ABS 088: Assessing and Validating Transcriptomic Divergence in Chordoma: Implications for Targeted Therapeutics in Primary and Recurrent Tumors

Victoria Chamberlain ¹ , Beatrice Campilan ¹ , Jonathan Arditi ¹ , Joselynn Wallace ² , Christian Godinez ¹ , Margot Martinez-Moreno ¹ , Patricia Sullivan ¹

¹ Brown Neurosurgery
² Brown COBRE

Van Wickle (2025) Volume 1, ABS 088

Introduction: Chordomas are rare, malignant tumors that arise from notochordal cells along the spinal axis, most commonly in the sacrococcygeal and clival regions. Though slow-growing, they are locally aggressive and difficult to treat, with a high recurrence rate and poor prognosis—median survival is 6 to 7 years. Due to their resistance to chemotherapy and limited response to radiation after recurrence, surgical resection followed by high-dose radiation remains the primary treatment, yet over half recur within 5 years and nearly 90% by 10 years. Current clinical challenges highlight the need for a better understanding of the molecular drivers of recurrence.
This thesis investigates transcriptomic differences between primary and recurrent chordomas to identify potential therapeutic targets. Using NanoString panels and RNA sequencing, we analyzed patient-derived tumor samples (4 primary, 3 recurrent for NanoString; 3 primary, 2 recurrent for RNA-seq). SPP1 (Osteopontin) emerged as consistently downregulated in recurrent tumors across both platforms. To validate this, we performed qPCR and ELISA on chordoma cell lines, confirming lower SPP1 expression in recurrent models compared to primary and notochordal-like control lines. These findings suggest that SPP1 may be specific to primary tumor biology, reinforcing the need to analyze primary and recurrent tumors separately.

Additionally, we identified CHi3L1 as downregulated in recurrence. Known for its roles in immune regulation and tumor progression, CHi3L1’s reduced expression may impair anti-tumor immunity and contribute to therapeutic resistance. Together, these results underscore the molecular divergence between primary and recurrent chordomas, and support SPP1 as a potential therapeutic target specific to early-stage disease. Understanding these differences may improve treatment strategies and enhance the success of targeted therapies.

Methods: Gene expression profiling was conducted on extracted RNA of 3 primary chordomas (2 from Chordoma Foundation, 1 from commercially available human cell line) and 2 recurrent chordoma from Chordoma Foundation using the GeneWiz RNA Sequencing and differential gene expression (DGE) analysis. DGE analysis was performed in nSolver and R, with KEGG pathway enrichment analysis conducted using the enrichR database. Genes selected for qPCR validation met two criteria: a significant differential expression (absolute log2FC ≥ 1.5) between chordoma samples and cell-derived notochordal controls, and biological relevance to pathways linked to extracellular matrix remodeling, immune evasion, and musculoskeletal processes. qPCR, normalized to percent expression of housekeeping (GAPDH), validated RNA Sequencing findings, focusing on expression changes between primary and recurrent chordomas compared to control notochordal cells.

Results: To validate RNA-seq and NanoString findings, qPCR showed higher SPP1 expression in the primary chordoma cell line JHC7 compared to recurrent UCH1 (mean ± SEM: 34.22 ± 9.828 vs. 0.66 ± 0.3008; p = 0.0628), with a moderate effect size (R² = 0.3683). ELISA analysis confirmed this trend, with JHC7 secreting higher SPP1 protein levels (4295 pg/mL ± 205) than UCH1 (1467 pg/mL ± 881; p = 0.0475). These results support the transcriptomic data, suggesting that SPP1 is highly expressed in primary chordomas and may serve as a biomarker specific to early tumor development.

Discussion: Our findings reveal significant molecular divergence between primary and recurrent chordomas, with SPP1 consistently downregulated in recurrence across transcriptomic and protein-level analyses. Although qPCR lacked statistical significance due to small sample size, ELISA confirmed significantly higher SPP1 protein expression in primary chordoma cells, supporting its role in early tumor development. SPP1 may promote tumor progression through immune modulation, ECM remodeling, and EMT. Its reduced expression in recurrence suggests a biological shift, limiting its utility as a recurrent disease target. Future studies should validate these findings with larger cohorts and explore downstream SPP1 signaling and interactions with EMT-related genes like CHi3L1.