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Molecular profiling of sacral chordomas through methylation, spatial transcriptomics and multiplexed
1Division of Precision Medicine, Department of Medicine, Grossman School of Medicine, New York University, New York.
Background:
Chordomas are rare bone malignancies originating from remnants of the notochord, primarily occurring at the base of the skull or sacrum. While typically slow growing with low-grade histology, chordomas can be locally aggressive and highly recurrent.
Materials And Methods:
We retrospectively identified 29 patients with sacral chordomas and utilized archival tissue to uncover novel insights into chordoma molecular heterogeneity, using a combination of DNA methylation profiling, spatial transcriptomics and multiplexed immunofluorescence.
Results:
Unsupervised clustering of methylation probes revealed two distinct epigenetic clusters, Cluster1 and Cluster2. Cluster2 was enriched for recurrent tumors and exhibited significant hypomethylation across most differentially methylated probes in intergenic and open sea regions. Multivariate linear regression analysis indicated that exon boundary and intergenic regions primarily drove these methylation changes. Digital Spatial Profiler (DSP) analysis identified differential gene expression among 9489 genes between tumor and stromal regions across 120 regions of interest, revealing 824 significantly differentially expressed genes. Tumor regions showed reduction of expression of major histocompatibility complex (MHC) class II genes and up-regulation of MHC class I genes compared with stroma. Multiplexed immunofluorescence revealed stromal enrichment of CD3+ and CD14+ cell populations, which was also associated with distinct survival groups. Stromal regions exhibited significant populations of immune-activated T cells and expression of immune checkpoint factors T-cell immunoglobulin and mucin-domain containing protein 3 and programmed cell death protein 1 (PD-1) in T-cell subsets. Stromal myeloid cells showed increased CD47 and PD-1 expression.
Conclusions:
Our study identified distinct epigenetic profiles in sacral chordomas, which were associated with recurrence, and revealed expression of checkpoint markers TIM3, CD47 and PD-1, warranting further investigation through functional validation.
Insights
Sacral chordoma epigenetics reveal two clusters linked to recurrence. Immune checkpoint markers like PD-1 were found in tumor stroma, suggesting new therapeutic targets for this rare bone cancer.
Area of Science:
- Oncology
- Molecular Biology
- Immunology
Background:
- Chordomas are rare, slow-growing bone malignancies originating from notochord remnants, primarily affecting the sacrum and skull base.
- Despite low-grade histology, chordomas can exhibit local aggressiveness and high recurrence rates.
- Understanding chordoma molecular heterogeneity is crucial for developing effective treatments.
Purpose of the Study:
- To investigate the molecular heterogeneity of sacral chordomas.
- To identify distinct epigenetic profiles and their association with tumor recurrence.
- To explore the tumor microenvironment, including immune cell infiltration and checkpoint marker expression.
Main Methods:
- Retrospective analysis of 29 sacral chordoma patient samples.
- DNA methylation profiling for epigenetic analysis.
- Digital Spatial Profiler (DSP) for transcriptomic analysis.
- Multiplexed immunofluorescence for immune cell profiling.
Main Results:
- Two distinct epigenetic clusters (Cluster1 and Cluster2) were identified via DNA methylation profiling, with Cluster2 associated with higher recurrence rates.
- Differential gene expression analysis revealed altered Major Histocompatibility Complex (MHC) class I and II gene expression between tumor and stromal regions.
- Stromal regions showed enrichment of immune-activated T cells and expression of immune checkpoint markers, including TIM3, CD47, and PD-1.
Conclusions:
- Distinct epigenetic profiles in sacral chordomas correlate with tumor recurrence.
- The expression of immune checkpoint markers (TIM3, CD47, PD-1) in the tumor microenvironment presents potential therapeutic targets.
- Further functional studies are warranted to validate these findings and explore therapeutic strategies.
