Abstract YAP and TAZ are Hippo pathway effectors that bind TEAD transcription factors to drive oncogenic programs. First-in-human trials of TEAD inhibitors (TEADis) showed activity and tolerability in pretreated mesothelioma patients, yet current trials focus on mesotheliomas and rare Hippo-altered tumors, despite the broad oncogenic role of YAP/TAZ in various solid cancers. Whether YAP/TAZ target gene signatures can identify tumors with high YAP/TAZ activity and potential TEADi sensitivity beyond these indications remains unclear. We profiled YAP/TAZ activity using a 22-gene signature across 2390 advanced pediatric and 3746 advanced rare cancers or cancers from young adults (<51y) from the INFORM and DKFZ/NCT/DKTK MASTER (MASTER) trials. Benchmarking against mesothelioma and YAP fusion-driven ependymoma revealed subsets of cancers across entity baskets with equal or higher YAP/TAZ activity independent of Hippo alterations. To dissect tumor-intrinsic versus stromal contributions, we performed spatial transcriptomics on MASTER samples using microarrays and the Xenium platform (n=106 cores from 89 tumors representing >70 histological subtypes). Tumor-cell YAP/TAZ scores correlated strongly with bulk scores (r=0.61), whereas fibroblast (r=0.23) and immune-cell (r=0.35) correlations were weak, indicating that bulk scores largely reflect tumor-cell activity. We highlight a MASTER patient with MET-amplified carcinoma in whom progression on the MET inhibitor capmatinib coincided with a marked YAP/TAZ-score increase. In MET-amplified HS746T gastric cancer cells, genetic YAP/TAZ activation reduced capmatinib sensitivity, partially reversed by TEAD inhibition, supporting an unrecognized YAP/TAZ-linked resistance mechanism. To evaluate predictive capacity of the YAP/TAZ signature, 23 cancer cell lines and 30 patient-derived spheroid cultures (PDSCs) were treated with IAG933 (Ω-loop-binding TEADi) or VT107 (TEAD autopalmitoylation inhibitor). Across compounds and models, expression of genes most strongly associated with TEADi response were enriched for YAP/TAZ targets, enabling refinement of a TEADi response signature. This refined signature correlated with area-under-the-drug-response-curve (AUC) values (IAG933: Pearson r=0.81 for cell lines, r=0.60 for PDSCs; VT107: r=0.46 and r=0.45). Notably, the refined signature derived from INFORM/MASTER tumors predicted TEADi response in matched PDSCs (n=13; r=0.70 for IAG933, r=0.72 for VT107), with IC50 values as low as 30 nM. Sensitive PDSCs included atypical rhabdoid tumor, colorectal, and pancreatic carcinoma - all lacking Hippo alterations and representing entities not typically considered YAP/TAZ-driven. In summary, these data provide a strong rationale for a transcription-based stratified clinical trial evaluating TEAD inhibition across pediatric and adult advanced cancers irrespective of Hippo alterations. Citation Format: Michael Wegert-Verhoeven, Mathea Fransisca, Sylvia Martin, Attila Jady, Daniela Richter, Malgorzata Oles, Timon A. Blindauer, Jan-Philipp Mallm, Jasmina Paluncic, Claudia Dagostino, Olga Ermakova, Annika Schneider, Matthew The, Annika Baude-Müller, Katja Beck, Maximilian Bullemer, Victor Didier Meza, Vivek Venkataramani, Ralf C. Bargou, Heiko Becker, Melanie Boerries, Armin Tuchscherer, DKFZ/NCT/DKTK MASTER consortium, Martin Wermke, Andreas Brunschweiger, Mohammed Al-Saeedi, Dirk Jäger, Olaf Witt, Denis Schapiro, Bernhard Küster, Andreas Hartig, Michael Allgaeuer, Alexander Brobeil, Christoph E. Heilig, Maria Veronica Teleanu, Simon Kreutzfeldt, Peter Horak, Daniel Hübschmann, Wolfgang Hartmann, Marcel Trautmann, Ina Oehme, Claudia R. Ball, Stefan Fröhling, Stefan M. Pfister, Hanno Glimm, Sebastian M. Dieter. A tumor-agnostic YAP/TAZ score predicts TEAD inhibitor sensitivity independent of Hippo alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1028.

Figure S3 shows a reciprocal regulation of YAP1/TAZ-TEAD and β-catenin-TCF in SySa cells via luciferase assays.

Synovial sarcoma (SySa) is a malignant soft tissue tumor that is characterized by an SS18::SSX fusion protein, which integrates into BAF chromatin remodeling complexes and alters global gene transcription. Despite its uniform genetic driver, SySa displays striking histomorphological and phenotypic heterogeneity, including spindle cell, glandular and poorly differentiated patterns. Prognosis is variable, with around 50% of patients developing metastases. Limited response to chemotherapy highlights the need for a better understanding of the underlying molecular mechanisms to guide alternative therapeutic strategies. Given the pivotal function of BAF complexes in SySa and their recently described impact on cellular differentiation processes, this study aims to investigate the role of SS18::SSX and specific BAF subunits in SySa differentiation. Nanostring analysis revealed that silencing of SS18::SSX and the GBAF subunit BRD9 modulates the cellular differentiation pathways. SS18::SSX and BRD9 were found to regulate epithelial–mesenchymal-transition (EMT)-associated factors of Snail and Slug on different levels, with SS18::SSX repressing E-Cadherin expression. Published single-cell RNA sequencing data were analyzed to validate our finding that BRD9 contributes to SySa EMT regulation. Our study provides novel insights into the multilayered regulation of key EMT players by SS18::SSX and BRD9 in SySa, thereby defining tumor phenotype and (potentially) prognosis.

Figure S1 shows that the SS18-SSX fusion protein regulates TEAD- and TCF-mediated transcriptional activity, both being important for SySa cell viability.

T-cell large granular lymphocytic leukemia (T-LGLL) is a rare hematologic neoplasm characterized by clonal expansion of CD3 + cytotoxic T lymphocytes and a highly heterogeneous clinical course. Conventional therapy primarily includes immunosuppressive regimen. However, optimal front-line approaches still need to be defined and refractory disease remains a clinical challenge. Thus, we here aimed to explore functional dependencies of T-LGLL as a basis for personalized therapeutic strategies. We performed functional apoptosis profiling and ex vivo drug treatment in a series of 8 clinically and genetically characterized T-LGLL patients from two German University hospitals. Our series of patients underscored the clinical and genetic heterogeneity of the disease. Genetically, only 2 patients harbored a STAT3 mutation. To identify targetable anti-apoptotic mechanisms, we performed selective functional BH3 profiling on the patients’ CD8 + T-cells harboring the malignant T-LGLL cells versus the same patients’ normal CD4 + T-cells. CD8 + cells in 50% of the patients (4/8) demonstrated a dominant functional dependence on MCL-1 as compared to the same patients’ normal T-cells. Accordingly, CD8 + T-LGLL cells from patients with enhanced MCL1 dependence significantly responded to AZD-5991 ex vivo while no response was observed in the remaining samples lacking enhanced MCL-1 dependence. Across clinically and genetically heterogeneous cases of T-LGLL, functional apoptosis profiling identified patients with CD8 + T-LGLL cells harboring a dominant dependence on MCL-1 as a potential therapeutic target.

Figure S5 shows that there is no interdependency between YAP1/TAZ and β-catenin activation in control cell lines.

Figure S6 shows that the mutual activation of YAP1/TAZ and β-catenin in SySa cells is impeded by knockdown of BAF complex subunits.

Figure S4 shows that induction of hyperactive YAP1/TAZ or β-catenin variants does not alter the other's protein levels.

Figure S2 shows that inhibition of YAP1, TAZ or β-catenin via siRNA-mediated knockdown or inhibitor treatment reduces each other's transcriptional activity.

Extraskeletal myxoid chondrosarcomas (EMCs) are rare mesenchymal neoplasms comprising less than 3% of all soft tissue tumors. EMCs arise mainly from the deep soft tissues of the extremities, accompanied by high rates of recurrence and metastases. The molecular hallmarks of EMCs are cytogenetic NR4A3 rearrangements, generating chimeric NR4A3 fusion oncoproteins. The most common reciprocal translocation t(9;22)(q22;q12) results in a fusion of the EWS RNA-binding protein 1 gene (EWSR1) to the nuclear receptor subfamily 4 group A member 3 gene (NR4A3 or TEC; approximately 75% of cases). Although the oncogenic NR4A3 fusion transcripts appear to play a crucial role in EMC tumorigenesis and progression, the specific biological function and the mechanism of action remains to be defined. Comprehensive genomic profiling (CGP) and reliable molecular characterization of solid tumors using Next-Generation-Sequencing (NGS) technology has become a key tool to facilitate biomarker-matched therapy selection. With a broad spectrum of therapies already approved or currently tested in clinical trials, rapid and scalable detection of an evolving number of therapeutically relevant genomic alterations and complex biomarkers is required. This study combined NGS-based CGP and fusion gene analysis of 69 paraffin-embedded EMC tissue samples to systematically map the genomic landscape of EMC. We used the all-in-one OncoDEEP® in-house kit, integrating both (i) an DNA NGS panel larger than 1MB powered by Twist Bioscience hybrid capture technology in combination with (ii) OncoDNA’s bioinformatic data analysis and clinical interpretation software suite (OncoKDM) resulting in an integrated theranostic report. The CE-IVD approved assay covers single-nucleotide variants (SNVs), copy number variants (CNVs), deletions and insertions (indels) and loss of heterozygosity (LOH) in 638 genes and facilitates the assessment of key complex biomarkers / signatures such as homologous recombination deficiency (HRD), tumor mutational burden (TMB), or microsatellite instability (MSI). Overall, more than 13, 600 variants have been identified, categorized as: pathogenic (0.1%), likely pathogenic (1.9%), variant of unknown significance (VUS; 13.3%), likely benign (6.3%) and benign (78.3%). TMB, HRD and MSI status were successfully assessed in more than 88% of all EMC samples. Furthermore, a novel NR4A3 fusion rearrangement was identified with the majority of EMC samples expressing the chimeric t(9;22) EWSR1::NR4A3 fusion transcript. This study provides a comprehensive genomic profile of EMC and uncovers novel genetic alterations, enhancing our understanding of its underlying pathogenesis. Gained genomic insights are anticipated to inform and refine future diagnostic criteria, potentially leading to more precise targeted therapies. Carl Philipp Schmitthenner, Franziska Evelt, Lucas Sebastian Scholl, Jessica Janke, Anna Kuntze, Santina Kirmse, Kim Falkenberg, Ilka Isfort, Ruth Berthold, Kornelius Kerl, Inga Grünewald, Eva Wardelmann, Wolfgang Hartmann, Marcel Trautmann. Comprehensive genomic profiling reveals novel insights into the genomic landscape of extraskeletal myxoid chondrosarcomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7173.

Superficial fibromas are a group of mesenchymal spindle cell lesions with pathomorphological heterogeneity and diverse molecular backgrounds. In part, they may be indicators of an underlying syndrome. Among the best-known entities of superficial fibromas is Gardner fibroma, a plaque-like benign tumor, which is associated with APC germline mutations and occurs in patients with familial adenomatosis polyposis (Gardner syndrome). Affected patients also have an increased risk to develop desmoid fibromatosis (DTF), a locally aggressive neoplasm of the deep soft tissue highly prone to local recurrences. Although a minority of DTFs occur in the syndromic context and harbor APC germline mutations, most frequently their underlying molecular aberration is a sporadic mutation in Exon 3 of the CTNNB1 gene. Up to date, a non-syndromic equivalent to Gardner fibroma carrying a CTNNB1 mutation has not been defined. Here, we present two cases of (sub-)cutaneous tumors with a hypocellular and collagen-rich Gardner fibroma-like appearance and pathogenic, somatic CTNNB1 mutations. We aim to differentiate these tumors from other fibromas according to their histological appearance, immunohistochemical staining profile and underlying somatic CTNNB1 mutations. Furthermore, we distinguish them from locally aggressive desmoid fibromatosis regarding their biological behavior, prognosis and indicated therapeutic strategies. Consequently, we call them CTNNB1-mutated superficial fibromas as a sporadic counterpart lesion to syndromic Gardner fibromas.

Supplementary Figure S1. WEE 1 expression correlates with histological grade of MLS.

Supplementary Figure S3. Supplementary Figure S3. In vivo efficacy of WEE 1 inhibition in MLS CAM xenografts.

Supplementary Table S4. Statistical correlation analysis by means of χ².

Gastrointestinale Stromatumoren (GIST) stellen seit über 20 Jahren ein Paradigma für die zielgerichtete Therapie mit Tyrosinkinaseinhibitoren dar. Eine elementare Voraussetzung für eine mögliche neoadjuvante oder adjuvante Behandlung bei lokalisierten GIST bzw. eine additive Therapie bei metastasierten GIST ist die molekulare Typisierung der Tumoren, idealerweise bereits bei Erstdiagnose. Zudem ist auf die Möglichkeit einer hereditären oder syndromalen Prädisposition zu achten, da sich hieraus auch therapeutische Konsequenzen und eine andere Nachsorgestrategie ergeben.

Supplementary Table S6. MK-1775 IC50 values of liposarcoma cell lines.

Zusammenfassung Gastrointestinale Stromatumoren (GIST) stellen seit über 20 Jahren ein Paradigma für die zielgerichtete Therapie mit Tyrosinkinaseinhibitoren dar. Eine elementare Voraussetzung für eine mögliche neoadjuvante oder adjuvante Behandlung bei lokalisierten GIST bzw. eine additive Therapie bei metastasierten GIST ist die molekulare Typisierung der Tumoren, idealerweise bereits bei Erstdiagnose. Zudem ist auf die Möglichkeit einer hereditären oder syndromalen Prädisposition zu achten, da sich hieraus auch therapeutische Konsequenzen und eine andere Nachsorgestrategie ergeben.

Abstract Introduction: Synovial sarcoma (SySa) is a rare malignant soft tissue tumor characterized by a specific reciprocal translocation t(X;18). The resulting chimeric SS18::SSX fusion protein drives SySa tumorigenesis by integrating into BAF chromatin remodeling complexes, changing their composition and dysregulating gene transcription. The role of BAF complexes in cancer steadily increases with ∼20% of all malignancies having alterations in BAF complex subunits. BAF complexes are multiprotein complexes with several interaction partners determining their localization and functionality. Since previous analyses revealed an induced activation of the transcriptional coregulators YAP1 and β-catenin in SySa, the aim of this study was to analyze if nuclear YAP1 and β-catenin are interacting with BAF complexes and if this has an impact on their transcriptional activity. Experimental procedures: Co-immunoprecipitation experiments on nuclear protein extracts and proximity ligation assays were performed to investigate interactions between YAP1, β-catenin, and BAF complex subunits in SySa cells. Knockdown of common and specific BAF complex subunits was conducted employing RNA interference. To assess changes in YAP1 and β-catenin transcriptional activities, TEAD and TOPFlash luciferase reporter assays were performed, respectively, and protein expression levels were detected by immunoblotting. Results: In SySa, protein-protein interaction experiments revealed nuclear interactions between β-catenin, YAP1, the SS18::SSX fusion protein and various BAF subunits. YAP1 and β-catenin’s transcriptional activities were found to be interdependent as they mutually enhanced each other’s activation. Knockdown of SS18::SSX as well as specific BAF complex subunits was associated with diminished transcriptional activities of these coregulators and, interestingly, substantially affected their mutual activation. This indicates that SS18::SSX-containing BAF complex assembly is crucial for interdependent YAP1 and β-catenin activation in SySa cells. Conclusions: This study reveals a significant role of the SySa-specific fusion protein and BAF chromatin remodeling complexes in mediating intertwined activation of YAP1 and β-catenin. Citation Format: Ilka Isfort, Ruth Berthold, Lorena Heinst, Anna Kuntze, Eva Wardelmann, Marcel Trautmann, Wolfgang Hartmann. The BAF complex mediates intertwined activity of YAP1 and β-catenin in synovial sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5638.

Supplementary Table S3. Individual clinicopathological characteristics and semi-quantitative immunohistochemistry results of MLS patients (n=49).