Single-cell analysis of accessible chromatin in human mammary epithelial cells using scATAC-seq [scATAC-seq]

Epigenome delineates lineage-specific transcriptional programs and restricts cell plasticity to prevent non-physiological cell fate transitions. Although cell diversification fosters tumor evolution and therapy resistance, upstream mechanisms that regulate the stability and plasticity of cancer epigenome remain elusive. Here, we show that 2-hydroxyglutarate (2HG) not only suppresses DNA repair but also mediates high-plasticity chromatin landscape. A combination of single-cell epigenomic and multi-omic approaches demonstrates that 2HG disarranges otherwise well-preserved stable nucleosome positioning and promotes cell-to-cell variability. 2HG induces loss of motif accessibility to luminal-defining transcriptional factors FOXA1, FOXP1 and GATA3 and a shift from luminal to basal-like gene expression. Breast tumors with high 2HG exhibit enhanced heterogeneity with undifferentiated epigenomic signatures linked to adverse patient prognosis. Further, ascorbate-2-phosphate (A2P) eradicates heterogeneity and impairs growth of high 2HG-producing breast cancer cells. These findings suggest 2HG as a key determinant of cancer plasticity and provide a rational strategy to counteract tumor cell evolution. Profiles of single-cell epigenomes were assayed using scATAC-seq across 3 samples.