Molecular Cancer Research

PurposeSWI/SNF (BAF) chromatin remodeling complex alterations are common in urothelial carcinoma, yet no biomarker-directed therapeutic strategies have been established for this population. We investigated whether BAF alterations delineate a biologically distinct, therapeutically actionable urothelial carcinoma subtype. Experimental DesignWe performed integrative genomic and transcriptomic analyses of 792 urothelial carcinoma tumors from the Oncology Research Information Exchange Network (ORIEN) and validated findings in the TCGA-BLCA cohort. Mechanistic studies incorporated RNA sequencing and ATAC-seq following histone deacetylase (HDAC) inhibition. Functional dependencies were assessed using patient-derived xenograft organoids and cell line models. Clinical relevance was explored in a biomarker-enriched investigator-initiated trial. ResultsApproximately half of urothelial carcinoma tumors exhibited BAF alterations, defining a previously unrecognized chromatin-altered molecular subtype characterized by activation of proliferative programs, loss of lineage identity, and altered metabolic signaling. This subtype was enriched for transcriptomic programs associated with HDAC inhibitor sensitivity and depleted of HDAC inhibitor resistance signatures. Mechanistically, HDAC inhibition induced widespread chromatin remodeling with reduced accessibility at AP-1 and TEAD-associated regions, and downregulation of E2F- and MYC-driven transcriptional networks. Functional studies confirmed enhanced HDAC inhibition sensitivity in ARID1A-mutated cell lines and a patient-derived organoid model. Early clinical observations demonstrated a durable responder treated with HDAC inhibitors and immunotherapy. ConclusionsBAF alterations define a chromatin-dependent tumor state in urothelial carcinoma that is selectively vulnerable to HDAC inhibition. Integrating genomic, epigenomic, functional, and early clinical evidence, these findings provide a rationale for biomarker-enriched clinical trials and HDAC inhibitor-based combination strategies in urothelial carcinoma.

AbstractNeuroendocrine prostate cancer (NEPC) is a highly aggressive and therapy-resistant subtype that arises from adenocarcinoma through lineage plasticity; however, the molecular mechanisms driving this transition remain incompletely defined. Insulinoma-associated protein 1 (INSM1), a zinc-finger transcription factor and established neuroendocrine lineage marker, has been implicated in a variety of neuroendocrine malignancies, yet its functional contribution to NEPC progression is not well understood. In this study, we demonstrate that INSM1 is consistently upregulated across NEPC patient tumors and experimental models, including both ASCL1 and NEUROD1 molecular subtypes, as revealed by integrated bulk and single-cell transcriptomic analyses. Functional studies revealed that INSM1 is sufficient to induce and necessary to maintain neuroendocrine lineage programs in prostate cancer, as overexpression promoted and depletion suppressed neuroendocrine-associated transcriptional networks. Mechanistically, pro-neural transcription factors, including ASCL1, NEUROD1, NEUROG3, and MYCN, directly or indirectly activate INSM1 expression, positioning it as a critical downstream effector of neuroendocrine lineage specification. Therapeutically, we identify homo-harringtonine (HHT), an FDA-approved protein synthesis inhibitor, as a potent suppressor of INSM1. HHT selectively reduces viability of INSM1-high NEPC cells at nanomolar concentrations, promotes ubiquitin-mediated degradation of INSM1, and significantly inhibits tumor growth in vivo. Notably, INSM1 depletion further enhances cellular sensitivity to HHT treatment. Collectively, our findings establish INSM1 as a key regulator of neuroendocrine plasticity and a promising therapeutic vulnerability in NEPC, providing a rationale for targeting INSM1 to suppress tumor progression.

Metastatic prostate cancer (PCa) continues to be a major cause of death in males, despite advances in treatment. Most treatment focuses on targeting the Androgen Receptor (AR), the main oncogene responsible for driving most prostate tumors. Despite these therapies targeting AR, the majority of patients still succumb to AR-driven disease. Therefore, there is a critical need for understanding how AR functions to promote prostate cancer growth and identify alternative therapeutic targets in AR-driven PCa. One avenue garnering attention is targeting epigenetic regulators that promote AR-activity; however, the importance of epitranscriptomic regulators, like those that modify mRNAs, is not well understood. Here, we identify a new role for the key catalytic subunit of the RNA N6-methyladenosine (m6A) transferase complex, METTL3, as an AR-coregulator. METTL3 is overexpressed in prostate tumors compared to normal tissue, and METTL3 protein is elevated in AR-expressing cell lines. Depletion of METTL3 significantly reduces proliferation of cancer cells and has no effect on the growth of non-transformed prostate epithelial cells, despite decreasing global m6A levels on mRNA. The catalytic activity of METTL3 is dispensable for the growth of both non-transformed and PCa cell lines, as pharmacologic inhibition of METTL3 does not inhibit proliferation, despite the reduction of global m6A on mRNA. Overexpression of both wild-type and catalytically inactive METTL3 mutants enhances cell viability and rescues cells in which METTL3 is knocked down. Finally, we report on direct interaction between AR and METTL3, their co-localization on chromatin, and reduced AR-cistromic occupancy within cells with METTL3 knockdown. Together, these findings identify a non-enzymatic role for METTL3 in supporting AR-driven transcriptional programs and PCa proliferation.

Merkel cell carcinoma (MCC) is a neuroendocrine skin tumor that is frequently driven by integration of Merkel cell polyomavirus (MCPyV). In MCC, the MCPyV genome is truncated, but expression of the viral tumor antigens, truncated large tumor antigen (LTT) and small tumor antigen (sT), is maintained and drives uncontrolled proliferation. We introduced constitutive expression of the MCPyV T antigens (TAs) into primary mouse dermal fibroblasts (MDFs) to determine whether these cells are susceptible to MCPyV-driven transformation. TA expression alone in MDFs induced key MCC markers, cytokeratin-20 (CK20) and Sry-box transcription factor 2 (SOX2), and promoted anchorage-independent growth indicative of cellular transformation. Subcutaneous implantation of TA-transformed fibroblasts produced high-grade MCC-like tumors that grew persistently in immunodeficient NSG mice but not in immunocompetent C57BL/6 mice. Serial in vivo passaging of the tumor cell line enhanced tumor growth, reduced expression of p53-target genes and MHC-1, and was accompanied by a shift in T antigen isoform expression, with decreased LTT and increased sT expression. Our data demonstrate that MCPyV-driven tumors acquire immune-evasive adaptions during tumor progression in vivo and suggest that the anti-tumor immune response exerts selective pressure in MCC that favors expression of sT rather than LTT. The model established in this study provides a unique platform for studying evolution of MCPyV-driven tumors under immune pressure and identifying mechanisms of immune evasion in MCC that could be used to develop new therapeutic strategies. Significance StatementMCPyV tumor antigen expression transforms mouse dermal fibroblasts to generate MCC-like tumors. Serial in vivo passaging reveals tumor evolution under immune pressure, providing a model to study immune evasion mechanisms in MCC.

Dysregulation of actin-binding protein Profilin1 (Pfn1) in tumor cells has prominent impacts on the tumor-intrinsic aspects of tumor progression. However, whether and how modulation of Pfn1 expression in tumor cells influences immune surveillance in cancer is not known. We utilized an inducible CRISPR/Cas9 knockout (KO) model to first demonstrate that triggering Pfn1 depletion in breast cancer cells leads to features of genomic instability (polyploidy, micronuclei, and DNA damage) and intrinsic defects in both homologous-recombination- and non-homologous end-joining-mediated double-stranded DNA repair. Pfn1-deficient breast cancer cells exhibit nuclear envelope abnormality and the accumulation of cytosolic DNA. This leads to activation of the nucleic acid-sensing cGAS-STING pathway and the type-I interferon (IFN) response including STING-mediated upregulation of pro-inflammatory chemokines. In an immunocompetent mouse model of breast cancer, triggering Pfn1 loss selectively in tumor cells promotes an immunogenic tumor microenvironment marked by a striking increase in intratumoral presence of CD8 T cells, leading to a robust tumor regression. Pfn1 knockout-induced tumor regression requires an intact immune system and can also be reversed by CD8+ T cell depletion. Based on these findings, we conclude that Pfn1 loss in tumor cells leverages a type I IFN response to drive a T-cell-mediated anti-tumor response in breast cancer. These findings for the first time reveal promising therapeutic opportunities in targeting Pfn1-driven pathways to enhance immunotherapeutic outcomes in breast cancer. Significance StatementExpression of actin-binding protein Profilin-1 is frequently altered in cancer; yet how these changes impact the immune response against tumors is unclear. Here we show that triggering Profilin-1 depletion in breast cancer cells promotes features of genomic instability, defects in DNA repair, and cytosolic release of DNA. This activates the cGAS-STING pathway, triggering a type I interferon response and immune-cell-attracting signals that drive a CD8+ T cell-mediated anti-tumor immune response and tumor regression in vivo. Therefore, Profilin-1 could be a novel actionable target for achieving immunological benefit in breast cancer. On a broader level, our studies establish a conceptual framework of how dysregulation of actin cytoskeletal proteins can harness nuclear damage-sensing signaling to augment anti-tumor immune response in cancer.

IDH1 R132 mutations are among the most frequent hotspot mutations in cancer, but their mutational origins have remained unclear. Here, we provide evidence that IDH1 R132C, the predominant IDH1 mutation in cholangiocarcinoma, acute myeloid leukemia, and melanoma, likely arises through APOBEC3-mediated mutagenesis. IDH1 R132C is a TpC>TpT substitution on the lagging-strand DNA template within a hairpin-forming sequence context, consistent with APOBEC3 susceptibility. In vitro assays showed that APOBEC3A can deaminate the relevant cytosine, and APOBEC3A and APOBEC3B were relatively highly expressed in tumor types with recurrent IDH1 R132C mutations. IDH1 R132G, a TpC>TpG substitution at the same site, may similarly result from APOBEC3 activity. By contrast, IDH1 R132H, the predominant IDH1 mutation in lower grade glioma and glioblastoma, is a CpG>TpG substitution at a methylated cytosine on the leading-strand DNA template, a pattern more consistent with DNA polymerase epsilon replication error. Concordantly, tumor types enriched for IDH1 R132H showed relatively low POLE expression. Together, these in vitro and bioinformatic analyses provide insight into the distinct mutational mechanisms that likely underlie recurrent IDH1 hotspot mutations in cancer.

Treatment-emergent neuroendocrine prostate cancer (NEPC) is an aggressive, therapy-resistant disease arising in up to 20% of castration resistant prostate cancers, yet robust biologically relevant preclinical models remain scarce. Here, we describe a technical blueprint for establishing an integrated platform of patient-derived models from visceral and bone metastases collected through a prostate cancer rapid autopsy program (PC RAP). We report the establishment and characterization of patient-derived xenograft (PDX) models from liver metastasis tissue, liver and bone metastasis-derived organoid lines (PDOs), and corresponding patient-derived organoid xenograft (PDOX) models. In addition, we established, to our knowledge, the first mesenchymal stem cell (MSC) cultures derived from neuroendocrine prostate cancer (NEPC) bone metastases. The PDOs preserved intratumoral heterogeneity, displaying both CRPC-NE and CRPC-adenocarcinoma features. These organoids retained neuroendocrine identity across multiple passages, with transcriptomic profiles concordant with the original patient tissue and matched PDX models generated at our institution and at the National Cancer Institute (NCI Patient-Derived Models Repository). To model the bone metastatic microenvironment, we generated novel organoid-based New Approach Methodologies (NAMs) by co-culturing PDOs with iPSC-derived bone marrow organoids, establishing a physiologically relevant vascularized organotypic model of PC bone metastasis. To extend our studies in vivo, we established preclinical models using the liver and bone metastasis-derived organoid models. The PDOX models were tumorigenic and developed spontaneous lymph node metastases, providing clinically relevant models for investigating lethal NEPC biology. Together, these complementary patient-derived models provide a robust and versatile platform for investigating NEPC biology, metastatic progression, and evaluating new therapeutic strategies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/740121v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@a4b747org.highwire.dtl.DTLVardef@1fcb778org.highwire.dtl.DTLVardef@7167e6org.highwire.dtl.DTLVardef@15c5b6d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINovel preclinical models of visceral and bone metastases established from a prostate cancer rapid autopsy program. C_LIO_LIThis study is the first to establish mesenchymal stem cell cultures from NEPC bone metastases. C_LIO_LIPDOs preserve heterogeneity, showing both CRPC-NE and CRPC-Adeno features, with transcriptomic profiles concordant with originator tissue and PDX models. C_LIO_LIPC RAP-derived organoids are tumorigenic in vivo and generate spontaneous lymph node metastases. C_LI

The expression and secretion of sulfated colonic-type mucins is a feature of high-risk metaplasias of the gastrointestinal foregut (Barretts esophagus, type III intestinal metaplasia of the stomach, and pancreatic intraepithelial neoplasia). Galectin-3 is a lectin that preferentially associates with galactose modified by a 3-O-sulfate relative to its unmodified counterparts and is upregulated as the tissue transitions to high-risk metaplasia, dysplasia, and cancer. Since both galectin-3 and sulfated glycotopes are aberrantly and concurrently overexpressed in high-risk premalignant and malignant tissue transformations, we sought to investigate the role of galectin-3 in the metaplastic reaction. We found that injury induces the expression of Lgals3 at the RNA and protein levels. Unlike cancer cell lines, we show that in vivo galectin-3 colocalized with sulfomucins in zymogenic granules of the gastric chief cell. Utilizing a synchronous, chemically-induced murine model that produces spasmolytic polypeptide expressing metaplasia, we found that galectin-3 facilitates cathartocytosis of the vesicles it resides in, but not organelles lacking LGALS3. Inhibition of cellular downscaling resulted in delayed expression of the metaplastic transcription factor Sox9 as well as proliferation. Here, we present a new role for galectin-3 in promoting the transition from normal, homeostatic tissue to metaplasia and our data suggest that cathartocytosis represents an unconventional secretory pathway for galectin-3, which has been a matter of controversy as galectins are not secreted via canonical pathways.

Understanding which genes are involved in mutagenesis is essential for developing cancer prevention and treatment strategies; establishing protectors of the genome has revolutionized cancer biology. Here, we describe metallothionein (MT) proteins as previously uncharacterized protectors against mutagenesis. MT is a heavy metal binding protein essential for zinc homeostasis and protection against heavy metal cytotoxicity. Because zinc binds approximately 10-15% of the proteome and is critical for processes such as DNA repair and mitochondrial health, MT loss is expected to disrupt these processes. We hypothesized that MT loss induces genomic instability by impairing DNA repair and mitochondrial function. In this study, the consequences of MT deficiency in high-grade serous ovarian cancer (HGSC) were investigated by knockdown of the most highly expressed MT, MT2A. Loss of MT2A resulted in the impaired DNA repair pathway base excision repair (BER), leading to increased mutagenesis. MT2A deficiency produced mitochondrial dysfunction, characterized by a decrease in mitochondrial membrane potential, glycolysis, oxidative phosphorylation, amino acids, and an imbalance of nucleobases. Together, these defects reflect cellular states associated with increased cancer aggressiveness. These findings identify MT as a fundamental hub maintaining genomic and metabolic integrity.

Multiple myeloma (MM) is a plasma cell malignancy that frequently harbors activating mutations in NRAS and KRAS oncogenes. Previous clinical trials targeting the Ras/MAPK oncogenic pathway with MEK inhibitors (MEKi) were met with limited efficacy, and newer generation of Ras inhibitors (RASi) have not been specifically evaluated in MM patients. To investigate the vulnerabilities of Ras-mutant MM to targeted therapies, we examined the sensitivity of a panel of human MM cell lines to the RASi RMC-6236 (daraxonrasib) and the MEKi trametinib. Although Ras-mutant MM cells are responsive to oncogenic Ras signaling and are sensitive to RAS inhibition, their sensitivity to MEK inhibition is heterogeneous. Mechanistic studies revealed that c-Myc protein is destabilized by MEK inhibition only in MEKi-sensitive MM cells but not in MEKi-resistant cells, and pharmacological and genetic stabilization of c-Myc is sufficient to confer MEKi resistance. In contrast, Ras inhibition reduced c-Myc protein across all MM cell lines tested, regardless of their dependency on the MAPK pathway, and c-Myc expression was insufficient to promote RASi resistance. Together, these findings demonstrate that c-Myc protein stability differentiates the response of Ras-mutant MM cells to Ras and MEK inhibition, and suggest that direct targeting of the Ras oncoprotein, rather than its downstream MAPK pathway, may present a more effective strategy.

Internal-tandem-duplication of the receptor tyrosine kinase FLT3 (FLT3-ITD) generates ligand-independent signaling and is highly recurrent in acute myeloid leukemias (AMLs). One way signaling pathways can quickly influence cell fates is by phosphorylating key fate-determining proteins to trigger their proteolysis. We investigated the master transcription factor (MTF) driver of granulo-monocytic lineage-fates, CEBPA, for regulation by this mechanism because we found high CEBPA mRNA but little CEBPA protein in FLT3-ITD versus FLT3-wildtype AML cells, and inhibiting FLT3-ITD signaling with tyrosine kinase inhibitors (TKI) rapidly rescued CEBPA protein. Mass spectrometry analyses of CEBPA and its interactome demonstrated prominent interactions with major ubiquitin-proteosome pathway (UPP) components UHRF1 and USP7. TKI treatments decreased CEBPA and USP7 phosphorylations at serine 21 and serine 18 respectively alongside shifts in CEBPA interactions from degradative ubiquitin-ligase UHRF1 toward protective deubiquitinase USP7. The rescued CEBPA activated granulocytic-differentiation. Supporting that the serine-phosphorylations were phospho-degrons, UPP-inhibitors (bortezomib, MG132) increased phosphorylated and total CEBPA and USP7. The MTF regulator of apoptosis p53 is a known USP7 client, therefore, we also evaluated p53 status: TKIs and UPP-inhibitors stabilized USP7 and p53, triggering apoptosis in addition to granulocytic-differentiation specifically in FLT3-ITD but not FLT3-wildtype AML cells. UPP-inhibitors produced these consequences in TKI-resistant FLT3-ITD AML cells also. These data predicted genetic loss-of-function to CEBPA or TP53 is redundant in the FLT3-ITD context, borne out by mutual exclusivity of the mutations in clinical series. In summary, FLT3-ITD signals for CEBPA and p53 proteolysis to block lineage-maturation and apoptosis, positioning UPP-inhibitors as therapeutic candidates acting downstream of TKIs. KEY POINTSO_LIThe oncoprotein kinase FLT3-ITD signals for CEBPA and p53 proteolysis and hence suppresses lineage-differentiation and apoptosis C_LIO_LIProteosome-inhibitors are candidate remedies to restore CEBPA and p53, acting downstream of presently used FLT3-ITD kinase inhibitors C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/738455v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@6ae211org.highwire.dtl.DTLVardef@12003bforg.highwire.dtl.DTLVardef@d62eb9org.highwire.dtl.DTLVardef@1958693_HPS_FORMAT_FIGEXP M_FIG C_FIG

Lung adenocarcinoma a progress from preinvasive lesions to invasive cancer; however, early evolutionary events in adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) remain poorly defined, particularly in East Asian populations enriched for EGFR mutations. We performed whole-exome sequencing on 67 Japanese patients (38 AIS, 29 MIA), including multiregion sampling in 13 cases to identify EGFR as predominant driver (61.2%), followed by RBM10 (19.4%) and TP53 (9.0%). Two evolutionary trajectories emerged: age-related and smoking-driven pathways. In the former, EGFR-mutant tumors frequently exhibited early whole-genome doubling (WGD) (24.4%) with clock-like signature. The smoking-driven pathway, typically involving KRAS mutations, displayed a tobacco-associated signature. Multiregion sequencing revealed that driver mutations (EGFR, KRAS, and MET) were shared trunk events across in situ and invasive regions, while secondary alterations arose subclonally. This study defines the genomic evolution of early lung adenocarcinoma in Japanese patients, identifying two evolutionary trajectories: an age-related pathway with EGFR-linked genome doubling and a smoking-driven pathway involving KRAS mutations. These findings elucidate mechanisms underlying progression from preinvasive lesions to invasive cancer in Asian populations.

Metastasis is the leading cause of death in breast cancer, yet the mechanisms controlling organotropism are not well defined. Coagulation has emerged as a biologically relevant contributor to metastatic progression, but mechanisms linking pro-thrombotic phenotypes to organ-specific metastasis remain unresolved, significantly hindering the development of novel treatments. Here, a serial transplantation approach was used to enrich for liver organotropism from a spontaneous mouse mammary tumor model with occasional liver and lymph node metastasis. Comparative transcriptomics between the enriched liver and lymph node metastases revealed strong upregulation of coagulation in liver metastases, due in part to loss of repression of FXII with knockout of the E2F5 transcription factor. In vitro clotting assays demonstrated that tumor-derived FXII was sufficient to induce fibrin(ogen) clot formation. Moreover, liver metastatic cells exhibit elevated lipid peroxide levels and impaired lipid droplet formation associated with a pro-coagulant phenotype. Inhibition of coagulation with low molecular weight heparin reduced the presence of circulating tumor cells and suppressed liver metastasis in the mouse model. Human electronic health record data supported the translational relevance of these findings. Together, these data reveal a new mouse model where loss of E2F5 has resulted in tumors with elevated expression of FXII that have a propensity for liver metastasis and illustrates that anti-coagulation dramatically reduces the liver-specific metastasis in breast cancer. HighlightsE2F5 conditional knockout model develops breast tumors with liver tropism Liver metastasis hijacks the intrinsic coagulation cascade mediated by tumor-derived FXII Liver metastatic cells displayed lipid metabolic alterations that contributed to a pro-coagulant phenotype Low molecular weight heparin blocks liver metastasis and significantly reduces circulating tumor cells

While recent research has increasingly focused on the role of fibroblasts and macrophages in osteosarcoma, the tumor vasculature remains poorly understood, particularly in metastatic disease. To address this gap, we performed single-nuclei multi-ome (RNA+ATAC) sequencing on 24 human metastatic osteosarcoma specimens. We found that endothelial cells adopt a hybrid endothelial-mesenchymal state resembling endothelial-to-mesenchymal transition (EndMT) and that a subset of diploid endothelial cells expresses osteoblastic transcriptional profiles and gene regulatory networks (GRN). Joint copy-number analysis further identified osteosarcoma cells with endothelial transcriptional programs and GRNs, consistent with vascular mimicry. In vitro assays and syngeneic lineage-tracing experiments validated that tumor educated endothelial cells acquire osteoblast-like features. Together, these findings reveal substantial plasticity among endothelial and osteosarcoma cells in human and murine metastatic osteosarcoma, provide new insight into the how the metastatic microenvironment shapes the tumor vasculature, and challenge current models of osteosarcoma biology.

Osteosarcoma (OS) and Ewing sarcoma (EWS) are the most common malignant bone tumors in children and adolescents, with survival rates around 25% in metastatic disease and few advances in treatment in decades. High DDX3 expression has been reported across various sarcoma subtypes. Depending on the context, DDX3 appears to have opposing roles in regulating the tumor immune microenvironment. Within macrophages, DDX3 promotes inflammatory cytokine expression and supports immune cell function. In contrast, in tumor cells DDX3 suppresses a pro-inflammatory state by unwinding dsRNAs, preventing a Type I interferon response. We show that inhibiting DDX3 with RK-33 leads to dsRNA accumulation, inducing a Type I interferon response and broader inflammatory gene expression changes across multiple sarcoma models, shifting macrophage polarization toward a pro-inflammatory M1-like phenotype. To evaluate whether this innate immune microenvironmental remodeling could translate into clinical benefit, we assessed the therapeutic efficacy of RK-33 alone or in combination with mifamurtide, an immunostimulant, in immune competent mouse models of osteosarcoma, with metastatic burden as the primary outcome. We found that in the absence of MYC over-expression, the combination treatment significantly reduced metastatic spread. These findings support targeting DDX3 as a novel innate immune based therapeutic strategy and highlight that the tumors molecular landscape critically influences therapeutic responsiveness.

Prostate cancer is a leading cause of cancer-related mortality in men, and effective treatment options are limited for advanced and metastatic disease. The sialoglycan immune checkpoint Siglec-15 has emerged as a key mediator of tumour-associated immune suppression in several malignancies; however, its expression and functional role in prostate cancer remain poorly defined. Here, using dual immunofluorescence and immunohistochemistry, we demonstrate that Siglec-15 is expressed by prostate tumour epithelial cells, immunosuppressive macrophage phenotypes, and bone-resorbing osteoclasts within the tumour microenvironment. Mechanistically, we show that direct Siglec-15 receptor crosslinking, either by antibodies or tumour cell-derived conditioned medium, promotes monocyte-to-macrophage differentiation, generating macrophages with immunosuppressive and pathogenic phenotypes. Using therapeutic antibodies, we show that Siglec-15 blockade suppresses supernatant-induced monocyte to macrophage differentiation, allowing for the recovery of CD8 T-cell activation. Furthermore, we reveal that macrophage colony-stimulating factor (M-CSF) driven monocyte-derived macrophage differentiation is partially dependent on Siglec-15 signalling, with Siglec-15 blockade enhancing CD8 T-cell responses. In addition, anti-Siglec-15 treatment suppressed osteoclast differentiation, highlighting a dual role for Siglec-15 in prostate cancer immune suppression and bone remodelling. Consistent with these in vitro findings, therapeutic Siglec-15 blockade significantly reduced subcutaneous tumour growth in a CD8 T-cell-dependent manner and prolonged survival in a mouse model of prostate cancer metastasis. Together, these findings identify Siglec-15 as a central regulator of the prostate cancer glyco-immune axis, linking tumour-associated macrophage immune suppression with osteoclast-mediated bone remodelling, providing a compelling rationale for the clinical development of Siglec-15-targeted therapies for patients with advanced disease.

High-grade serous ovarian carcinoma (HGSOC) is characterized by widespread peritoneal dissemination and poor long-term survival, largely driven by metastatic relapse following initial response to chemotherapy. Defining the molecular programs that enable tumor progression from the primary ovarian site to metastatic niches remains a key challenge. Here, we leverage patient-derived organoids (PDOs) coupled with single-cell RNA sequencing (scRNA-seq) to interrogate tumor evolution and identify regulators of metastatic competence in HGSOC. We profiled PDOs and matched formalin-fixed paraffin-embedded (FFPE) tumor samples from ovarian and omental disease sites across seven patients. Single-cell transcriptomic analysis revealed conserved and patient-specific cellular states and enabled reconstruction of inferred trajectories of tumor progression. Comparative trajectory analysis identified gene expression programs associated with metastatic transition from ovarian to omental tumors. Among these, the heparan sulfate proteoglycan AGRIN emerged as a consistently upregulated gene along the metastatic axis. Cell-cell communication analyses suggested that AGRIN-mediated signaling involves both epithelial tumor cells and stromal components, implicating the extracellular matrix in shaping metastatic behavior through mechanotransduction and integrin-associated pathways. Functional validation using genetic depletion of AGRIN in ovarian cancer cell lines demonstrated reduced migratory and invasive capacity, supporting a causal role for AGRIN in promoting metastatic phenotypes. Together, these findings identify AGRIN as a regulator of metastatic competence in HGSOC and highlight extracellular matrix-associated signaling as a key driver of disease progression. More broadly, this study demonstrates that PDO-based single-cell transcriptomic approaches can uncover actionable regulators of metastasis and provide a scalable framework for therapeutic target discovery across cancer types. SignificancePatient-derived organoids analyzed by single-cell transcriptomics reveal dynamic tumor evolution and uncover AGRIN as a regulator of metastatic competence in HGSOC, demonstrating the utility of living tumor models for therapeutic target discovery.

BackgroundApurinic/apyrimidinic endonuclease 1/redox factor-1 (Ref-1/APE1) is a central regulator of redox-dependent transcriptional signaling that promotes pancreatic ductal adenocarcinoma (PDAC) progression, therapeutic resistance, and metabolic adaptation. While pharmacologic inhibition of Ref-1 suppresses tumor growth and alters cellular metabolism, immediate molecular events linking Ref-1 inhibition to downstream cellular adaptation remain poorly understood. We therefore sought to characterize proteome-wide signaling responses induced by second-generation Ref-1 redox inhibitor, APX2014. MethodsWe applied an integrated multiplexed proteomics workflow to simultaneously quantify global protein abundance together with cysteine oxidation, phosphorylation, and lysine acetylation in Pa03C PDAC cells following acute treatment (30-120 min) with selective Ref-1 redox inhibitor APX2014. Differential post-translational modification (PTM) analysis, pathway enrichment, structural mapping of regulated sites, and functional mitochondrial substrate utilization assays were performed to define early signaling responses. ResultsAPX2014 induced rapid and extensive remodeling of PTM landscape while producing minimal changes in global protein abundance. Cysteine oxidation represented the earliest and most sustained response, accompanied by widespread phosphorylation and delayed lysine acetylation. Integrated pathway analyses identified mitochondrial translation, respiratory electron transport, TCA cycle metabolism, and mitochondrial redox homeostasis as the earliest and most consistently regulated processes. Functional mitochondrial assays confirmed impaired utilization of TCA cycle substrates following APX2014 treatment. Coordinated PTM remodeling was observed on Ref-1-associated signaling proteins, including NF-{kappa}B1 and p53, revealing simultaneous regulation of oxidation, phosphorylation, and acetylation within functionally important domains. Early redox-sensitive protein networks were also associated with subsequent disruption of mitotic organization. ConclusionsIntegrated multi-PTM proteomics reveals that pharmacologic Ref-1 redox inhibition rapidly rewires regulatory signaling networks before detectable changes in protein abundance. Our findings identify mitochondrial redox remodeling as an early consequence of Ref-1 inhibition, providing systems-level insight into how Ref-1-targeted therapies disrupt metabolic and stress-adaptive programs in pancreatic cancer. This work establishes a framework for understanding the molecular basis of Ref-1-directed therapeutics and highlights integrated PTM profiling as a powerful strategy for defining early drug response mechanisms. These findings provide a strong translational rationale for advancing next-generation Ref-1 redox inhibitors such as APX2014, developed from the first-in-class inhibitor APX3330 currently in clinical trials, and underscore the broader therapeutic potential of targeting Ref-1 redox signaling in pancreatic cancer.

Mutations in isocitrate dehydrogenase 1 (IDH1) drive the early stages of gliomagenesis while simultaneously imposing replication stress that creates targetable vulnerabilities. Using both in vitro and in vivo models, we show that inhibition of poly(ADP-ribose) glycohydrolase (PARG) induces a poly(ADP-ribose) (PAR)-dependent augmentation of radiosensitivity in IDH1-mutant glioma cells. Metabolic repletion of NAD+ fails to rescue this effect, indicating that the vulnerability cannot be explained solely by NAD+ depletion. Instead, PARG inhibition profoundly alters replication fork progression and S-phase kinetics in IDH1-mutant cells. Mechanistically, ionizing radiation preferentially activates replication fork-associated damage response proteins DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and X-ray repair cross-complementing protein 1 (XRCC1) in IDH1-mutant cells, a response partially reversed by pharmacologic inhibition of mutant IDH1. Importantly, pharmacologic inhibition of DNA-PKcs with AZD7648 during irradiation disrupts fork-associated repair signaling and markedly enhances cytotoxicity in IDH1-mutant glioma models. Together, these findings identify a PAR-dependent replication fork vulnerability that can be therapeutically exploited to selectively enhance radiosensitivity in IDH1-mutant gliomas. Statement of significanceIDH-mutant gliomas harbor intrinsic replication stress yet lack targeted radiosensitization strategies. We identify a PAR-dependent replication fork vulnerability in which disruption amplifies radiation cytotoxicity by deregulating S-phase fork signaling. Pharmacologic DNA-PKcs inhibition exploits this dependency, providing a genotype-selective approach to enhance radiotherapy in IDH-mutant glioma.

Lung squamous cell carcinoma (LUSC) is an aggressive malignancy characterized by high cellular plasticity and few targeted treatment options. TNIK overexpression is common in LUSC and promotes tumor growth, with TNIK inhibition sensitizing LUSC to radiotherapy, though the underlying mechanisms are not well defined. Through transcriptomic analyses and functional assays, we identified TNIK as a regulator of a MYC-dependent transcriptional network that coordinates epithelial-mesenchymal plasticity and cell proliferation in LUSC. Depletion of TNIK reprogrammed LUSC cells from a hybrid epithelial/mesenchymal state towards an epithelial, senescent-like state characterized by reduced cell migration, invasion, reduced DNA synthesis, and enhanced {beta}-galactosidase activity. Using a small-molecule screen approach, we found that TNIK inhibitors cooperated with agents suppressing the histone methyltransferase and MYC binding partner EZH2, which further suppressed partial epithelial-to-mesenchymal transition (pEMT). Mechanistically, we identified MYC as a key downstream TNIK effector in LUSC cells: MYC depletion phenocopied the effects of TNIK loss on pEMT and senescence, and restoring MYC expression bypassed the effects of TNIK depletion. Collectively, these results implicate TNIK in the mechanisms linking epithelial-mesenchymal plasticity with proliferation and evasion of senescence and provide insights into future strategies for the clinical deployment of TNIK inhibitors in LUSC and other TNIK-dependent malignancies.