Introduction: Chordomas are rare, slow-growing, malignant tumors of the spine that remain challenging to treat due to high recurrence rates despite interventions such as en bloc resection and radiation. With limited treatment options for recurrent chordomas, our study investigates transcriptomic differences between patient-derived primary and recurrent chordomas to uncover molecular drivers of recurrence. Leveraging transcriptomics and qPCR (quantitative polymerase chain reaction), we profiled potential targets for therapeutic intervention.
Methods: Gene expression profiling was conducted on 7 patient-derived sacral chordomas (4 primary, 3 recurrent) using the Nanostring nCounter PanCancer Pathways Panel, covering 770 cancer-related transcripts. Differential expression 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 notochordal controls, and biological relevance to pathways linked to proliferation, extracellular matrix remodeling, immune evasion, and musculoskeletal processes. qPCR, normalized to GAPDH and analyzed by ΔΔCt, validated Nanostring nCounter findings, focusing on expression changes between primary and recurrent chordomas compared to control notochordal cells.
Results: Transcriptomic profiling identified 56 significantly differentially expressed genes (17 upregulated and 39 downregulated, p< 0.05), including four with log2 fold-change >1.5 (ANXA2P2, TNFRSF12, P3H2, ITGA3) and thirteen with log2 fold-change < -1.5 (e.g. Chi3l1, NRXN3, CDH2, AREG, MYH11). The upregulation of ANXA2P2, a pseudogene of Annexin A2 (ANXA2), suggests a potential regulatory role in processes associated with recurrence. qPCR validation confirmed the Nanostring nCounter results, with ANXA2P2 showing an 8.92-fold increase in expression in recurrent sacrococcygeal chordoma cells (U-CH1) relative to primary sacral chordoma (U-CH12 and JHC7) commercial cell lines, supporting its potential involvement in recurrence-related molecular mechanisms.
Conclusion : Our findings suggest that recurrent chordomas exhibit distinct gene expression patterns, promoting growth, bone matrix remodeling, and immune evasion. qPCR validation supports these differences, with further investigation warranted to elucidate recurrence pathways and explore potential therapeutic targets. Understanding genetic drivers in chordoma progression may offer new strategies for managing recurrence.
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