UNLABELLED: MYC is amplified on extrachromosomal DNA (ecDNA) or homogeneously staining regions (HSR) in group 3 medulloblastoma (G3-MB), conferring a poor prognosis. A better understanding of the mechanisms underlying MYC expression in ecDNA and HSRs could be leveraged to develop improved treatments for G3-MB. Using a structure-function approach, we identified and characterized an enhancer (ecMYC E1) that drives MYC activation specifically in G3-MB with MYC-amplified ecDNA or HSRs. The ecMYC E1 locus exhibited enhancer hallmarks exclusively in MYC-amplified G3-MB but not in other MYC-dependent cancer cell lines, including those with MYC amplification. Silencing of the ecMYC E1 enhancer significantly reduced MYC transcription, which was compensated for by increases in ecDNA copy number. Neuronal differentiation 1 and bromodomain-containing protein 4 interacted with each other and bound to ecMYC E1, looping the enhancer to the MYC promoter. Together, these findings define a mechanism that regulates amplified MYC gene expression within ecDNA or HSRs specifically in G3-MB. SIGNIFICANCE: Combined structural and functional approaches identified a conserved enhancer activating MYC transcription exclusively in MYC-amplified ecDNA- and HSR-positive group 3 medulloblastoma, providing a potential therapeutic target for suppressing MYC.

Cell surface proteins offer significant cancer therapeutic potential attributable to their accessible membrane localization and central roles in cellular signaling, yet their promise remains largely untapped due to technical challenges inherent to profiling them. Here, we employ N-glycoproteomics to analyze 85 patient-derived xenografts (PDXs), constructing Glyco PDXplorer—an in vivo pan-cancer atlas of cancer-derived surface proteins. We develop a target discovery pipeline to prioritize proteins with favorable expression profiles for immunotherapeutic targeting and validate FAT2 as a squamous-cancer-enriched surface protein minimally detected in normal tissue. Functional studies reveal that FAT2 is essential for head and neck squamous cancer (HNSC) cell growth and adhesion through regulation of surface architecture and integrin-PI3K signaling. Chimeric antigen receptor (CAR)-T cells targeting FAT2 demonstrate anti-tumor activity. This work lays the foundation for developing FAT2-targeted therapies and represents a pivotal platform to inform therapeutic target discovery across cancers. Graphical abstract Highlights•Pan-cancer landscape of cancer-derived cell surface proteins detected in vivo•Discovery pipeline to prioritize proteins as immunotherapy target candidates•Validation of FAT2 as an SCC surface protein with minimal normal tissue expression•FAT2 CAR-T cells demonstrate anti-tumor activity in pre-clinical models Govindarajan et al. leverage N-glycoproteomics and PDX models to decode the in vivo cancer cell surfaceome and establish Glyco PDXplorer—a target discovery platform. The identification and validation of FAT2 as a previously undescribed, actionable antigen demonstrates the utility of Glyco PDXplorer for uncovering therapeutic vulnerabilities.

Hsp90 is a molecular chaperone that is often overexpressed across multiple cancer types and has a potential value as a prognostic marker as well as a therapeutic target. Given the high interest in Hsp90 therapies, positron emission tomography or PET imaging of Hsp90 can be a valuable tool for patient selection. The limitations of the previously developed Hsp90 tracers prompted us to evaluate the recently developed brain-permeable [ 11 C]HSP990 PET probe to advance the development of Hsp90-targeted therapeutics. Given the brain accumulation of [ 11 C]HSP990 probe, application for glioblastoma imaging of this tracer is of particular interest. In vitro [ 11 C]HSP990 binding was assessed in breast cancer and glioma cell lines including patient-derived cells using Hsp90 inhibitors and RNA interference knockdown of Hsp90 isoforms. Saturation binding studies were conducted on these cells and tumour tissue homogenates, and autoradiography was performed on tissue sections. Ex vivo biodistribution and in vivo dynamic µPET/CT studies were performed in healthy mice and tumour-bearing mice, including immunocompromised subcutaneous human U87 and MDA-MB-231models and immunocompetent intracranial murine NS/CT-2A models at baseline and following a pre-treatment with Hsp90 inhibitors. High Hsp90-specific tracer uptake was observed in breast cancer and glioma cells, with Hsp90β inhibition resulting in the most substantial reduction in uptake. In vivo uptake was high in U87 tumours but low in MDA-MB-231, presumably due to the differences in Hsp90 expression in tumour tissue versus cultured cells. Differences in maximum binding capacity or B max across cell and tissue types support this hypothesis, especially given that the affinity measured as dissociation constant K d remained similar across all tissue types. Despite high NS/CT-2A tumour uptake in vitro, no contrast between the healthy brain tissue and the NS/CT-2A glioma was observed in vivo due to the high uptake by the healthy brain. [ 11 C]HSP990 is a promising tracer for identifying Hsp90-overexpressing tumours and may hold potential for patient stratification, prognosis, and therapy monitoring of novel Hsp90 therapeutics. High healthy brain uptake of this tracer precluded the differentiation of the tumour in the intracranial NS/CT-2A tumour model, therefore [ 11 C]HSP990 might not be a suitable tracer for the glioblastoma imaging. Tracer with a longer half-life might be needed to compare the washout of the tracer from the brain and the tumour tissue over several hours to identify a suitable imaging window. The online version contains supplementary material available at 10.1186/s41181-025-00386-z.