Oncogene

The Hippo pathway effector YAP1 is a potent oncogenic driver in triple-negative breast cancer (TNBC) and its activity is restrained by the scaffold protein Angiomotin-p130 (AMOT). AMOT is itself short-lived, being targeted for proteasomal degradation by NEDD4-family E3 ubiquitin ligases that dock at its L/P-PxY motifs. Here we identify Profilin1 (PFN1), an actin-binding protein with established actin-independent tumour-suppressive signalling functions in TNBC as a direct binding partner and stabilizer of AMOT. PFN1 and AMOT are co-immunoprecipitated, they share 70 common interactors and NEDD4 is one of them. Protein-protein docking shows the interaction of PFN1 on the first PPxY motif of AMOT, through its actin-binding domain. We further show that PFN1s binding leaves the AMOT LPTY motif and both coiled-coil domains entirely unoccupied. Site-directed mutagenesis of AMOT PPxY motifs shows that PFN1 binding is unaffected by substitution of the PPxY tyrosines Y242 and Y287, either alone or in combination, indicating that PFN1 engages through its actin-binding domain. Functionally, PFN1 stabilizes AMOT as shown by cycloheximide-chase assay in TNBC. PFN1 induction increases cytoplasmic retention of YAP1, reduces TEAD occupancy at the CTGF promoter and thereby suppresses TNBC cell migration. Thus, this study suggests that PFN1 deregulates tumour cells migration by interacting with AMOT through its actin-binding domain, stabilizing AMOT and thereby arresting YAP in the cytoplasm, which might be an important therapeutic target to regulate TNBC.

Fluoropyrimidine-based chemotherapies, including 5-fluorouracil (5-FU) and floxuridine (FuDR), are widely used in cancer treatment, but their efficacy is limited by adaptive resistance driven by TYMS upregulation. The upstream mechanisms controlling TYMS expression remain poorly defined. Here, we identify INPPL1 (SHIP2) as a critical regulator of TYMS expression and fluoropyrimidine response in breast cancer cells. We show that SHIP2 enhances basal and drug-induced TYMS expression at the transcriptional level independently of its phosphatase activity. Mechanistically, SHIP2 increases SRC levels and nuclear accumulation of {beta}-catenin, driving TYMS expression. Inhibition of SRC or {beta}-catenin suppresses TYMS induction and restores sensitivity to FuDR. Importantly, SHIP2 rewires TYMS regulation from a P53-dependent program to a {beta}-catenin-driven pathway, enabling sustained TYMS expression under chemotherapeutic stress. Consistent with this model, differential sensitivity to SHIP2 depletion correlates with baseline TYMS levels across cell lines. Analysis of patient cancer datasets reveals that high INPPL1 expression correlates with increased TYMS levels and poor clinical outcomes. These findings identify SHIP2 as a non-canonical regulator of TYMS and a potential therapeutic target to overcome fluoropyrimidine resistance.

Osteosarcoma (OS) is the most common primary malignant bone tumour and is characterised by aggressive growth, early metastasis, and a very stagnant clinical outcome. Although epigenetic dysregulation has been implicated in OS progression, the mechanisms linking epigenetic alterations to metastatic signalling remain unclear. Here, we identified the lysine-protein demethylase 6A (KDM6A/UTX) as a critical suppressor of OS metastasis and uncovered a novel regulatory axis involving the Hippo/YAP and Wnt/{beta}-catenin signalling. Initial bioinformatics analyses revealed frequent KDM6A alterations and significantly reduced expression in OS patient datasets, which correlated with metastatic disease and poor prognosis. Functional inhibition of KDM6A by pharmacological inhibitors and siRNA induced a hyper-invasive phenotype, marked by elevated mesenchymal markers, enhanced cytoskeletal remodelling, increased transendothelial adhesion and decreased chemotherapeutic drug sensitivity. Importantly, restoration of KDM6A expression effectively counteracted these effects. Mechanistically, KDM6A loss activated Wnt/{beta}-catenin signalling, resulting in nuclear translocation of {beta}-catenin and transcriptional activation of genes associated with stemness and invasion. Therefore, inhibition of {beta}-catenin reversed the invasive phenotype. Further analysis revealed that KDM6A regulated Hippo signalling through epigenetic control of the negative regulator of Yes-Associated Protein (YAP)-LATS1. KDM6A inhibition led to enrichment of H3K27me3, a repressive mark, at the LATS1 promoter. Accumulated YAP was predominantly localised in the cytoplasm, where it interacted with GSK3{beta} and contributed to the stabilisation of {beta}-catenin by preventing its proteasomal degradation. Collectively, our findings identify a novel KDM6A-LATS1-YAP-{beta}-catenin signalling axis that drives metastatic progression in OS.

MLL3 (Mixed-Lineage Leukemia 3), also known as KMT2C, is one of the most frequently altered epigenetic regulators in breast cancer. MLL3 loss-of-function leads to accelerated tumor onset and growth and increased metastasis. As a large multi-domain protein, MLL3 functions as a histone methyltransferase and a nuclear protein adaptor interacting with other epigenetic proteins. Since breast cancer MLL3 mutations are often truncating mutations that lead to protein degradation, whether the MLL3 tumor suppressor activity depends on its catalytic activity or non-catalytic chromatin adaptor function remains unclear. Here, using CRISPR genetically engineered mouse mammary stem cell organoid-based breast tumor models, we dissected dosage-dependent and domain-specific functions of MLL3 in breast tumor suppression. MLL3 heterozygous loss breast tumor models revealed that MLL3 is haplo-insufficient for breast tumor suppression. Interestingly, homozygous catalytic-dead MLL3-Y4792A mutation did not accelerate tumor onset, growth, or metastasis. By contrast, G367V mutation in the PHD2 domain, which disrupts the BAP1 complex binding without affecting MLL3 protein stability, accelerated tumor onset and growth, phenocopying MLL3 loss. Mechanistically, MLL3 loss impaired chromatin localization of UTX, and genetic depletion of UTX accelerated breast tumor progression in MLL3-wildtype but not MLL3-deficient cells. Integrated RNA-seq, CUT&TAG, and ATAC-seq analyses further showed that transcriptional changes induced by MLL3 loss were more closely associated with promoter-proximal alterations in H3K27Ac, H3K27me3, and chromatin accessibility than with putative MLL3-dependent enhancer regions. Together, these findings reveal that MLL3 suppresses breast tumor initiation through a dosage-sensitive, catalytic-independent adaptor function that regulates promoter-proximal epigenetic states.

Structural AbstractO_ST_ABSBackgroundC_ST_ABSTriple-negative breast cancer (TNBC) represents a major clinical challenge due to its aggressiveness, heterogeneity and limited availability of effective targeted therapy. We investigated whether LRP-1, a multifunctional cell-surface endocytic and signaling receptor, contributes to TNBC progression. MethodsUsing CRISPR-Cas9, LRP-1-deficient murine 4T1 and human HS578-T TNBC cells were used. Functional consequences were assessed through migration, invasion, and 3D spheroid assays, imaging of focal adhesions and actin organization, atomic force microscopy, and plasmin activity assays. Global molecular reprogramming was analyzed by label-free quantitative proteomics and secretomics. LRP-1-deficient or proficient 4T1 cells were implanted orthotopically in immunocompetent mice; tumor progression was monitored longitudinally while peritumoral collagen architecture and immune microenvironment composition were characterized by second harmonic generation imaging and immunohistochemistry. ResultsWe show that LRP-1 loss reduces TNBC aggressiveness, as reflected by decreased migration and invasive capacity, reduced spheroid evasion, and significant morphological changes in focal adhesion and actin structure. LRP-1-deficient cells became stiffer and showed lower LOXL-4 levels, while pericellular proteolytic activity remained unchanged, suggesting other proteases mechanism. Multi-omic analysis revealed alterations in extracellular matrix (ECM), epithelial-mesenchymal transition, and inflammatory pathways. In vivo, LRP-1-deficiency reduced tumor progression and peritumoral collagen deposition, while increasing CD8+ T and Natural Killer cell infiltration, together with a cytokine profiling compatible with a more immune-permissive microenvironment. ConclusionsLRP-1 act as a key contributor in TNBC progression through matrix remodeling, mechano-adaptation, and immune exclusion. Positioning it as a candidate biomarker for TNBC patients who are likely to benefit from stroma-targeting therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/732906v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1b595c2org.highwire.dtl.DTLVardef@7b208aorg.highwire.dtl.DTLVardef@1956e54org.highwire.dtl.DTLVardef@17e55d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

The role of UBE2N in myeloid cell-mediated immune suppression in cancer remains undefined. Here, we examined the function of UBE2N in myeloid cell-mediated tumor progression using a temporally inducible myeloid-specific knockout model (LysMCreERUbe2nfl/fl). Temporally induced deletion of Ube2n in myeloid cells (Ube2nMyeKO) significantly hindered growth of YUMM1.7 melanoma. This was accompanied by reduced myeloid cell burden within the tumor microenvironment. We observed altered abundance of PD-1, PD-L1, and SPP1 in the Ube2nMyeKO tumor microenvironment at the tissue level. In vitro analysis showed that knock-in expression of a catalytically deficient UBE2NC87S mutant in bone marrow-derived macrophages (BMDMs) markedly decreased expression of Spp1. We observed decreased SPP1 secretion in Ube2nMyeKO BMDM-conditioned media (CM). Treatment with Ube2nMyeKO BMDM-CM decreased co-expression of PD-1, TIM-3, and LAG-3 on chronically stimulated T cells. Antibody-mediated neutralization of SPP1 in Ube2nWT BMDM-CM decreased PD-1 expression on CD8+ T cells. Together, these findings suggest a role for myeloid UBE2N in YUMM1.7 progression.

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.

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.

ZNF217 is an established oncogenic transcription factor that promotes cancer progression and therapeutic resistance; however, the mechanisms regulating ZNF217 protein abundance remain poorly understood. Here, we identify ubiquitin-specific peptidase 15 (USP15) as a critical regulator of ZNF217 stability and define a reciprocal USP15-ZNF217 signaling loop that sustains malignant phenotypes in ovarian cancer. Stable overexpression of ZNF217 in OVCA420 ovarian cancer cells enhanced proliferation, epithelial-mesenchymal transition, migration, invasion, and extracellular matrix adhesion. Notably, ZNF217 overexpression increased USP15 protein abundance without altering USP15 mRNA levels, whereas ZNF217 depletion reduced USP15 protein levels, suggesting post-transcriptional regulation. Conversely, USP15 depletion markedly reduced ZNF217 protein abundance while increasing ZNF217 mRNA levels, indicating that USP15 regulates ZNF217 predominantly at the post-transcriptional level. Proteasome inhibition restored ZNF217 protein levels following USP15 depletion, further demonstrating that USP15 promotes ZNF217 protein stability. Functionally, USP15 depletion in ZNF217-overexpressing ovarian cancer cells suppressed proliferation and multiple metastatic phenotypes, including migration, invasion, extracellular matrix adhesion, anoikis resistance, and multicellular aggregate formation. In vivo, USP15 depletion significantly reduced tumor progression and metastatic burden and prolonged survival in mice bearing ZNF217-driven ovarian tumors. Furthermore, USP15 depletion enhanced the sensitivity of ZNF217-overexpressing cells to carboplatin, paclitaxel, and doxorubicin. Collectively, these findings identify USP15 as an upstream regulator of ZNF217 protein stability and reveal a positive-feedback loop between USP15 and ZNF217 that reinforces oncogenic signaling. Targeting USP15 may therefore represent an indirect therapeutic strategy for suppressing ZNF217-driven ovarian cancer, particularly given the challenges associated with directly targeting oncogenic transcription factors.

Metastatic dissemination represents the major determinant of poor clinical outcome across cancer entities. Yet, how driver oncogenes shape transcriptional programs facilitating metastasis is poorly understood. In Ewing sarcoma (EwS) - a highly aggressive pediatric bone and soft-tissue sarcoma driven by chimeric FET::ETS transcription factors - low activity of the fusion oncoproteins is thought to promote metastasis, but the underlying molecular mechanisms remain largely elusive. Here, using spatially resolved functional transcriptomics in EwS patient tumors, we identify a distinct transcriptional state at the invasive tumor front, that in contrast to the tumor core, is characterized by lower FET::ETS activity and induction of the multifunctional shuttle LIM domain only protein 7 (LMO7). Integrating these data with clinical information reveals that high LMO7 expression is associated with poor outcomes. Gene network analysis of patient tumors and integrated proteomic and transcriptomic profiling of EwS cell lines following inducible LMO7 silencing highlight LMO7 as a central regulatory hub orchestrating epithelial-mesenchymal transition (EMT) and cytoskeletal remodeling in EwS. Functional experiments demonstrate that LMO7 silencing decreases clonogenicity and migratory capacity in vitro and suppresses primary tumor growth and metastatic dissemination in vivo. Collectively, these findings identify LMO7 as a clinically relevant effector of FET::ETS fusions in EwS, and illustrate how integrating functional, spatial and clinical data can uncover oncogene-driven effectors of metastasis.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers and more evidence suggests that glucose metabolism plays a significant role in the development and progression with glycosylation at multiple sites potentially being a key characteristic. However, the underlying mechanisms remain insufficiently studied. Here, we first confirmed the presence of O-GlcNAc glycosylation modifications at Thr50 on PKM, which is highly expressed in PDAC and strongly correlated with poor prognosis. Further, we found that PKM expression was significantly positively correlated with CDC27 levels, and mutation of the Thr50 O-GlcNAc site in PKM abolished the upregulation of CDC27. We confirmed that O-GlcNAc-modified PKM enhances nuclear translocation of ARNT, which binds to the CDC27 promoter to upregulate its expression. Finally, we demonstrated that reduced expression of CDC27, as a key component of the APC/C complex, leads to downregulation of ubiquitination at the K11 site of PPP2CA, resulting in upregulation of PPP2CA expression, in turn, reduces AKT phosphorylation, ultimately driving PDAC regression by inhibiting aerobic glycolysis. Thus, we delineate a novel O-GlcNAcylation-dependent pathway where PKM drives PDAC progression through ARNT-mediated CDC27 transcriptional activation and AKT-mediated glycolysis.

Oncogenic NPM-ALK drives aberrant signaling networks that promote malignant phenotypes; however, the molecular mechanisms linking oncogenic signaling to downstream cellular programs remain incompletely understood. Among candidate regulatory factors, transglutaminase 1 (TGM1) has not been functionally characterized in this context. Here, we investigated the role of TGM1 in NPM-ALK-expressing cells by combining proximity-dependent proteomics with functional analyses. Using a TurboID- based approach, we mapped the TGM1-associated protein network and identified extensive remodeling of this network upon NPM-ALK expression. Proteomic analyses revealed that NPM-ALK reduced TGM1-associated proteins involved in genome maintenance and DNA repair, while enhancing associations with proteins linked to cytoplasmic translation and PI3K-AKT signaling pathways. Consistent with these findings, TGM1 deficiency impaired cell proliferation without significantly affecting cell viability, indicating a specific role in maximal proliferative capacity. Furthermore, proteomic and functional analyses suggested a link between TGM1 and AKT signaling pathways. Together, these findings suggest that oncogenic NPM-ALK reprograms the TGM1 interactome toward oncogenic signaling and transcriptional states, positioning TGM1 within signaling networks associated with proliferative cellular phenotypes.

BRAF mutant colorectal cancer (CRC) remains difficult to treat despite the clinical use of combined BRAF and EGFR inhibition, highlighting a need to define tumour-intrinsic mechanisms that limit therapeutic response. Here, using genome-wide CRISPR-Cas9 screening in BRAF-mutant CRC cells, we identify MEN1, encoding the chromatin-associated protein Menin, as a selective determinant of sensitivity to combined encorafenib and cetuximab (EC). MEN1 loss markedly enhanced EC-mediated inhibition of cell proliferation and ERK activity while having comparatively little effect in untreated cells, and re-expression of Menin restored resistance. Transcriptomic and chromatin profiling revealed that Menin supports the transcriptional response associated with MAPK signalling. Menin occupied promoters of MAPK/BRAF-responsive genes and EC treatment caused widespread displacement of Menin from chromatin. Phosphoproteomic analysis demonstrated extensive remodelling of MAPK signalling following EC treatment, whereas proximity proteomics showed that the Menin-associated protein complexes remained largely intact despite loss of Menin chromatin occupancy. Importantly, MLL1 loss did not reproduce the sensitising effect of MEN1 deletion, and pharmacological Menin inhibition with revumenib failed to phenocopy either genetic MEN1 loss or acute Menin degradation, indicating that this phenotype is independent of Menin-MLL activity. Together, these findings identify a previously unrecognised, MLL-independent role for Menin in buffering the response of BRAF-mutant CRC cells to MAPK pathway inhibition and suggest targeting Menin, rather than disruption of its interaction with MLL, may provide a strategy for enhancing the response to BRAF-targeted therapy for CRC.

Malignant melanoma is frequently driven by constitutive activation of the RAS-RAF-MEK1/2-ERK1/2 pathway, yet adaptive signaling limits the long-term efficacy of MAPK-targeted therapies. Although activation of the MEK5-ERK5 pathway has emerged as a mechanism of resistance to RAF-MEK1/2-ERK1/2 inhibition, whether ERK5 inhibition reciprocally activates the canonical MAPK cascade and the molecular basis of this crosstalk remain unknown. Here, we show that genetic and pharmacological inhibition of ERK5 induces further activation of the MEK1/2-ERK1/2 pathway in BRAFV600E melanoma cells. Based on our previous transcriptomic analyses, we investigated the role of the small GTPase R-Ras, identified among the genes upregulated following ERK5 silencing. Accordingly, R-Ras mRNA and protein levels increased upon both genetic and pharmacological ERK5 inhibition, whereas R-Ras silencing abolished ERK1/2 hyperactivation and potentiated the anti-proliferative and pro-apoptotic effects of ERK5 targeting. Conversely, inhibition of the RAF-MEK1/2-ERK1/2 pathway increased R-Ras expression and ERK5 activation, both of which were prevented by R-Ras depletion. Besides ERK1/2, overexpression of a constitutively active mutant of R-Ras promoted ERK5 activation, placing R-Ras upstream of both signaling cascades. Finally, the pan-Ras inhibitor RMC-6236 potentiated the antitumor activity of either ERK5- or RAF-MEK1/2-ERK1/2-targeted therapies in either two-dimensional cultures or melanoma spheroids. Collectively, these findings identify R-Ras as a central regulator of reciprocal rewiring between ERK1/2 and ERK5 pathways under targeted MAPK inhibition. Functional disruption of this signaling circuit enhances melanoma cell death, providing a mechanistic rationale for co-targeting R-Ras together with MAPK signaling to limit adaptive responses to targeted therapy in BRAFV600E melanoma.

BET bromodomain inhibitors block binding of BET family bromodomains 1 and 2 (BD1, BD2) to chromatin and have demonstrated clinical activity in NUT carcinoma (NC), a BRD-NUT fusion-driven cancer, but toxicity from BD1 inhibition has limited their effectiveness. We investigated whether selective inhibition of BRD4 bromodomain 2 (BD2) could retain antitumor activity while reducing toxicity. NC cells were uniquely sensitive to the novel BRD4-BD2 inhibitor DC-9476 and other BD2-selective inhibitors, which induced differentiation and growth arrest. A CRISPR knockout screen identified the BRD4-targeting E3 ligase SPOP as the top resistance hit. BD2 inhibition, but not BD1-selective or pan-BET inhibition, triggered SPOP-dependent proteasomal degradation of BRD4 and BRD4-NUT; SPOP loss prevented degradation and largely rescued BD2 inhibitor-induced differentiation and growth arrest. Unexpectedly, BRD4 and BRD4-NUT remained chromatin-associated during BD2 inhibition, whereas BD1 or pan-BET inhibition displaced them. Together with evidence that ectopic BRD4-NUT expression sensitizes BRD4 to degradation, these findings support a model in which BRD4-NUT megadomains create a high-density, degradation-competent SPOP substrate pool of BRD4 and BRD4-NUT upon BD2 inhibition, whereas pan-BET inhibition disperses this substrate and limits efficient degradation. In preclinical NC models, BD2-selective inhibition achieved greater tumor growth inhibition and survival benefit than pan-BET inhibition, revealing a therapeutic vulnerability.

Ewing Sarcoma (ES) is an aggressive neoplasm arising in bones and soft tissues driven by the oncogenic fusion EWSR1::FLI1. Through epigenetic deregulation, EWSR1::FLI1 generates de novo super-enhancers that control the expression of key genes for tumor cell maintenance. By an integrative in silico analysis, we identified the subunit of the Mediator complex MED13L and RERE, a member of the atrophin family of arginine-glutamic acid dipeptide repeat-containing proteins, as genes regulated by EWSR1::FLI1-bound super-enhancers. We confirmed that EWSR1::FLI1 regulates MED13L and RERE expression in ES cell lines and showed that these proteins are highly expressed in Ewing primary tumors. Besides the well-established role of the Mediator complex in transcriptional regulation given its association with the RNA polymerase II, in ES cells the DNA binding sites of MED13L overlap with those of RERE and EWSR1::FLI1 in genes that control protein translation and alternative splicing (AS). Accordingly, the expression of various spliceosome components is co-regulated by MED13L, RERE and the oncogene, leading to AS in ES cells. We identified RBM39, a splicing factor downregulated after MED13L and RERE depletion, as a direct transcriptional target of EWSR1::FLI1. Consistently, in vitro viability experiments using indisulam, which induces selective DCAF15-dependent proteosome degradation of RBM39, demonstrate ES cells highly and specifically sensitive to RBM39 inhibition. In vivo experiments with mice xenografted with ES cells show complete tumor regression with indisulam, highlighting the potential of this approach as a novel and promising therapeutic strategy for Ewing sarcoma. STATEMENT OF SIGNIFICANCEEwing sarcoma (ES) is characterized by FET::ETS oncoproteins that act as pioneer transcription factors. Here, we identified two genes controlled by EWSR1::FLI1-bound super-enhancers, MED13L and RERE, and characterized the mechanism by which these proteins cooperate with the oncogene to regulate RNA metabolism and ribosomal processes in ES cells. These findings have led to the identification of the splicing factor RBM39 as a vulnerability in ES, as supported by the extraordinary sensitivity of these tumors to monotherapy with RBM39 degrader indisulam.

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.

Hypoxia and NF-{kappa}B signaling are well-established drivers of cancer progression and treatment failure, yet the oxygen-dependent regulation of non-canonical NF-{kappa}B signaling remains poorly defined. Here, we identify hypoxia-inducible factor prolyl-4-hydroxylase-1 (HIF-P4H-1/EGLN2) as a key modulator of the non-canonical NF-{kappa}B pathway. Using integrated biochemical, genetic, proteomic, and transcriptomic analyses across human cell lines, mouse models, and clinical tumor samples, we demonstrate that HIF-P4H-1 directly interacts with and hydroxylates IKK at proline 367, thereby promoting its ubiquitination and proteasomal degradation. Loss or inhibition of HIF-P4H-1 results in accumulation of IKK, impaired NF-{kappa}B2/p100 processing to p52, destabilization of NF-{kappa}B-inducing kinase (NIK), and suppression of non-canonical NF-{kappa}B-dependent survival gene expression. Structural modeling and mutagenesis identify proline 367 hydroxylation as a critical determinant of IKK turnover. Analysis of TCGA cohorts reveals an inverse correlation between HIF-P4H-1 and IKK expression, with elevated HIF-P4H-1 associating with advanced tumor stage and reduced overall survival in clear cell renal cell carcinoma. Functionally, targeting HIF-P4H-1 sensitizes cancer cells to cell death and impairs proliferation, clonogenic growth, and migration. Together, our findings define a previously unrecognized oxygen-dependent mechanism regulating non-canonical NF-{kappa}B signaling through direct control of IKK stability and nominate the HIF-P4H-1-IKK axis as a potential therapeutic vulnerability in hypoxia-adapted malignancies.

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.

The scaffold protein TKS4 plays a role in the development of several cancers. Alternative splicing of the TKS4 gene generates two isoforms, TKS4L and TKS4b; however, their distinct expression patterns and functional roles have not yet been characterized. We have shown that TKS4 isoforms were differentially expressed across human cell lines and breast cancer (BC) tumor samples. Both TKS4L and TKS4L/TKS4b mRNA ratios were significantly altered in tumors compared with adjacent tissues. We identified six novel binding SH3-domain-containing partners for TKS4L, none of which interact with TKS4b, suggesting their functional differences. Tyrosine phosphorylation of both isoforms was induced by Src(Y527F) kinase overexpression, enabling binding to the SH2 domains of signaling proteins. Interestingly, TKS4b significantly accumulated in the nucleus, while TKS4L was primarily present in the cytosol in MCF-7 cells. TKS4b overexpression enhanced MCF-7 cell migration. Both TKS4 isoforms exhibit oncogenic properties by promoting epithelial-mesenchymal transition in BC cells, highlighting their potential as targets for therapeutic intervention.