Functional Characterization of Breast Cancer-Associated Histone Mutations

Cancer-related somatic histone mutants are present in 4% of diverse tumor types and display a similar genomic prevalence to other somatic mutations in cancer, but they are not well characterized. We curated and characterized 17 of the most frequently recurring missense mutations in histone H2A, H2B, and H3 genes in breast cancers occurring at glutamate (E), aspartate (D), serine (S), and arginine (R) residues. Many of these mutants co-occur with PIK3CA mutations in breast cancers. We expressed these breast cancer-associated histone mutants in MCF-7 and MDA-MB-468 breast cancer cells, or MCF-10A mammary epithelial cells, and screened them for effects on oncogenic phenotypes in a variety of cell- and tumor-based assays (i.e., proliferation, migration, invasion, competitive outgrowth, transformation). In addition, we examined the effects of selected mutants on DNA damage, gene expression, and histone modifications. We observed varying phenotypic and functional effects. Some of the histone mutants promoted cancer-related phenotypes, with H2B-E76Q, H3-E97K, and H3-E105K eliciting strong oncogenic phenotypes, alterations in gene expression, and context-dependent growth enhancement in a PI3K-activated background. We further showed that the H2B-E76Q and H3-E105K mutants exhibit reduced ADP-ribosylation compared to their cognate wild-type histones, resulting in altered H3-S10 phosphorylation and H3-K27 acetylation in cells. Our results indicate that some histone mutants can promote oncogenic effects in breast cancers, contributing to cancer pathogenesis and tumor progression. Implications: These findings identify a subset of breast cancer-associated histone variants with oncogenic activity, highlighting the role of histone mutations in promoting tumor phenotypes through epigenomic alterations and signaling crosstalk.