The tumor microenvironment (TME) actively contributes to pancreatic ductal adenocarcinoma (PDAC) pathogenesis through dynamic bidirectional tumor-stroma interactions. Here, we demonstrated that ATM-deficient tumor epithelium reprograms the TME in a genotype-specific manner to enhance cancer aggressiveness. In genetically engineered mouse models, pancreatic stellate cell (PSC) and cancer-associated fibroblast (CAF) co-culture systems, single-nucleus multiomics, and human PDAC models, tumoral loss of ATM serine/threonine kinase drove CAFs toward αSMA+ myofibroblastic (myCAF) differentiation, independently of p53 status. The myCAFs, in turn, promoted cancer aggressiveness and chemoresistance. Mechanistically, ATM deficiency increased reactive oxygen species and contractility signaling, enhancing TGF-β1 secretion. Pharmacological TGF-β inhibition reversed myCAF differentiation, sensitized tumors to chemotherapy, and impaired tumor progression in both murine and human ATM-null models. These findings reveal that ATM-deficient tumors shape a cancer-promoting niche via TGF-β signaling and identify dual targeting of intrinsic and extrinsic vulnerabilities as a promising precision oncology strategy.

Despite the availability of RAS inhibitors and the dependence of >90% of pancreatic ductal adenocarcinomas (PDAC) on oncogenic KRAS mutations, resistance to KRAS inhibition remains a serious obstacle. We showed here that PI3K plays a major role in this resistance through upstream activation of wild-type RAS signaling - beyond its known KRAS effector function. The combination of proximity labeling, CRISPR screening, live-cell imaging, and functional assays revealed that PI3K orchestrates phosphoinositide-mediated GAB1 recruitment to the plasma membrane, nucleating assembly of RAS signaling complexes that activate MAPK in an EGFR/SHP2/SOS1-dependent manner. Inhibiting PI3K enhanced sensitivity to mutant-specific KRAS inhibitors in PDAC cells, including in cells with clinically identified PIK3CA mutations. These findings refine RAS-PI3K signaling paradigms, reveal that PI3K-driven wild-type RAS activation drives resistance to KRAS inhibition, and illuminate avenues for augmenting KRAS-targeted therapies in PDAC.

Arginine biosynthesis is frequently suppressed in cancer due to loss of ASS1 expression, rendering cancer cells reliant on extracellular arginine. This feature has driven the development of systemic arginine-depleting strategies, which are clinically safe but offer limited clinical benefit. Here, we demonstrated that under arginine scarcity, cancer cells with low ASS1 expression resort to aberrant mRNA translation, characterized by ribosomal frameshifts and amino acid misincorporations. While aberrant proteins originated from most arginine codons, the predominant effect was observed at AGA. This codon preference was caused by a selective decrease in tRNAArg(UCU) levels following arginine deprivation, linked to METTL1-mediated tRNA modification. Proteomics and immunopeptidomics analyses validated that arginine shortage induced aberrant protein production at the endogenous level. T cell receptor (TCR) T cells that specifically recognize these HLA-presented mistranslated peptides efficiently killed cancer cells after arginine deprivation. These results lay the foundation for improved cancer therapies by combining systemic arginine-depleting strategies with TCR-based targeting of non-classical neoantigens.

Emerging evidence implicates human endogenous retroviruses (HERVs) in cellular senescence and stemness suppression, suggesting that they may also play a role in tumor cell senescence. In this study, we identified the histone methyltransferase DOT1L as a key epigenetic repressor of HERV-K in adenocarcinoma of the esophagogastric junction (AEG). Comparison of expression of HERV and epigenetic regulators in AEG using two independent datasets revealed an inverse correlation between DOT1L and HERVs, and DOT1L was also overexpressed in AEG and correlated with poor clinical prognosis. Pharmacological inhibition of DOT1L in vitro and in vivo diminished H3K79 methylation, reactivated HERV-K expression, and triggered STING-dependent innate immune signaling, thereby inducing tumor cell senescence and conferring potent antitumor effects. By promoting the assembly and secretion of HERV-K-derived retrovirus-like particles (RVLPs), DOT1L inhibition propagated senescence to neighboring tumor cells via STING pathway activation. Together, this study not only establishes DOT1L as a druggable epigenetic target in AEG but also proposes a therapeutic strategy that leverages HERV-K and RVLPs to drive tumor cell senescence and intercellular senescence transmission for antitumor therapy.

Analysis of tumors using single-cell and spatial modalities is critical to advance our understanding of cancer. The growth of technologies that enable these studies provides an increasing number of single cell datasets. Integrating such data across studies will increase the impact of individual studies and speed cancer research. Most existing integration approaches are tailored to transcriptomic data and assume large sets of shared features, an assumption that fails for lower-dimensional proteomic measurements. Here, we developed CellFuse, a deep learning-based integration framework that unifies antibody-based proteomic datasets including high-dimensional cytometry, CITE-seq, and spatial proteomics data. Leveraging supervised contrastive learning, CellFuse learned a shared embedding space that enabled accurate cross-modality cell type prediction and robust label transfer across tumor samples and experimental conditions. Applied to datasets spanning peripheral blood, bone marrow, and lymphoma, CellFuse consistently outperformed existing approaches in recovering clinically relevant populations, including rare malignant and immune subsets. In solid tumors, it reconstructed spatially resolved microenvironments, capturing interactions between malignant, stromal, and immune cells that correlated with treatment response. By enabling scalable, modality-agnostic integration, CellFuse provides a powerful tool to uncover prognostic cell states and delineate the architecture of the tumor-immune ecosystem with translational relevance, driving cancer discoveries.

Pancreatic ductal adenocarcinoma (PDAC) carries an extremely poor prognosis, in part resulting from cellular heterogeneity that supports overall tumorigenicity. Cancer-associated fibroblasts (CAF) are key determinants of PDAC biology and response to systemic therapy, and multiple CAF subtypes have been defined. However, defining the effects of patient-specific CAF heterogeneity and plasticity on tumor cell behavior is required to better characterize the role of CAFs in PDAC. Here, we used multi-omic analyses to characterize the tumor microenvironment (TME) in tumors from patients undergoing curative-intent surgery for PDAC. In these same patients, matched tumor organoid and CAF lines were established to functionally validate the impact of CAFs on the tumor cells. CAFs promoted epithelial-mesenchymal transition (EMT) and a switch in tumor cell classification from classical to basal subtype. Furthermore, CAF-specific interleukin 8 (IL-8) functioned as a modulator of tumor cell subtype. Finally, neighborhood relationships between tumor cells and T cell subsets were defined, demonstrating a distinct spatial coordination among CAF and tumor cell subtypes. Overall, this study provides data supporting CAF signaling as a regulator of the cellular and behavioral heterogeneity in the PDAC TME. These findings can be used to explore rational approaches to improve therapies for this difficult-to-treat disease.

Androgen receptor engenders a sex-biased tumor microenvironment in head and neck cancer by suppressing CD8+ T-cell function, which can be overcome with androgen deprivation therapy to delay tumor progression.

CCL5 hiCD4+ T cells with memory-like activated characteristics enhance antitumor immunity in bladder cancer by reprogramming macrophages, supporting the potential of these cells as biomarkers and targets to enhance immunotherapy efficacy.

The N-terminal domain of VGF is required for sustaining mitochondrial fusion and oxidative phosphorylation to support metabolic adaptation in lung cancer brain metastases, underscoring a potentially targetable mechanism to impair brain colonization.

KO-2806 salvages RAS inhibitor activity by controlling parallel mTORC1 in RAS inhibitor-resistant tumors in which vertical inhibition of MAPK is insufficient to restore sensitivity, providing a combination strategy for resistant patients.