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Updated: Jul 23, 2025
Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients
Published on: June 16, 2017
DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and
Szymon Baluszek1, Paulina Kober1, Natalia Rusetska2
1Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.
Abstract:
Chordomas are rare tumors of notochord remnants, occurring mainly in the sacrum and skull base. Despite of their unusually slow growth, chordomas are highly invasive and the involvement of adjacent critical structures causes treatment challenges. Due to the low incidence, the molecular pathogenesis of this entity remains largely unknown. This study aimed to investigate DNA methylation abnormalities and their impact on gene expression profiles in skull base chordomas. 32 tumor and 4 normal nucleus pulposus samples were subjected to DNA methylation and gene expression profiling with methylation microarrays and RNA sequencing. Genome-wide DNA methylation analysis revealed two distinct clusters for chordoma (termed subtypes C and I) with different patterns of aberrant DNA methylation. C Chordomas were characterized by general hypomethylation with hypermethylation of CpG islands, while I chordomas were generally hypermethylated. These differences were reflected by distinct distribution of differentially methylated probes (DMPs). Differentially methylated regions (DMRs) were identified, indicating aberrant methylation in known tumor-related genes in booth chordoma subtypes and regions encoding small RNAs in subtype C chordomas. Correlation between methylation and expression was observed in a minority of genes. Upregulation of TBXT in chordomas appeared to be related to lower methylation of tumor-specific DMR in gene promoter. Gene expression-based clusters of tumor samples did not overlap with DNA methylation-based subtypes. Nevertheless, they differ in transcriptomic profile that shows immune infiltration in I chordomas and up-regulation of cell cycle in C chordomas. Immune enrichment in chordomas I was confirmed with 3 independent deconvolution methods and immunohistochemistry. Copy number analysis showed higher chromosomal instability in C chordomas. Nine out of eight had deletion of CDKN2A/B loci and downregulation of genes encoded in related chromosomal band. No significant difference in patients' survival was observed between tumor subtypes, however, shorter survival was observed in patients with higher number of copy number alterations.
Insights
Skull base chordomas exhibit distinct molecular subtypes based on DNA methylation, influencing gene expression and chromosomal instability. These subtypes, C and I, show unique methylation patterns and cellular characteristics, impacting tumor behavior and patient outcomes.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Chordomas are rare, invasive tumors arising from notochord remnants, primarily affecting the skull base and sacrum.
- Their slow growth and invasiveness present significant treatment challenges, complicated by largely unknown molecular pathogenesis.
- Understanding the molecular underpinnings of chordomas is crucial for developing targeted therapies.
Purpose of the Study:
- To investigate DNA methylation abnormalities and their impact on gene expression in skull base chordomas.
- To identify distinct molecular subtypes of chordomas based on methylation patterns.
- To correlate molecular findings with clinical characteristics and patient survival.
Main Methods:
- Genome-wide DNA methylation profiling using methylation microarrays.
- RNA sequencing for gene expression profiling.
- Copy number analysis and immunohistochemistry for validation.
Main Results:
- Two distinct chordoma subtypes (C and I) identified based on DNA methylation patterns: C chordomas showed hypomethylation with CpG island hypermethylation, while I chordomas were generally hypermethylated.
- Subtype C chordomas exhibited higher chromosomal instability and cell cycle gene upregulation, whereas subtype I chordomas showed immune infiltration.
- TBXT upregulation correlated with decreased promoter methylation in chordomas.
- No significant survival difference between methylation subtypes, but increased copy number alterations were associated with shorter survival.
Conclusions:
- Skull base chordomas comprise at least two distinct molecular subtypes with differing methylation, gene expression, and chromosomal instability profiles.
- These molecular differences, particularly immune infiltration in subtype I and cell cycle dysregulation in subtype C, may influence tumor behavior.
- Further research into these subtypes could lead to more personalized treatment strategies for chordoma patients.
