Deep sequencing of 360 primary breast tumors identified 9 genes with recurrently mutated promoters.

  • Major finding: Deep sequencing of 360 primary breast tumors identified 9 genes with recurrently mutated promoters.

  • Concept: Mutations in a FOXA1 promoter hotspot promote E2F binding and enhanced expression.

  • Impact: Deep-sequencing studies in large cohorts may uncover additional functionally relevant promoter mutations.

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Genomic studies have identified numerous protein-coding mutations that promote tumorigenesis, but less is known about the contribution of mutations in noncoding regions.

Rheinbay and colleagues performed deep sequencing of 360 primary breast tumors and matched normal samples and developed computational methods to identify recurrent promoter mutations in breast cancer. This analysis identified nine genes with excessive or clustered promoter mutations: FOXA1 (altered in 2.9% of patients), TBC1D12 (in 3.9%), RMRP/CCDC107 (a bidirectional promoter; in 2.5%), NEAT1 (in 1.4%), LEPROTL1 (in 1.7%), ALDOA (in 1.7%), ZNF143 (in 3.6%), CITED2 (in 0.8%), and CTNNB1 (in 1.4%). The observed mutations occurred at single-site hotspots or in tight clusters. In reporter assays, the majority of mutations in the NEAT1, TBC1D12, ZNF143, ALDOA, and LEPROTL1 promoters reduced promoter activity. In contrast, mutations in the FOXA1 and RMRP promoters increased gene expression, suggesting increased recruitment of transcriptional activators. The FOXA1 promoter mutations increased binding of the E2F family transcription factors E2F1 and E2F3, and the E2F3 cofactor DP1, leading to enhanced FOXA1 expression and activation of downstream ER signaling, allowing breast cancer cells to grow in low-estrogen conditions. Thus, cells overexpressing FOXA1 were more resistant to the ER-antagonist fulvestrant, which is used to treat hormone receptor–positive breast cancer, than control cells. In patients with breast cancer, the mutation rate in promoter hotspots was similar to the rate of coding mutations in well-characterized cancer drivers such as PIK3CA, AKT1, and TP53. Taken together, these findings suggest that recurrent promoter mutations in patients with breast cancer can alter protein binding and transcription to promote breast tumorigenesis and may explain the activation or inactivation of cancer genes in patients who lack coding mutations. Further analysis of promoter mutations in patients with cancer may lead to the identification of additional cancer-promoting genes and potential therapeutic targets.

Rheinbay E, Parasuraman P, Grimsby J, Tiao G, Engreitz JM, Kim J, et al. Recurrent and functional regulatory mutations in breast cancer. Nature 2017;547:55–60.