Premium
The DNA methylation signature of EpCAM‐/CD49f‐ breast cancer stem cells correspond with worse clinical severity in basal‐like breast cancers
Author(s) -
Rizzo Paris,
Benson Layne,
Shull Austin
Publication year - 2021
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2021.35.s1.04846
Subject(s) - dna methylation , cpg site , cancer research , biology , methylation , epigenetics , breast cancer , cancer stem cell , cancer , microbiology and biotechnology , genetics , dna , gene , gene expression
The metastatic potential in breast cancer can correspond with the uncontrolled expansion of mammary stem cells identified by loss of epithelial markers EpCAM and CD49f. These populations identified as breast cancer stem cells (CSCs) can be important from a prognostic standpoint, thus characterizing the CSC‐specific epigenetic events would be of great interest with DNA methylation playing such a critical role in cell fate. To accomplish this characterization, we compared the 450K DNA methylation profile of EpCAM‐/CD49f‐ cells from the isogenic MCF10A p53‐/PTEN‐ breast cell line against the corresponding EpCAM+/CD49f+ and EpCAM‐/CD49f+ subpopulations to determine a CSC‐specific DNA methylation signature. Additionally, we overlapped the profiles from 16 established breast cancer cell lines of varying aggressiveness to determine how these cells relate epigenetically with the isolated CSCs. Based on unsupervised PCA and matrix dissimilarity clustering, we identified distinct groups that cluster based on EpCAM‐/CD49f‐ enrichment status, with a group of CSC‐rich cells clearly clustering together. This grouping was interesting as these CSC‐rich cell line all contained both a TP53 mutation and a PI3K/AKT pathway alteration. From the clustered groups, we performed differential DNA methylation analysis between varying genomic regions and discovered that DNA methylation changes varied by location between CSC‐rich and CSC‐poor cell lines (ANOVA FDR p ‐value <0.01). Specifically, CpG islands in promoter‐associated regions were differentially hypermethylated in CSC‐rich cells, yet non‐CpG islands in promoters as well as gene body regions demonstrated extensive hypomethylation in CSCs. Additionally, when comparing CpG island vs non‐CpG island promoter methylation, genes with CpG island promoter hypermethylation were enriched for cell differentiation genes (ex: CDH1, IRF6, CLDN7), whereas non‐CpG island promoter hypomethylation were enriched for immune regulation and inflammation genes (ex: TLR9, IL32, IL27). Furthermore, correlation between differentially methylated regions and EpCAM‐/CD49f‐ enrichment showed that hypomethylation significantly correlated with an increase in EpCAM‐/CD49f‐ positive cells. Additionally, these hypomethylation events were present in the TCGA breast cohort with hypomethylation events being preferentially enriched in both basal‐like tumors and tumors harboring TP53 mutations. Lastly, several genes with lower overall DNA methylation corresponded with worse progression‐free survival including RBM47 , PLEKHA7 , DOK7 , and OVOL1 . In conclusion, we identified a DNA methylation signature in EpCAM‐/CD49f‐ breast CSCs and demonstrated that these CSC‐associated epigenetic events shed light on the clinically severe phenotype in basal‐like breast cancers.