NEW YORK – An international team led by researchers at Memorial Sloan Kettering Cancer Center investigated genome-wide chromatin recruitment, chromatin accessibility, and transcriptional networks in breast cancer models harboring recurrent mutations in the FOXA1 gene, and found that patients with these mutations have distinct chromatin profiles and don't respond as well to aromatase inhibitor therapy as patients without the mutations.
In a study published on Thursday in Cancer Cell, the researchers noted that FOXA1 has frequently been found to be mutated in estrogen receptor-positive breast cancer. The gene is a pioneer factor that binds to condensed chromatin allowing the recruitment of other transcription factors to DNA, and it can displace linker histones to maintain enhancer nucleosomes accessible for other transcription factors to bind, they said. Because of that, FOXA1 reprograms ER recruitment at cis-regulatory elements, affecting cell growth and response to endocrine therapies like PI3K inhibitors.
The researchers first studied the prevalence of FOXA1 mutations in breast cancer using a cohort of 4,952 patients who had been profiled with the Memorial Sloan Kettering-integrated mutation profiling of actionable cancer targets (MSK-IMPACT) platform. FOXA1 mutations occurred at a frequency of nearly 4.2 percent in all patients and nearly 4.9 percent in metastatic tumors, they found.
The researchers performed several analyses using a curated cohort of 1,918 tumors from 1,756 breast cancer patients with detailed clinical annotation. Among their findings, they noted that hotspot mutations in PIK3CA, the catalytical subunit of PI3K, were significantly enriched in the FOXA1-altered cases. Among the different FOXA1 alterations, missense substitutions were the most prevalent. Further, FOXA1 hotspot mutations were more common in metastatic ER-positive cases than in primary ER-positive breast cancers, and were mutually exclusive with mutations in ESR1, which are well-known drivers of endocrine therapy resistance.
Given this mutual exclusivity, they next studied whether the presence of FOXA1 mutations in breast cancers would be associated with clinical outcome after anti-estrogen therapy. The team analyzed all 6,136 tumors from the patients with FOXA1 mutations in the MSK-IMPACT clinical series and filtered the patients treated with single-agent endocrine therapy. The analysis included 17 eligible patients with metastatic breast cancers whose tumors harbored missense FOXA1 mutations in the tumor samples collected before the start of an aromatase inhibitor and 287 metastatic breast cancer with pretreatment FOXA1 wild-type tumors as controls.
They found that patients harboring FOXA1 missense mutations had significantly shorter progression-free survival of 4.6 months compared to 12.2 months for patients with wild-type FOXA1.
The researchers also performed atomistic molecular dynamics simulations to explore the effects of FOXA1 mutations on their interaction with DNA. They found that most mutations retained canonical interactions between wild-type FOXA1 and DNA, but that several mutations conferred structural alterations. Specifically, the mutation SY242CS showed neomorphic properties that included the ability to open distinct chromatin regions and activate an alternative cistrome and transcriptome. The team's structural models predicted that SY242CS confers a conformational change that mediates stable binding to a non-canonical DNA motif.
Further analyses indicated that genes upregulated by the SY242CS mutation are related to proliferation and tumorigenesis, and that the mutation provided FOXA1 with the capacity to alter the chromatin accessibility and activate a unique cistrome, which in turn triggered the expression of an alternative transcriptome.
The FOXA1 SY242CS variant “grants a cellular growth advantage in line with the transcriptomic signatures that this mutant induces, which in concert may contribute to [aromatase inhibitor] resistance," the authors wrote. "Other SY242CS-specific gene signatures include increased lipid synthesis which may be a potential energy source to sustain the increased proliferation rate for this mutant."