N Nature Cancer · Dec 04, 2025 Retargeted oncolytic viruses engineered to remodel the tumor microenvironment for glioblastoma immunotherapy Glioblastoma (GBM) is an aggressive, immunotherapy-resistant brain tumor. Here, we engineered an oncolytic virus platform based on herpes simplex virus 1 for GBM viroimmunotherapy. We mutated the highly cytopathic MacIntyre strain to increase spread and oncolytic activity, limit genetic drift, prevent neuron infection and enable PET tracing. We incorporated microRNA target cassettes to attenuate replication in healthy brain cells. Moreover, we engineered the gD envelope protein to specifically target GBM using EGFR-specific or integrin-specific binders. Lastly, we incorporated five immunomodulators to remodel the tumor microenvironment (TME) by locally expressing IL-12, anti-PD1, a bispecific T cell engager, 15-hydroxyprostaglandin dehydrogenase and anti-TREM2 to target T cells and myeloid cells in the GBM TME. A single intratumoral injection increased survival in GBM preclinical models, while promoting tumor-specific T cell, natural killer cell and myeloid cell responses in the TME. In summary, we engineered a retargeted, safe and traceable oncolytic virus with strong cytotoxic and immunostimulatory activities for GBM immunotherapy. Cancer Cancer therapy Tumour immunology biology
N Nature Cancer · Nov 19, 2025 SMMILe enables accurate spatial quantification in digital pathology using multiple-instance learning Spatial quantification is a critical step in most computational pathology tasks, from guiding pathologists to areas of clinical interest to discovering tissue phenotypes behind novel biomarkers. To circumvent the need for manual annotations, modern computational pathology methods have favored multiple-instance learning approaches that can accurately predict whole-slide image labels, albeit at the expense of losing their spatial awareness. Here we prove mathematically that a model using instance-level aggregation could achieve superior spatial quantification without compromising on whole-slide image prediction performance. We then introduce a superpatch-based measurable multiple-instance learning method, SMMILe, and evaluate it across 6 cancer types, 3 highly diverse classification tasks and 8 datasets involving 3,850 whole-slide images. We benchmark SMMILe against nine existing methods using two different encoders—an ImageNet pretrained and a pathology-specific foundation model—and show that in all cases SMMILe matches or exceeds state-of-the-art whole-slide image classification performance while simultaneously achieving outstanding spatial quantification. Cancer Cancer imaging Computational biology and bioinformatics Tumour biomarkers Tumour heterogeneity
N Nature Cancer · Nov 14, 2025 Characterization of the tumor microbiome of brain metastases and glioblastoma reveals tumor-type-specific and location-specific microbial signatures Brain tumors, including glioblastoma multiforme (GBM) and brain metastases, present a notable clinical challenge. Recent research highlights the presence of intratumor bacteria across many tumor types, yet the microbiome of brain tumors remains largely underexplored. Here we show that the microbiome of 322 brain tumors differs markedly by tumor type and location. Using multiple approaches to visualize, culture and sequence bacterial communities, we found that brain metastases harbor higher bacterial richness and diversity than GBM, with distinct microbial compositions. Moreover, metastases in posterior brain regions exhibited greater diversity than those in anterior regions. Pathway analysis revealed enrichment of bacterial metabolic pathways associated with tumor spread and metastasis in brain metastases while GBM was enriched with pathways supporting alternative phosphorus use. These findings provide valuable insights into the microbial landscape of brain tumors, highlighting tumor-type-specific and location-specific variation and suggesting potential roles for bacteria in brain tumor biology. Cancer Cancer microenvironment CNS cancer Microbiome
N Nature Cancer · Nov 06, 2025 Spatiotemporal control of SMARCA5 by a MAPK–RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration Acute pancreatitis-induced acinar-to-ductal metaplasia involves global chromatin remodeling and contributes to normal tissue regeneration. Oncogenic KRAS hijacks this process to promote PDAC formation. Here we show that regeneration and KRASG12D-driven oncogenesis can be decoupled from tissue regeneration through a chromatin remodeler, SMARCA5. We show that SMARCA5 maintains KRASG12D-dependent chromatin accessibility at regions specifically required for malignancy, without affecting chromatin opening that occurs during normal regeneration. Without SMARCA5, regeneration can be restored in the presence of KRASG12D. Mechanistically, regeneration-related or malignancy-related chromatin remodeling activities occur in a time-sensitive manner. The activity of SMARCA5 is controlled spatiotemporally by transcription factor RUNX1, which only accumulates at sufficient levels with sustained MAPK signals. We further show that inhibition of the SMARCA5-containing NoRC complex specifically inhibits the growth of PDAC organoid but not that of normal tissue derived from patients. Cancer Chromatin remodelling Pancreatic cancer
N Nature Cancer · Nov 01, 2025 Cryoablation plus sintilimab and lenvatinib in advanced or metastatic intrahepatic cholangiocarcinoma: a phase 2 trial Treatment options for advanced or metastatic intrahepatic cholangiocarcinoma (ICC) are limited. In this single-arm, phase 2 trial (CASTLE-01,NCT05010668), 28 participants with advanced or metastatic ICC who have progressed after chemotherapy were treated with cryoablation, followed by anti-PD1 sintilimab (200 mg every 3 weeks) plus lenvatinib (8–12 mg per day) 2 weeks later. The objective response rate assessed by Response Evaluation Criteria in Solid Tumors version 1.1 was 75.0% (95% confidence interval (CI): 59–91%), meeting the prespecified primary endpoint. Secondary endpoints of disease control rate, median progression-free survival and overall survival were respectively 100% (95% CI: 100–100%), 16.8 months (95% CI: 11.5–not reached (NR)) and 25.4 months (95% CI: 13.3–NR). Treatment was well tolerated. Post hoc multiomics analysis of paired pretreatment and on-treatment tumor biopsies suggested that cryoablation increased the tumor immunogenicity and dendritic cell activation, followed by triggering continuous replenishment of intratumoral CD8+PD1hieffectors from peripheral blood. The addition of lenvatinib transitioned endothelial cells into inflamed venules to boost lymphocyte influx and targeted tumor stroma to promote CD8+PD1hieffectors penetrating into tumor cell nests. Therefore, cryoablation combined with sintilimab plus lenvatinib represents a promising approach for the treatment of advanced or metastatic ICC. These findings also support the notion that cryoablation may trigger abscopal antitumor immunity in ICC when combined with lenvatinib and PD1 blockade. ClinicalTrials.gov registration:NCT05010668. Biliary tract cancer Cancer Cancer immunotherapy Gastrointestinal cancer
N Nature Cancer · Oct 27, 2025 SCRN1 confers hepatocellular carcinoma resistance to ferroptosis by stabilizing GPX4 via STK38-mediated phosphorylation Systemic therapy is the optimal choice for individuals with unresectable or advanced hepatocellular carcinoma (HCC). However its effectiveness is constrained by resistance. Ferroptosis is a unique form of regulated cell death and plays an essential role in HCC systemic therapy. Here we identified that secernin-1 (SCRN1) was closely associated with ferroptosis resistance and poor prognosis in HCC. Specifically, high expression of SCRN1 enhances the interaction of phosphokinase serine/threonine kinase 38 (STK38) and glutathione peroxidase 4 (GPX4) to promote the phosphorylation of GPX4 at S45. This phosphorylation impairs heat shock protein family A member 8 (HSC70) recognition and degradation of GPX4 by chaperone-mediated autophagy, which further alleviates lipid peroxidation and ferroptosis. Our findings reveal a critical mechanism by which tumor cells antagonize ferroptosis through enhanced GPX4 phosphorylation and provide potential targets and strategies for HCC treatment. Cancer Cell death Lysosomes Phosphorylation
N Nature Cancer · Oct 23, 2025 MEF2D-expressing cancer precursors reprogram tissue-resident macrophages to support liver tumorigenesis Cancers often originate from precursor cells within an inflamed microenvironment; however, the mechanisms by which these precursors manipulate the niche to promote tumorigenesis remain unclear. By combining single-cell and spatial transcriptomic analyses of precancerous lesions in hepatocellular carcinoma, here we show that elevated myocyte enhancer factor 2D (MEF2D)-expressing cancer precursors reprogram liver-resident macrophages, Kupffer cells (KCs), to create a growth-supportive environment. MEF2D levels induce an oncogenic and secretory phenotype in these precursors by epigenetic reprogramming, which is crucial for tumor initiation in murine models and human samples. This results in a KC-rich niche through paracrine activation of neuropilin 1 (NRP1) signaling on stem-like KC subtype-2 (KC2), driving its differentiation into KC subtype-1 (KC1)-like cells. Pro-inflammatory KC1s release cytokines, particularly IL-6, to enhance an MEF2D-mediated tumor-promoting program in nearby cancer precursors. Targeting NRP1 signaling disrupts the KC2-to-KC1-like differentiation and reduces niche inflammation, thereby inhibiting liver tumorigenesis in male mice. Thus, preventing aberrant KC subtype conversion in the precancerous microenvironment is a viable strategy for early cancer prevention. Cancer Cancer microenvironment Cancer prevention Hepatocellular carcinoma
N Nature Cancer · Oct 23, 2025 Engineering T cells with a membrane-tethered version of SLP-76 overcomes antigen-low resistance to CAR T cell therapy Chimeric antigen receptor (CAR) T cells can mediate durable complete responses in individuals with certain hematologic malignancies, but antigen downregulation is a common mechanism of resistance. Although the native T cell receptor can respond to very low levels of antigen, engineered CARs cannot, likely due to inefficient recruitment of downstream proximal signaling molecules. We developed a platform that endows CAR T cells with the ability to kill antigen-low cancer cells consisting of a membrane-tethered version of the cytosolic signaling adaptor molecule SLP-76 (MT-SLP-76). MT-SLP-76 can be expressed alongside any CAR to lower its activation threshold, overcoming antigen-low escape in multiple xenograft models. Mechanistically, MT-SLP-76 amplifies CAR signaling through recruitment of ITK and PLCγ1. MT-SLP-76 was designed based on biologic principles to render CAR T cell therapies less susceptible to antigen downregulation and is poised for clinical development to overcome this common mechanism of resistance. Majzner and colleagues show that engineering T cells with a membrane-tethered version of the signaling adaptor molecule SLP-76 alongside a chimeric antigen receptor (CAR) enhances CAR T cell activity against low-antigen-density tumors. Cancer Cancer immunotherapy Immunotherapy
N Nature Cancer · Oct 07, 2025 A cellular and spatial atlas ofTP53-associated tissue remodeling defines a multicellular tumor ecosystem in lung adenocarcinoma Tumor protein p53 (TP53) is the most frequently mutated gene across many cancers and is associated with shorter overall survival in lung adenocarcinoma (LUAD). Here, to define howTP53mutations affect the LUAD tumor microenvironment (TME), we constructed a multiomic cellular and spatial atlas of 23 treatment-naive human lung tumors. We found thatTP53-mutant malignant cells lose alveolar identity and upregulate highly proliferative and entropic gene expression programs consistently across LUAD tumors from resectable clinical samples, genetically engineered mouse models, and cell lines harboring a wide spectrum ofTP53mutations. We further identified a multicellular tumor niche composed ofSPP1+macrophages and collagen-expressing fibroblasts that coincides with hypoxic, prometastatic expression programs inTP53-mutant tumors. Spatially correlated angiostatic and immune checkpoint interactions, includingCD274–PDCD1andPVR–TIGIT, are also enriched inTP53-mutant LUAD tumors and likely engender a more favorable response to checkpoint blockade therapy. Our systematic approach can be used to investigate genotype-associated TMEs in other cancers. Cancer Cancer genetics Cancer microenvironment Non-small-cell lung cancer
N Nature Cancer · Oct 03, 2025 Aberrant expression of SLAMF6 constitutes a targetable immune escape mechanism in acute myeloid leukemia Immunotherapy has shown limited success in acute myeloid leukemia (AML), indicating an incomplete understanding of the underlying immunoregulatory mechanisms. Here we identify an immune evasion mechanism present in 60% of AML cases, wherein primitive AML cells aberrantly express the lymphoid surface protein SLAMF6 (signaling lymphocyte activation molecule family member 6). Knockout ofSLAMF6in AML cells enables T cell activation and highly efficient killing of leukemia cells in coculture systems, demonstrating that SLAMF6 protects AML cells from recognition and elimination by the immune system in a mode analogous to the programmed cell death protein–ligand (PDL1/PD1) axis. Targeting SLAMF6 with an antibody against the SLAMF6 dimerization site inhibits the SLAMF6–SLAMF6 interaction and induces T cell activation and killing of AML cells both in vitro and in humanized in vivo models. In conclusion, we show that aberrant expression of SLAMF6 is a common and targetable immune escape mechanism that could pave the way for immunotherapy in AML. Acute myeloid leukaemia Antibody therapy Cancer Tumour immunology
N Nature Cancer · Sep 25, 2025 SMAD4 induces opposite effects on metastatic growth from pancreatic tumors depending on the organ of residence The role of driver gene mutations in sustaining tumor growth at metastatic sites is poorly understood.SMAD4inactivation is a paradigm of such mutations and a hallmark of pancreatic ductal adenocarcinoma (PDAC). To determine whether metastatic tumors are dependent onSMAD4inactivation, we developed a mouse model of PDAC that enables spatiotemporal control ofSmad4expression. WhileSmad4inactivation in the premalignant pancreas facilitated the formation of primary tumors,Smad4reactivation in metastatic disease suppressed liver metastases but promoted lung metastases. These divergent effects were underpinned by organ-biased differences in the tumor cells’ chromatin state that emerged in the premalignant pancreas and were distinguished by the dominance of KLF4 versus RUNX1 transcription factors. Our results show how epigenetic states favored by the organ of residence can influence the output of driver mutations in metastatic tumors, which has implications for interpreting tumor genetics and therapeutically targeting metastatic disease. Cancer Cancer epigenetics Metastasis Pancreatic cancer
N Nature Cancer · Aug 28, 2025 MIRO2-mediated mitochondrial transfer from cancer cells induces cancer-associated fibroblast differentiation Cancer-associated fibroblasts (CAFs) are key components of the tumor microenvironment that commonly support cancer development and progression. Here we show that different cancer cells transfer mitochondria to fibroblasts in cocultures and xenograft tumors, thereby inducing protumorigenic CAF features. Transplantation of functional mitochondria from cancer cells induces metabolic alterations in fibroblasts, expression of CAF markers and release of a protumorigenic secretome and matrisome. These features promote tumor formation in preclinical mouse models. Mechanistically, the mitochondrial transfer requires the mitochondrial trafficking protein MIRO2. Its depletion in cancer cells suppresses mitochondrial transfer and inhibits CAF differentiation and tumor growth. The clinical relevance of these findings is reflected by the overexpression ofMIRO2in tumor cells at the leading edge of epithelial skin cancers. These results identify mitochondrial transfer from cancer cells to fibroblasts as a driver of tumorigenesis and provide a rationale for targeting MIRO2 and mitochondrial transfer in different malignancies. Cancer Cancer microenvironment Organelles
N Nature Cancer · Aug 27, 2025 An MRI–pathology foundation model for noninvasive diagnosis and grading of prostate cancer Shao et al. developed an MRI–pathology-based foundation model to assess the pathology of prostate cancer for diagnosis and grading of tumors. The model is noninvasive and outperforms current pathological assessments.
N Nature Cancer · Aug 21, 2025 Colorectal cancer cells hijack a brain–gut polysynaptic circuit from the lateral septum to enteric neurons to sustain tumor growth The bidirectional interaction between the brain and peripheral tumors is critical but poorly understood. Here we show GABAergic neurons in the lateral septum, a key brain region implicated in emotional regulation, connect via a polysynaptic circuit to enteric cholinergic neurons that send nerve fibers into the tumor microenvironment, which were then hijacked by colorectal cancer cells to sustain tumor growth in mice. Functionally, activation of this septo-enteric circuit induces GABA release from enteric cholinergic neurons, which in turn activates epsilon-subunit-containing GABAAreceptors on tumor cells. Notably, chronic restraint stress potentiates activity within this circuit, exacerbating tumor progression. Clinically, patients with colorectal cancer exhibiting elevated neuronal activity in the septal region present with larger primary tumors. Collectively, our findings uncover a stress-sensitive septo-enteric polysynaptic pathway exploited by cancer cells to promote tumor growth, underscoring the previously unrecognized role of lateral septum-mediated neural circuitry and psychological stress in cancer progression. Cancer Neuroscience Rectal cancer
N Nature Cancer · Aug 21, 2025 A sphingolipid-derived paclitaxel nanovesicle enhances efficacy of combination therapies in triple-negative breast cancer and pancreatic cancer Taxol and Abraxane, the US Food and Drug Administration-approved paclitaxel (PTX) formulations, have revealed hypersensitivity due to excipients and mediocre efficacy due to insufficient tumor penetration, respectively. Here we developed a sphingolipid-derived PTX nanovesicle (paclitaxome) via covalently conjugating PTX to sphingomyelin, which improved pharmacokinetics and enhanced efficacy in metastatic triple-negative breast cancer and pancreatic cancer female mice and reduced myelosuppression. To bolster tumor penetration and reduce phagocytosis, we engineered a cationization-enabled transcytosis machinery by installing an ultra-pH-sensitive azepane (AZE) probe into paclitaxome and masked nanovesicle surface with a CD47 ‘self’ peptide (CD47p). The resulting CD47p/AZE–paclitaxome synchronized the co-delivery of gemcitabine or carboplatin to boost tumor inhibition and eradicate metastasis in late-stage KPC-Luc pancreatic cancer model and prevent tumor relapse and extend survival in postsurgical 4T1-Luc2 triple-negative breast cancer model in female mice. CD47p/AZE–paclitaxome also outperformed previous promising PTX nanoformulations. Finally, the series of nanoparticle modifications was applied to camptothecin, demonstrating its generalizability. Cancer Cancer therapy Drug delivery Nanotechnology in cancer
N Nature Cancer · Aug 19, 2025 Evolutionary trajectories of IDH-mutant astrocytoma identify molecular grading markers related to cell cycling The evolutionary processes that drive malignant progression of IDH-mutant astrocytomas remain unclear. Here, we performed multiomics on matched initial and recurrent tumor samples from a cohort of 105 patients and overlaid the data with detailed clinical annotation. We identified overlapping features associated with malignant progression that are derived from three molecular mechanisms: cell cycling, tumor cell (de)differentiation and remodeling of the extracellular matrix. Together, they provide a rationale of the underlying biology of tumor malignancy. DNA methylation levels decreased over time, predominantly in tumors with malignant transformation, and co-occurred with poor prognostic genetic events. We identified a DNA methylation-based signature strongly associated with survival, which allows objective, molecular-based grading of IDH-mutant astrocytomas to aid clinical decision making. Our findings were validated on large, independent cohorts of IDH-mutant astrocytoma samples. Lastly, in this retrospective study, we found little effect of radiotherapy or chemotherapy on the molecular features associated with malignant progression. Cancer Cancer genomics CNS cancer Tumour heterogeneity
