Abstract C036: Comprehensive chordoma cell systems: Profiling brachyury-independent persistence and stem-like transitions in novel patient-derived sacral culture models

Abstract Chordomas, rare and malignant tumors of the spine, are notable for their highly morbid and slow-growing nature accompanied by high recurrence rates despite en bloc resection. Once maximal safe radiation dosing and surgical options are exhausted, no proven clinical treatments remain. At present, significant transcriptomic divergence persists between tumor subtypes, with molecular profiles remaining poorly studied. Given its rarity and heterogeneity, limited preclinical models comprehensively capture the genetic and phenotypic landscape of its tumorigenesis. To address the need for reliable model systems, we established two novel patient-derived chordoma cell lines from primary sacral tumor samples collected intraoperatively from patients at a single institution. Molecular characterization was performed using quantitative PCR to assess the expression of brachyury, a key chordoma marker, alongside stemness and EMT-related markers. In particular, CHI3L1, SPP1, and PTEN–genes identified as differentially expressed through ongoing NanoString and RNA-seq analyses. Both retrospective chart and systematic literature reviews were conducted to contextualize transcriptomic results. Search terms in PubMed included ("chordoma" AND ("brachyury" OR "chi3l1" OR "spp1" OR "pten")) in all literature published between 2005 and 2025, yielding 264 articles. We report successful establishment of two chordoma cell lines from pathologically confirmed sacral tumors. Genetic profiling across multiple passages bears marked resemblance to existing commercial in vitro primary models and retains chordoma-like morphology in culture. Our findings reveal that brachyury varies significantly throughout the culturing period, yet cell doubling endures, suggesting an enrichment of stem cell populations over time. Such variability is crucial for informing optimal passage selection for future characterization studies and implies influence between brachyury expression and stem cell populations, potentially underlying tumor recurrence dynamics. Initial findings indicate that these novel patient-derived cell lines represent a valuable tool for exploring chordoma biology and stem-like transition. While brachyury expression is often absent at tumor margins in histologic sections, recurrence still occurs, suggesting that chordoma cells may persist through stem-like states despite losing brachyury expression. Our data support the idea that chordoma cells can undergo a stem-like transition, contributing to recurrence even in the absence of brachyury. Clinically, this variability may underscore why recurrent or dedifferentiated chordomas exhibit distinct brachyury expression. As our institutional biobanking efforts continue to expand, we are establishing additional cell lines from diverse chordoma subtypes–including recurrent and metastatic tumors–to better encapsulate the disease spectrum and further elucidate mechanisms underlying tumor recurrence. Citation Format: Beatrice Campilan, Christian Godinez, Margot Martinez-Moreno, Ziya Gokaslan, Patricia Sullivan. Comprehensive chordoma cell systems: Profiling brachyury-independent persistence and stem-like transitions in novel patient-derived sacral culture models [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr C036.