Endothelial cell-specific DNA methylation alterations identified in breast cancer with epigenetic deconvolution

Abstract

DNA methylation alterations are epigenetic modifications that regulate gene expression and contribute to carcinogenesis. Technical challenges and high costs limit the use of single-cell sequencing approaches to measure and understand cell-specific DNA methylation alterations in the tumor microenvironment (TME). Using cell type deconvolution (HiTIMED) and an interaction testing framework (CellDMC), we identified DNA methylation alterations in tumor endothelial cells (TECs) from measures in bulk biospecimens. Alterations in TECs contribute to abnormal angiogenesis, resulting in disorganized, leaky blood vessels that can hinder drug delivery and immune access. We hypothesize that TECs in the TME exhibit distinct DNA methylation patterns compared to normal endothelial cells, driving phenotypic changes that support tumor growth and vascular dysfunction. We used genome-scale DNA methylation data and a testing and validation set design (tumor, n=1,080; nontumor, n=415) to identify TEC-specific DNA methylation alterations in breast cancer. Between cohorts, we validated 4,562 TEC-specific CpGs (4,163 hypermethylated and 399 hypomethylated), and found that many map to genes regulating angiogenesis and endothelial function. Integration with mRNA data from tumor samples in both discovery and validation sets revealed genes whose expression correlates with TEC-specific DNA methylation patterns and endothelial cell proportions, highlighting potentially novel therapeutic targets. This study demonstrates the utility of cellular deconvolution to uncover cell lineage-specific epigenetic changes in cancer using bulk specimen, and identifies TEC-specific methylation alterations as novel potential targets for therapeutic intervention.