Prognosis-Linked FOXA1 Mutations Alter DNA Binding and Transcription

FOXA1 is frequently mutated in estrogen receptor–positive (ER⁺) breast cancer and encodes a pioneer transcription factor that is required for most ER–DNA binding. Arruabarrena-Aristorena and colleagues found that common missense mutations in FOXA1 were correlated with shorter progression-free survival in patients with ER⁺ breast cancer treated with aromatase inhibitors. Mutations of note affected the DNA-binding C-terminal forkhead domain and included one in β strand 3 (SY242CS) and three in Wing2 (H247Y, S250F, and F266L). In ER⁺ breast cancer cell lines grown in low-estrogen conditions, Wing2 mutations conferred increased proliferation and anchorage-independent growth capabilities. Additionally, in mice with low (basal-level) estrogen levels, xenografts expressing SY242CS-mutant or F266L-mutant FOXA1 exhibited greater growth than xenografts expressing wild-type FOXA1. In vitro, FOXA1 harboring mutations in the Wing2 subdomain had greater binding to ER loci upon estrogen stimulation, and Wing2 mutations caused increased transcription of estrogen response genes. In contrast, SY242CS-mutant FOXA1 occupied thousands of new binding sites on chromatin whether in the presence or absence of estrogen stimulation, and the SY242CS mutation led to increased expression of different genes than those induced by mutations in the Wing2 region, with particular enrichment of transcription of cholesterol, adipogenesis, and proliferation gene signatures—but not estrogen response gene signatures. Notably, the novel binding sites were characterized by a different motif from that bound by wild-type FOXA1, and almost half of the new FOXA1 binding sites observed with the SY242CS-mutant protein exhibited increased chromatin accessibility, consistent with a mechanism in which SY242CS-mutant FOXA1′s affinity for an alternate motif leads to chromatin opening and subsequent transcription at aberrant sites. In agreement with this notion, the top 50 most upregulated genes in SY242CS-mutant cells had substantial overlap with the atypically accessible chromatin sites and aberrant FOXA1 binding sites caused by the SY242CS mutation. Together, these findings demonstrate the clinical relevance of FOXA1 mutations in ER⁺ breast cancer and illustrate two mechanisms by which these mutations cause altered FOXA1 activity.

Arruabarrena-Aristorena A, Maag JLV, Kittane S, Cai Y, Karthaus WR, Ladewig E, et al. FOXA1 mutations reveal distinct chromatin profiles and influence therapeutic response in breast cancer. Cancer Cell 2020 Sep 3 [Epub ahead of print].

• ©2020 American Association for Cancer Research.