROUND: Monounsaturated fatty acid (MUFA) metabolism promotes cancer progression and survival by regulating membrane lipid composition, maintaining lipid homeostasis and preserving redox balance. A growing body of evidence indicates that altered MUFA metabolism promotes tumour growth while protecting cancer cells from ferroptosis.
    AIM: This review summarises current knowledge on the contributions of MUFA metabolism to carcinogenesis, regulation of ferroptosis and treatment response across different cancers. Further, we discussed the emerging treatment strategies targeting MUFA metabolic pathways.
    METHODS: Relevant experimental and clinical studies investigating MUFA metabolism, lipid metabolic reprogramming, ferroptosis and therapeutic interventions in cancer were comprehensively reviewed and critically analysed.
    RESULTS: Enhanced de novo MUFA synthesis and incorporation into membrane phospholipids increase the MUFA-to-polyunsaturated fatty acid (PUFA) ratio, thereby reducing the availability of oxidation-prone PUFAs, limiting lipid peroxidation, and protecting cancer cells from ferroptosis. MUFA-driven membrane remodelling enhances membrane fluidity and activates oncogenic signalling pathways, including epithelial-mesenchymal transition (EMT), cancer cell migration, invasion and metastasis. These effects are mediated by the dysregulated expression of key lipogenic enzymes and signalling pathways that reprogramme lipid metabolism to meet the metabolic demands of cancer cells. Multiple studies have shown that MUFA metabolism is a promising therapeutic target. Furthermore, the inhibition of stearoyl-CoA desaturase-1 (SCD1) and fatty acid synthase (FASN), key enzymes in MUFA metabolism, sensitises cancer cells to ferroptosis by enhancing lipid peroxidation.
    CONCLUSION: MUFA metabolism is a key regulator of cancer progression and ferroptosis resistance. Targeting MUFA metabolic pathways is a promising therapeutic strategy. However, mechanistic studies are required to elucidate the molecular mechanisms underlying sensitivity to ferroptosis and to optimise clinical applications.
    Keywords:  FASN; MUFA; SCD1; ferroptosis; lipid metabolism; redox homeostasis
    DOI:  https://doi.org/10.1155/omcl/9604592
  15. Dev Cell. 2026 Oct 14. pii: S1534-5807(26)00351-5. [Epub ahead of print]61(10): 1952-1968.e5
      The mesenchymal-amoeboid transition (MAT) enhances cancer cell migration and therapy resistance during dissemination through mechanically confined spaces. Using an in vitro MAT induction system combining physical confinement with a non-adhesive environment to mimic interstitial migration, we introduce "long-term MAT" (L-MAT) to describe cells sustaining MAT under prolonged pressure and show that L-MAT triggers receptor-interacting protein kinase 3 (RIPK3)-independent necroptosis. Mechanistically, the PIEZO1-STAT1 axis upregulates mixed lineage kinase domain-like pseudokinase (MLKL), whose membrane accumulation drives necroptosis in cells otherwise resistant to death-receptor signaling. Before membrane rupture, L-MAT cells show progressive migration restriction; MLKL-knockout cells bypass this checkpoint and persist as surviving clones. Spatial transcriptomics of patient tumors shows MLKL expression correlates with PIEZO1 activation and immunogenicity in less aggressive regions, while advanced malignant and metastatic clones show reduced MLKL. These findings establish MLKL as a conditional tumor checkpoint and identify the PIEZO1-STAT1-MLKL axis as a predictive biomarker and therapeutic target.
    Keywords:  MLKL; PIEZO1; RIPK3-independent necroptosis; amoeboid migration; mechanical confinement; mesenchymal-amoeboid transition; necroptosis; spatial transcriptomics; tumor checkpoint; tumor evolution
    DOI:  https://doi.org/10.1016/j.devcel.2026.09.003
  16. Phys Rev E. 2026 Sep;114(3-1): 034410
      Cell migration plays a fundamental role in numerous physiological processes, including embryonic development, wound healing, and cancer metastasis. While cell-cell adhesion is known to regulate motion by shaping cell morphology and intercellular force balance, its dynamic, rate-dependent contributions to tissue behavior remain poorly understood. In this study, we examine how the dissipative nature of cell-cell adhesion influences tissue dynamics and collective migration using an extended vertex model with explicit junctional viscosity. Our findings reveal a nontrivial interplay between two distinct components of adhesion: An interfacial adhesion energy (energetic, rate-independent) contribution, which sets the effective junctional tension, and a dissipative (rate-dependent) contribution, which controls resistance to relative motion during cell rearrangements. We show that increasing the energetic component promotes migration by modifying cell shape and lowering the barrier to neighbor exchanges, whereas strengthening the dissipative component induces jamming and suppresses cell motion. Linear rheological analysis further demonstrates that, in the unjammed regime, vertex-model tissues exhibit power-law viscoelastic behavior, with adhesion modulating the power-law exponent and thereby controlling the spread of relaxation timescales. Together, these findings clarify the dual role of adhesion in governing tissue mechanics and rheology and provide a mechanistic framework for understanding the balance between fluidity and rigidity in epithelial monolayers.
    DOI:  https://doi.org/10.1103/f6mt-tkgl
  17. Redox Biol. 2026 Sep 29. pii: S2213-2317(26)00419-2. [Epub ahead of print]97 104420
      Ferroptosis resistance contributes to pathological skin scarring, but the underlying regulatory mechanisms remain unclear. Here, we identified a novel selective autophagy pathway NEURL1-SQSTM1/p62-SLC40A1 that controls fibroblast ferroptosis and scar formation. SLC40A1 is upregulated in human scars, conferring ferroptosis resistance by promoting iron efflux. Mechanistically, NEURL1 mediates K63-linked ubiquitination of SLC40A1, enabling its recognition by SQSTM1 for lysosomal degradation. A microneedle system co-delivering curcumin (autophagy activator) and siSLC40A1 effectively activates this axis, induces ferroptosis, and alleviates scarring in vivo. Our findings reveal a new therapeutic target and strategy for pathological scars.
    Keywords:  Autophagy; Ferroptosis; Microneedles; Pathological scars; SLC40A1
    DOI:  https://doi.org/10.1016/j.redox.2026.104420
  18. bioRxiv. 2026 Sep 29. pii: 2026.09.28.755133. [Epub ahead of print]
      Ether glycerophospholipids (ether lipids) are a subclass of glycerophospholipids that are synthesized at the peroxisome and constitute nearly 20% of the total phospholipid content in metazoans. Biochemically, ether lipids have an alkyl chain attached by an ether bond at the sn-1 position of the glycerol backbone (alkyl-ether) primarily containing choline or ethanolamine head groups. Some ether lipids contain a cis bond adjacent to the ether linkage (alkenyl-ether) and are commonly referred to as plasmalogens. While the importance of ether lipids in humans is clear, highlighted by the severity of inherited peroxisomal disorders caused by ether lipid deficiency, the molecular roles of these lipids remain poorly understood. Here, we identify a link between ether lipid metabolism, peroxisome degradation, and oxygen availability. We find Fatty acyl-CoA-reductase 1 (FAR1), the rate-limiting enzyme in peroxisomal ether lipid metabolism, acts as a peroxisome receptor necessary for peroxisome degradation when oxygen is limiting. Hypoxia increases choline ether lipid abundance, promotes autophagy activation, and peroxisome degradation. Mechanistically, FAR1 binds ATG8-family protein LC3B and is necessary and sufficient to control peroxisome degradation under hypoxia. FAR1's enzymatic function as well as its capacity to bind LC3B is necessary to degrade peroxisomes under hypoxia. Similarly, loss of multiple components of peroxisomal ether lipid metabolism blocks peroxisome degradation under hypoxia in cells and in vivo. In mouse models of chronic HIF activation, Far1 is a direct HIF target gene and is necessary for peroxisome degradation in this setting. Increasing ether lipids using ether lipid precursors activates autophagy and promotes autophagy-dependent cardioprotection against ischemic injury. This work reveals FAR1 as a critical regulator of peroxisome homeostasis in the setting of oxygen limitation.
    DOI:  https://doi.org/10.64898/2026.09.28.755133
  19. STAR Protoc. 2026 Oct 10. pii: S2666-1667(26)00550-2. [Epub ahead of print]7(4): 104897
      In mouse models of pancreatic ductal adenocarcinoma, surgical removal of orthotopic tumors typically involves removing the primary tumor along with the spleen. Here, we present a protocol for surgical removal of the tumor in the tail of the pancreas while preserving the spleen. We describe steps for implantation of mouse pancreatic cancer cells followed by the identification and removal of the orthotopic tumor. We also outline perioperative treatment strategies for tumor recurrence.
    Keywords:  Cancer; Immunology; Model Organisms
    DOI:  https://doi.org/10.1016/j.xpro.2026.104897
  20. Phys Rev E. 2026 Sep;114(3-1): 034406
      Substrate curvature and cell-substrate adhesion are two key physical determinants of directional collective cell migration, yet their joint regulatory mechanism remains unresolved. Here, we establish a physical framework based on the instantaneous force balance to reveal the dominance switching mechanism between these two factors in collective cell migration. Higher curvature sets a threshold that gates migration initiation by redistributing forces, while adhesion primarily governs curvature-independent migration velocity after cells surpass the threshold by mediating the balance between driving and resistive forces. This framework yields experimentally consistent predictions for in vitro systems and helps understand a diversity of physiological and pathological processes that involve collective cell dynamics.
    DOI:  https://doi.org/10.1103/79s4-d9d2
  21. Methods Mol Biol. 2026 ;3057 171-187
      Recent advances in volume electron microscopy have permitted unprecedented visualizations and in-depth quantitative analyses of mitochondrial network structure in skeletal muscle. Nanoscale, 3D analyses of skeletal muscle mitochondria have provided novel insights into how mitochondria interact among themselves and with other skeletal muscle cell organelles, such as the sarcoplasmic reticulum and the sarcomere. The identification of mitochondria within volume electron microscopy datasets and the downstream analyses of segmented structures remain two major bottlenecks in the analysis of 3D mitochondrial network structure at the nanoscale. Here, we provide a step-by-step guide on how to use machine learning programs to segment skeletal muscle mitochondria from volume electron microscopy datasets, followed by instructions on several types of 3D analyses of individual mitochondria and mitochondrial network structure that can be performed using ImageJ. We highlight key quality-control steps to ensure precise and accurate segmentation and analyses and to enhance reproducibility across groups.
    Keywords:  Focus Ion Beam Scanning Electron Microscopy; Mitochondria; Skeletal muscle; Volume electron microscopy
    DOI:  https://doi.org/10.1007/978-1-0716-5396-8_14
  22. ACS Chem Biol. 2026 Oct 15.
      Cell membranes are composed of both bilayer and nonbilayer lipids, whose molecular shape and interactions support or oppose their packing into flat bilayer sheets. While the role of the former in maintaining membrane structural integrity is clear, a growing body of data highlights the importance of nonbilayer lipids in membrane function, including fission and fusion processes in trafficking, and the dynamics of membrane-associated proteins. In this review, we provide a comprehensive overview of nonbilayer lipids and their roles in membrane biology, disease, and drug delivery. First, we introduce the lipid chemistry that gives rise to intrinsic curvature and curvature elastic stress (CES), and we survey the chemical diversity of nonbilayer lipids across organelles and cell types. Second, we discuss relevant methodological advances for characterizing the physicochemical properties of nonbilayer lipids, including X-ray scattering, lipidomics, and molecular dynamics. We then examine how nonbilayer lipids contribute to membrane fusion and fission and how the CES they generate modulates membrane protein localization and function. Next, we consider how the biophysical principles governing nonbilayer lipid behavior can inform the rational design of lipid nanoparticle formulations for therapeutic delivery. Finally, we explore how cells regulate lipid intrinsic curvature as a distinct homeostatic parameter and discuss the implications of its dysregulation in liver disease, neurodegeneration, and mitochondrial dysfunction. We highlight developments in methods spanning the interface between chemistry and biology that can help investigate the function and regulation of nonbilayer lipid chemistry, with far-reaching potential to answer questions in human health, disease, and drug delivery.
    DOI:  https://doi.org/10.1021/acschembio.6c00629
  23. Oncogene. 2026 Oct 16.
      KRAS is mutated in 30% of all human cancers. Small molecule inhibitors targeting KRAS with distinct mechanisms-of-action and variable specificities have entered the clinic, but their full effect on the RAS signaling network remains unclear. Here, we described the impact of RAS inhibition on the KRAS interactome using Proximity-dependent Biotin Identification. Two inhibitors were used: panRAS-ON, which forms a ternary complex between cyclophilin and RAS in the GTP-bound state; panKRAS-off, which binds to the KRAS switch II pocket. RAS inhibitors were found to significantly alter 16.5% of proteins in proximity to KRAS. Despite their distinct modality, the KRAS inhibitors induced highly correlated changes in the KRAS interactomes. Among KRAS-proximal proteins, Afadin was highly affected by RAS inhibition. AFDN is a key regulator of cell motility, invasion, and metastasis. Analysis of AFDN phosphorylation revealed that AKT only partially modulates p-Ser1718, while KRAS inhibition sufficiently abolished EGF-mediated AFDN phosphorylation. Silencing AFDN in a KRAS-driven non-small cell lung cancer model abolished chemotaxis and disrupted directional migration in an EGF-driven wound healing model. We demonstrated that KRAS is a central node in regulating growth factor-induced cell migration, and that KRAS inhibition plays a broader role than MAPK-mediated cell proliferation and survival.
    DOI:  https://doi.org/10.1038/s41388-026-04017-y
  24. Protein Sci. 2026 Nov;35(11): e70822
      Although biological membranes exhibit complex and dynamic organization, the mechanistic role of molecular crowding in governing lateral membrane heterogeneity remains poorly characterized experimentally. Here, we provide direct experimental visualization showing that crowding-induced condensation of membrane-anchored macromolecules above the bilayer interface reorganizes membrane dynamics and gives rise to spatially heterogeneous lipid mobility. Both PEGylated lipids and membrane-anchored proteins undergo surface-density-driven condensation on supported lipid bilayers (SLBs), forming immobile regions that constrain lipid diffusion. Notably, the condensation threshold varies inversely with poly(ethylene glycol) chain length and surface density, defining a quantitative relationship between molecular size and crowding strength. To directly visualize these crowding-induced structures, we employed a nanodisc-mediated lipid delivery ("nanodelivery") approach, revealing a clear correspondence between condensed crowder regions and diffusion barriers reminiscent of the picket-fence model of live-cell membranes. Similar behavior in protein-crowded SLBs demonstrates the generality of this crowding-driven mechanism. Using minimal two-layer and three-layer reconstituted architectures, we further demonstrate that surface density and macromolecular crowding above the membrane function as tunable control parameters that drive phase transitions within membrane-tethered macromolecular layers, independent of anchoring chemistry, while the underlying lipid bilayer remains laterally continuous. Extension of this framework to living cells reveals analogous suppression of membrane mobility under high surface-density conditions, indicating that this crowding-induced reorganization is not restricted to SLBs model systems. Together, these findings establish surface-density-driven phase transitions of membrane-anchored macromolecules as a general physical mechanism underlying lateral membrane inhomogeneity and position nanodelivery as a versatile approach for interrogating membrane organization across synthetic and biological systems.
    Keywords:  PEGylated lipids; lateral membrane heterogeneity; membrane phase transition; molecular crowding; nanodisc‐mediated lipid delivery
    DOI:  https://doi.org/10.1002/pro.70822
  25. Biochem Soc Trans. 2026 Oct 28. 54(10): 1497-1511
      Autophagy is the cell's recycling system; it removes unwanted or dysfunctional cellular material, thereby preventing damage. Importantly, it is a key pro-survival pathway during periods of stress, for instance, during nutrient scarcity. As it can support nutrition during starvation, it is not surprising that autophagy is controlled by nutrient availability. As a result, diet-based strategies to modify autophagy have attracted considerable scientific and public interest, although what is presented to the public is often not supported by a solid scientific foundation. Evidence from animal models is compelling: several of these interventions robustly activate autophagy and are linked to improved lifespan and healthspan. Data from humans, however, are much more limited. Many human studies rely on measurement of steady-state levels of autophagy genes or proteins, metrics that do not independently establish pathway activity. Far fewer have measured autophagic 'flux', the more rigorous readout of turnover, and where they have, findings are often negative or inconclusive. Here, we review the human research on popular nutritional interventions purported to change autophagy-including prolonged fasting, intermittent fasting, calorie restriction, and altered macronutrient intake-and contrast these findings with the preclinical evidence that has shaped public expectations. We highlight key gaps in the literature, particularly the scarcity of flux-based measurements and the reliance on blood as a proxy for autophagy in other, less accessible tissues. Refining how we monitor autophagy in humans should be a key priority for the field and is ultimately needed to establish whether and how diet modulates human autophagy.
    Keywords:  autophagy; calorie restriction; fasting; intermittent fasting
    DOI:  https://doi.org/10.1042/BST20260632
  26. Nat Immunol. 2026 Oct 14.
      Most patients with solid tumors fail to sustain antitumor immunity, in part because immune cells cannot outcompete cancer cells inside the immunosuppressive tumor microenvironment. Here, we show the lipid-sensing transcription factor PPARδ is a compartment-specific determinant of cancer-immune fitness balance and immunotherapy efficacy. Activating PPARδ in cancer cells promotes their growth and impairs antitumor immunity, whereas activating it in immune cells drives tumor suppression and overrides tumor-promoting effects of cancer-intrinsic activation. Mechanistically, PPARδ enhances CD8+ T cell fitness against cancer through effector-associated chromatin remodeling and Cpt1a-mediated fatty acid oxidation. Therapeutically, PPARδ-activated CD8+ T cells sensitize immunotherapy-resistant microsatellite stable metastatic colorectal cancer to checkpoint blockade in mice, and pharmacological or genetic PPARδ activation enhances human chimeric antigen receptor T cell function. These findings identify compartment-specific PPARδ activity as a targetable driver of immune cell fitness that can be harnessed to improve outcomes in immunotherapy-resistant tumors.
    DOI:  https://doi.org/10.1038/s41590-026-02685-2
  27. Cancer Discov. 2026 Oct 13.
      To evaluate the functional relevance of mutations newly detected in breast cancer metastases, we analyzed genomic data from 662 paired and ~6,000 unpaired primary and metastatic tumors. These analyses indicate that metastasis-specific mutations are frequently acquired post-dissemination, with a disproportionate contribution from APOBEC-mediated mutagenesis. Metastasis-specific mutations converged on a set of pathways that were highly recurrent, distinct from those altered in primary tumors, and dependent on metastatic site. 95% of patients harbored metastasis-specific mutations within a minimum set of 10 pathways. Remarkably, more than half the variation in metastatic latency across patients was explained by the relative timing of mutation acquisition within implicated pathways before versus after dissemination. These findings support a "mutability-dependent" model of metastasis in which functionally consequential mutations accumulate after primary tumor dissemination and contribute to metastatic outgrowth, with latency reflecting the time required for DTCs to acquire the remaining driver mutations needed to achieve metastatic competence.
    DOI:  https://doi.org/10.1158/2159-8290.CD-25-2090
  28. Nucleic Acids Res. 2026 Oct 13. pii: gkag967. [Epub ahead of print]
      Proteome-wide association studies (PWASs) have emerged as a powerful approach for investigating associations between genetically regulated proteins and complex traits, offering valuable insights into the mechanisms linking genetic variation, protein abundance, and phenotypes. Despite the rapid expansion of PWAS research, no resource currently exists to systematically collect, integrate, and organize publicly accessible PWAS findings and related knowledge, limiting efficient use and exploration of these valuable assets. To address this urgent need, we introduce PWAS Atlas (https://ngdc.cncb.ac.cn/pwas/), a comprehensive knowledgebase that consolidates literature-curated information and large-scale, standardized PWAS analyses. The PWAS Atlas encompasses 40 609 associations among 4585 genes/proteins and 763 traits, derived from 118 publications and 841 GWAS datasets. It implements interactive knowledge graphs that reveal associations among genes, proteins, tissues, and traits, as well as online comparative analysis tools that enable systematic comparisons across multiple genes or traits. PWAS Atlas also provides a user-friendly web platform for browsing, searching, exploring, and downloading data. By enabling standardized retrieval, visualization, comparison, and reuse of PWAS information, PWAS Atlas serves as an extensive resource for investigating protein-trait associations and deriving insights into disease biology.
    DOI:  https://doi.org/10.1093/nar/gkag967
  29. Protein Sci. 2026 Nov;35(11): e70820
      Protein-nucleic acid (protein-Nu) interactions are crucial for many cellular processes and biological functions. Crosslinking mass spectrometry (XL-MS) has emerged as a powerful method for identifying these interactions. However, the analysis of protein-Nu XL-MS data requires an integrated workflow from raw data processing to results inspection and validation. Existing workflows for protein-Nu XL-MS often require switching between tools and considerable manual processing. Here, we introduce NuXLApp, an interactive web-based application for data processing and results visualization in protein-Nu XL-MS studies. NuXLApp integrates the protein-Nu crosslink search engine "NuXL," machine-learning models for peptide property prediction, and interactive result visualization within a reproducible workflow. It enables rapid validation of false discovery rate-controlled crosslink spectrum match-level identifications and facilitates collaboration and intuitive exploration of experimental results. In addition, NuXLApp generates a spectral library from identified protein-Nu crosslinks to enable quantitative analysis of crosslinks using data-independent acquisition (DIA). NuXLApp supports discovery-driven identification of protein-nucleic acid crosslinks and enables DIA-based follow-up experiments for their quantitative analysis. NuXLApp is open-source and available via the OpenMS WebApps platform at https://nuxl.webapps.openms.de/.
    Keywords:  computer science; data processing; false discovery rate; mass spectrometry; proteomics; raw data; search engine; visualization; web application; web application framework
    DOI:  https://doi.org/10.1002/pro.70820
  30. Cell Rep. 2026 Oct 14. pii: S2211-1247(26)01229-5. [Epub ahead of print]45(10): 118150
      Fatty acids require conjugation with coenzyme A (CoA) for their incorporation into membrane lipids. Of these, very-long-chain fatty acids (VLCFAs), the precursors of yeast ceramides, are particularly hydrophobic. Yet, it remains unresolved where and how the sole VLCFA-CoA synthetase Fat1 activates them. Here, we show that lipid droplets (LDs) are both the site of free VLCFA storage and their place of activation. Free VLCFAs preferentially partition into LDs in molecular simulations and in vitro reconstitutions, whereas Fat1 targets the LD surface in cells via an N-terminal amphipathic helix. Structural predictions identify an essential hydrophobic cavity in Fat1 that connects the active site to the membrane, suggesting that VLCFAs shuttle directly from the LD core into the enzymatic pocket. Our model explains how the organelle targeting of a fatty acid activator evolved to match the biophysical properties, and consequently, the subcellular localization of its highly hydrophobic substrate.
    Keywords:  CP: cell biology; CP: metabolism; Fat1; VLCFA; fatty acyl-CoA synthetase; lipid droplets; very-long-chain fatty acids
    DOI:  https://doi.org/10.1016/j.celrep.2026.118150
  31. Phys Rev E. 2026 Sep;114(3-1): 034409
      Membrane extrusion experiments offer a powerful framework for investigating cell surface mechanics. However, providing a robust physical interpretation of the observed force-extension curves (FECs) remains a significant challenge. In this work, we introduce a minimal statistical-mechanical model for cellular membrane extrusion that accounts for discrete lipids, adhesion molecules, and the finite-size elasticity of the loading device. Focusing on a peeling geometry to isolate the essential physics of extrusion, we derive exact analytical expressions for the force-extension relations under two loading conditions: isometric (constant extension) and isotensional (constant force). Our results elucidate how lipid-lipid interactions, adhesion energies, and device stiffness govern the emergence of a mechanically induced conformational transition, providing a formal interpretation of the characteristic mechanical signatures reported in membrane-extrusion experiments, including force peaks, plateau regimes, and relaxation patterns. A central outcome of our analysis is that the isometric and isotensional conditions provide qualitatively different FECs of the same membrane system. This finding carries profound physical implications, suggesting that distinct experimental protocols applied to the same membrane may yield different mechanical responses.
    DOI:  https://doi.org/10.1103/6ypm-2k66
  32. Nat Biomed Eng. 2026 Oct 14.
      Single-cell resolution spatial transcriptomics provides a great opportunity to explore the complex cellular contents in different tissues. Here we introduce SpatialZoomer, a spectral graph-based method that applies a set of low-pass filters to efficiently extract spatial molecular features from spatial transcriptomics data at multiple resolutions or scales, including the single cell scale, the niche scale with dozens of closely interacting cells and the domain scale with spatially organized cell contents. The corresponding critical scales can be automatically identified by partitioning a cross-scale similarity map. Results show that SpatialZoomer can identify disease-progression signals at specific scales in Alzheimer's disease and spatial context-dependent cell subtypes in tumour microenvironment. The extracted multi-scale features also uncovered spatially heterogeneous niches in cancer. SpatialZoomer achieves comparable or superior performance to existing methods for single-scale tasks, and it also has the advantages of high computational efficiency and low hardware requirements.
    DOI:  https://doi.org/10.1038/s41551-026-01800-w
  33. Med. 2026 Oct 13. pii: S2666-6340(26)00329-6. [Epub ahead of print] 101326
      The advent of precision oncology has brought substantial advancements in cancer therapy, yet it has been accompanied by equally complex resistance mechanisms. Among these mechanisms, histological transformations can compromise the effectiveness of targeted therapies, resulting in a loss of clinical benefit following initial success. Understanding these evolutionary processes is crucial for developing the next generation of cancer treatments that can effectively combat resistance. This review examines histological transformation as a key mechanism of resistance to anticancer therapies, driven by various forms of tumor plasticity, and explores into the underlying processes and mechanisms that drive these changes. We also discuss how precision oncology and an appreciation of cancer plasticity can be leveraged to overcome histological transformation and lead to improved patient outcomes.
    Keywords:  EMT; cancer; cancer stemness; plasticity; precision oncology; recurrence; resistance; targeted therapy
    DOI:  https://doi.org/10.1016/j.medj.2026.101326
  34. bioRxiv. 2026 Sep 29. pii: 2026.09.23.753830. [Epub ahead of print]
      Aging progresses asynchronously across organs, motivating the development of organ-resolved aging clocks. Direct assessment of organ aging in living humans, however, is largely impractical. Here, we construct tissue-specific transcriptomic aging clocks and infer organ biological age from paired whole-blood (blood-organ age) and tissue RNA sequencing data in the GTEx project. We observe high variability both in the strength of aging signatures across organs and in the ability to predict organ age and organ scores from blood. Pathway analysis shows that organ aging clocks are dominated by biological processes that differ across tissues. Age-associated multi-organ modules identified in an aging multi-organ network correlation analysis and organ age features causally mediated through organ-blood-organ transcriptomic interactions support a role for systemic signaling in coupling organ aging processes. Given the established role of cellular senescence as a driver of tissue dysfunction and its tissue-specific accumulation during aging, we extend this framework to estimate burden of organ-level senescence and hallmarks of aging. Using senescence- and hallmark-associated gene sets, we derive tissue-specific senescence and hallmark scores (organ scores) and demonstrate that these burdens across multiple organs can be inferred from blood transcriptomes (blood-organ scores). Finally, in pursuit of extending these models to other blood omics and alternative non-invasive assessments, we evaluate whether blood methylation (methylation-blood-organ age and scores) and facial photographs (facial-blood-organ age and scores) can serve as proxies for blood-organ age and blood-organ scores in independent cohorts (Edifice Health and Health and Retirement Study). The methylation- and facial-blood-organ age and scores were associated with mortality in additional testing cohorts (Framingham Heart Study and IMDB-WIKI dataset). These results establish a cross-modal framework for inferring organ-specific aging and senescence from minimally invasive data.
    DOI:  https://doi.org/10.64898/2026.09.23.753830