Epigenomic disorder and partial EMT impair luminal progenitor integrity in Brca1-associated breast tumorigenesis

Defects in double-strand repair mechanisms - both through germline or somatic inactivation of repair genes - is a hallmark of basal-like breast cancers. In this genetically-unstable context, a recurrent major shift in cell identity occurs within the mammary epithelium. Basal-like BRCA1 tumors have indeed been proposed to originate from luminal progenitor cells yet tumor-initiating events remain poorly understood. Here, we map the state transitions leading luminal progenitors to tumor formation, using a mouse model launching tumorigenesis in multiple LP cells. We identify a population of cycling p16-expressing cells, emerging from the luminal progenitor compartment, undergoing partial epithelial-to-mesenchymal transition and losing luminal identity. Pseudo-temporal analyses position these cells as a transitory state between aberrant Brca1-deficient luminal progenitors and growing tumor cells. Concomitant to p16 activation, we show that LP cells undergo an epigenomic crisis attested by the general re-organization of their heterochromatin. They accumulate multiple H3K27me3 micro-foci - reminiscent of the formation of senescence-associated heterochromatin foci (SAHFs) - and lose their inactive X (Xi). Both p16 activation and heterochromatin reorganization are hallmarks of human basal-like breast tumors, we propose that these events occur during initial LP transformation and are scars of an initial transitory senescent-like state. Single-cell RNA-seq was performed mammary gland samples from n=3 Cre Negative (Brca1+/+ Tp53 +/+) and n= 8 Cre Positive (Brca1-/- Tp53 -/-) samples at different histological stages : young mice (2-3 months old), mice with millimitric tumors (5-5.4 months) and tumor samples at different sizes (6 months).