Abstract LB194: Methylation subtypes of skull base chordoma

Abstract Background: Chordoma is a rare bone tumor with a high recurrence partially due to incomplete tumor resection. Recent studies suggest that chordoma is a heterogeneous disease that may comprise of molecular subtypes manifesting distinct clinical outcomes. Molecular classification may improve our knowledge of chordoma biology and patient stratification. However, due to its rareness, tumor profiling data is limited. The aim of this study was to identify molecular subtypes of chordoma that may improve clinical management using methylation profiling data. Methods: Genomic DNA was extracted from fresh frozen tissues in 67 patients with skull-base chordoma from Beijing Tiantian Hospital, China. DNA was then profiled using an Infinium Methylation 850K BeadChip array. CpG sites involving low-quality data (CpG detection with p > 0.01), those on the X and Y chromosomes, and the sites overlapping with single-nucleotide polymorphisms were removed. RNA sequencing (RNA-Seq) data was available for 51 out of 67 tumor samples. Results: We conducted unsupervised clustering analysis using the top 8000 most variable methylation probes and identified two distinct clusters (Cluster 1 n = 40, Cluster 2 n = 27). Thirty-three significant differentially methylated regions (DMRs, p-adj < 0.05) were identified between the two clusters using Bumphunter. Gene set enrichment analysis (GSEA) Hallmark analysis identified four enriched pathways of interest: IL6 JAK STAT3 Signaling, Mitotic Spindle, TGF Beta Signaling, and Apical Junction among genes included in these DMRs (p-adj < 0.05). We used RNA-Seq data to identify significant correlations between methylation probes and gene expression associated with DMR genes (n=30 genes; n=150 probes). We found probes in four genes of interest (HOXA3, MBP, NEDD4L, and TEX14) showed consistent negative correlations with gene expression levels. HOXA3 encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation in pathways that are highly relevant to chordoma development. Previous research has cited HOX complex inhibition in highly therapy resistant chordoma relapses. NEDD4L is associated with regulation of the epithelial NA+ channels and plays an important role in regulating tumor cell function through ubiquitinating substrates. MBP is involved in nervous system development, while the role of TEX14 in cancer is less understood. Conclusion: Our results confirmed findings from previous studies that chordoma is molecularly heterogeneous. In addition to immune pathways, we showed that the two subtypes also demonstrated different epigenetic regulation in mitosis and cell adhesion related genes/pathways. Next, we will expand the analysis by including more samples to increase statistical power and to associate our epigenetic findings with patient outcomes. Our goal is to build a reliable classifier to facilitate clinical management. We will integrate whole genome/exome sequencing data to identify potential epigenetic drivers. Citation Format: Gulzar N. Daya, Yujia Xiong, Mingxuan Li, Hela Koka, Xiaoyu Wang, DiFei Wang, Shilpa Katta, Jiwei Bai, Xiaohong R. Yang. Methylation subtypes of skull base chordoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB194.