Biology subjects

Geyer, F. H.

Publications and source records attributed to Geyer, F. H..

8 recordsLinked to original sources

bioRxiv2026

Oncogenic fusions induce an extensive cancer-restricted cryptic proteome in Ewing sarcoma

How tumors generate a cryptic "dark" proteome absent from healthy tissues, and whether it can be reversibly activated, remains unclear. In Ewing sarcoma, all tumors are driven by EWSR1::ETS fusions, making it a tractable model to study dark proteome activation. Integrating matched transcriptomes, translatomes and proteomes from 48 patient tumors with long-read RNA sequencing, single-cell Ribo-seq, proteomics and immunopeptidomics in cell line models, we show that EWSR1::FLI1 acts as a reversible switch recurrently inducing hundreds of cancer-specific neoproteins. Many arise from canonical coding regions via intragenic transcription start sites, generating truncated or out-of-frame neoproteins. We uncover a fusion-dependent increase in ribosomal readthrough into poly(A) tails, generating a stable 80-amino-acid TRPM4 neoprotein that, despite lacking a stop codon, is the most abundant tumor-specific microprotein across patients. Proteomic, immunopeptidomic, and immunofluorescence analyses validate neoproteins as tumor-restricted antigens, revealing a therapeutically actionable cancer dark proteome controlled by one oncogenic fusion.

cancer biology↗

bioRxiv2026

EXO1 Facilitates MiDAS and Prevents Genome Instability and Cell Death in Ewing Sarcoma

Ewing sarcoma (EwS) is an aggressive malignancy driven by EWSR1::ETS fusions, predominantly EWSR1::FLI1. Previous efforts using both direct and indirect approaches to target these chimeric oncoproteins have yielded limited clinical benefit. Although EWSR1::FLI1 is a well-known source of replication stress and genome instability, targeting DNA damage response (DDR) factors that mitigate these effects remain poorly understood. Here, we identified a marked dependency of EwS cells on exonuclease 1 (EXO1). We demonstrate that EXO1 is essential for EwS cell survival and tumor growth, highlighting its potential as a novel therapeutic target. Intriguingly, we unveil that EXO1 loss impairs mitotic DNA synthesis (MiDAS), promoting EWSR1::FLI1-associated genome instability and cell death. Collectively, our results support the idea that targeting DDR factors, which counteract replication stress and/or DNA damage induced by fusion oncoproteins, represents a promising therapeutic option for EwS.

cancer biology↗

bioRxiv2025

Targeting CXADR-mediated AKT signaling suppresses tumorigenesis and enhances chemotherapy efficacy in Ewing sarcoma

Distant metastasis is the leading cause of mortality in Ewing sarcoma (EwS) - a malignant bone or soft-tissue cancer mainly affecting children, adolescents, and young adults. Despite continuous efforts in understanding its pathogenesis, the molecular mechanisms driving EwS metastasis remain poorly understood, thus limiting the potential for therapeutic progress. Here, we identify the tight junction component Coxsackievirus and Adenovirus receptor (CXADR) as a critical regulator of cancer progression and metastasis in EwS. Differential gene expression analysis of patient tumors from two independent cohorts revealed that elevated CXADR levels are associated with metastatic disease and poor overall survival. In functional experiments, conditional CXADR knockdown reduced the growth of EwS cell line models in vitro, and suppressed local tumorigenesis. Notably, CXADR knockdown completely abrogated metastasis formation in vivo. Integration of transcriptome profiling and mechanistic studies uncovered that CXADR promotes the activation of AKT signaling, likely through complex formation with PTEN. Consequently, pharmacological targeting of AKT using the FDA-approved pan-AKT inhibitor Capivasertib showed CXADR-dependent cytotoxicity, with enhanced efficacy if combined with the EwS standard-of-care chemotherapeutic agent Vincristine. Collectively, our findings establish CXADR as a prognostic and predictive biomarker in EwS, highlighting AKT inhibition combined with chemotherapy as a promising strategy for patients with high CXADR expression. Together, these findings support a precision medicine approach combining molecular stratification and targeted therapies to improve patient outcomes in metastatic EwS.

cancer biology↗

bioRxiv2025

Exploration of oncogenic cooperation between germline variation and somatic mutation in prostate cancer progression

Prostate carcinoma (PCa) is the most common cancer of men, associated with a still unresolved issue of accurate risk-stratification. While recent advances in omics technologies have provided clues as to how molecular changes shape the onset and progression of PCa, it remains largely unclear whether germline variants and somatic mutations cooperate to contribute to PCa progression and outcome. Thus, we explored whether oncogenic cooperation between regulatory germline variants and somatic driver mutations can help explain why some PCa patients develop a more aggressive phenotype, which may have implications for risk-adapted medical treatment. Here, by employing an integrative functional genomics approach, we identified receptor-type protein-tyrosine phosphatase kappa (PTPRK) as a TMPRSS2::ERG (TE)-modulated gene associated with PCa progression whose expression is controlled by cooperation of the TE-fusion with a regulatory single nucleotide polymorphism (SNP). Analysis of available clinically annotated patient cohorts demonstrated that PTPRK is overexpressed in TE-positive PCa tumors and associated with higher Gleason scores and metastatic disease. TE knockdown in PCa cell lines reduced PTPRK expression, while ectopic overexpression of the fusion in TE-negative PCa cell lines and prostatic epithelium cells induced its expression. Functionally, PTPRK silencing inhibited cellular proliferation, cell cycle progression, and clonogenic growth of PCa cells, which was mirrored by dysregulation of corresponding gene and protein signatures in global transcriptomic and phospho-proteomic analyses after PTPRK knockdown. Analysis of TE ChIP-Seq and Hi-C data from PCa cells highlighted a proximal TE-bound DNA element whose TE-dependent enhancer activity was validated in reporter assays and which could be abrogated by a regulatory SNP. Collectively, our results provide evidence of how exploration of oncogenic cooperation may help to identify novel biomarkers and potentially druggable pathways and highlight the role of the regulatory genome in PCa progression.

cancer biology↗

bioRxiv2025

cIAP1 inhibitor of apoptosis is a tumor suppressor in Ewing sarcoma

Ewing sarcoma (EwS) is a highly aggressive pediatric malignancy driven by EWSR1::ETS fusion oncoproteins -primarily EWSR1::FLI1- which deregulate genes essential for differentiation, proliferation, and cell survival. To uncover key downstream targets of this fusion involved in cell differentiation, we combined transcriptomic profiling of EwS cell lines following EWSR1::FLI1 inhibition with gene ontology analysis, a clinically annotated gene expression dataset derived from EwS patient material and network analyses. This integrative approach identified inhibitor of apoptosis protein 1 (cIAP1, alias BIRC2) as an EWSR1::FLI1-suppresed gene. Despite its known oncogenic role in many cancers, cIAP1 showed minimal expression in EwS. Using inducible cIAP1 re-expression models in EwS cells, we demonstrated that cIAP1 re-expression suppresses proliferation, clonogenic growth, and 3D spheroid formation in vitro. Transcriptomic and proteomic analyses revealed that low cIAP1 expression enhances proliferation-related gene signatures, which are inhibited upon cIAP1 re-expression. In vivo xenograft models revealed that cIAP1 re-expression significantly reduces tumor growth, mitotic activity, and Ki-67 positivity, while increasing tumor necrosis and apoptosis. These findings highlight an unexpected tumor-suppressive role for cIAP1 in fusion-driven sarcomas, contrasting with its pro-survival function in other cancers. Collectively, our results identify cIAP1 as a prognostically relevant, EWSR1::FLI1-regulated hub whose re-expression disrupts tumor progression, offering a potential therapeutic strategy to restore tumor-suppressive pathways in EwS.

cancer biology↗

bioRxiv2025

EWSR1::ETS-low cells promote metabolic reprogramming of the tryptophan-kynurenine-AHR axis, immunosuppression, and poor outcome in Ewing sarcoma

The extent to which dynamic changes in oncogene activity shape cancer cell metabolism and drive disease progression remains poorly understood. Ewing sarcoma (EwS), driven by EWSR1::ETS fusion transcription factors, constitutes an ideal model to interrogate this question, as fluctuations in fusion activity direct divergent transcriptional programs. While EWSR1::ETS-high cells display a rather sessile but proliferative phenotype, EWSR1::ETS-low cells are more invasive. Yet, the mechanisms underlying these different phenotypes remain poorly characterized. Here, by employing an integrative functional metabolomics approach, we link reduced EWSR1::ETS activity in primary EwS tumors to adverse clinical outcome and pronounced activation of the aryl hydrocarbon receptor (AHR) pathway. Low EWSR1::ETS states foster tryptophan catabolism and accumulation of the AHR agonist kynurenine, which in turn promotes an immunosuppressive tumor microenvironment characterized by impaired natural killer (NK) cell cytotoxicity and enrichment of immunoregulatory infiltrates. Functionally, AHR silencing restores NK cell-mediated tumor recognition, while also directly suppressing EwS cell proliferation, clonogenicity, and spheroid growth in plasma-like media. Genetic inhibition of AHR reduces tumor burden and metastatic competence in xenograft models. These findings reveal a mechanistic link between oncogene fluctuation, amino acid metabolism, and immune evasion, positioning AHR as a central mediator of EwS progression and a tractable therapeutic vulnerability.

cancer biology↗

bioRxiv2024

Super-enhancer-driven CACNA2D2 is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT)

Desmoplastic small round cell tumor (DSRCT) is a highly aggressive cancer predominantly occurring in male adolescents and young adults. The lack of a comprehensive understanding on the biology of the disease is paralleled by its dismal survival rates (5-20%). To overcome this challenge, we first identified and prioritized urgently needed resources for clinicians and researchers. Thus, we established genome-wide single-cell RNA-sequencing and bulk proteomic data of in vitro and in vivo-generated knockdown models of the pathognomonic DSRCT fusion oncoprotein (EWSR1::WT1) and combined them with an original systems-biology-based pipeline including patient data and the largest histology collection of DSRCTs and morphological mimics available to date. These novel tools were enriched with curated public datasets including patient- and cell line-derived ChIP-seq, bulk and single-cell RNA-seq studies resulting in a multi-model and multi-omic toolbox for discovery analyses. As a proof of concept, our approach revealed the alpha-2/delta subunit of the voltage-dependent calcium channel complex, CACNA2D2, as a highly overexpressed, super-enhancer driven, direct target of EWSR1::WT1. Single-cell and bulk-level analyses of patient samples and xenografted cell lines highlighted CACNA2D2 as a critical component of our newly established EWSR1::WT1 oncogenic signature, that can be employed to robustly identify DSRCT in reference sets. Finally, we show that CACNA2D2 is a highly sensitive and specific single biomarker for fast, simple, and cost-efficient diagnosis of DSRCT. Collectively, we establish a large-scale multi-omics dataset for this devastating disease and provide a blueprint of how such toolbox can be used to identify new and clinically relevant diagnostic markers, which may significantly reduce misdiagnoses, and thus improve patient care.

cancer biology↗

bioRxiv2024

Glutaredoxin 3 (GLRX3) confers a fusion oncogene-dependent vulnerability to Ewing sarcoma

Ewing sarcoma (EwS) is a highly aggressive bone and soft-tissue associated cancer for which there are no effective targeted therapeutics available. Genetically, EwS is driven by aberrantly active EWSR1::ETS fusion transcription factors, most commonly EWSR1::FLI1. Despite their unique expression in EwS, all attempts to effectively target these fusion oncoproteins clinically were not yet successful, wherefore alternative targets are required. Here, we functionally characterize the evolutionarily conserved oxidative stress regulator glutaredoxin 3 (GLRX3) as a EwS-specific and EWSR1::FLI1-dependent vulnerability. Through integration of transcriptome-profiling, conditional drug screens in 3D cultures, and functional experiments, we discover that GLRX3 promotes EwS growth in vitro and in vivo, and that it has a key role in mitigation of oxidative stress and maintenance of iron homeostasis. These GLRX3 functions can be exploited in both GLRX3-high and -low expressing EwS cells by targeted therapeutics including CDK4/6 inhibitors and inducers of apoptotic and ferroptotic cell death. Collectively, our results exemplify how the interplay of an evolutionarily conserved oxidative stress regulator with a dominant oncogene can promote malignancy but provide opportunities for predictive diagnostics and personalized therapy.

cancer biology↗