Epigenetic heterogeneity in breast tumours informs diagnosis and prognosis.

A recurrent basal-like cell subpopulation with a conserved epigenetic signature is found within treatment-naive human luminal breast tumours, linked to loss of luminal identity.

• Why it matters: Intratumour epigenetic heterogeneity complicates diagnosis and long-term disease-free survival, and luminal tumours may still harbor aggressive basal-like programs.
• What they did: Using a single-cell epigenetic cytometry by time-of-flight approach on luminal tumours after surgical resection, the study identifies basal-like cells and validates them via whole-genome DNA methylation deconvolution. It compares single-cell proteomic and genomic profiling of histone 3 lysine 4 monomethylation and trimethylation, and tests blood cell-free nucleosome profiling for a liquid biopsy signal.
• The result: Histone 3 lysine 4 marks associate with loss of luminal identity, and the basal epigenetic signature measured in blood is linked to prognosis, enabling relapse-risk identification.

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