Molecular Profiling of Clear Cell Carcinoma of the Breast Reveals Novel Targetable Biomarkers

Background: Although clear cell morphology may be seen in various subtypes of breast cancer, a pure variant of clear cell carcinoma (usually glycogen-rich) is a very rare primary breast malignancy. It is characterized by the neoplastic cells with abundant and clear cytoplasm that contains glycogen. A recent SEER study highlighted the aggressive clinical behavior of this rare cancer. Apart from the steroid receptors profile (ER-positive in 33-75%, PR positive in 30-43% and HER2 positive in 0-44%) status, no information is available regarding its molecular features and targetable biomarkers. Design: Nine pure (>90% clear cell morphology) clear cell carcinomas of the breast were comprehensively profiled using massively parallel DNA and RNA sequencing (NGS), in-situ hybridization and immunohistochemistry. Results: Steroid receptors ER and AR were positive in 8/9 and 7/9 cases, respectively. AR was positive in 6/7 cases without the presence of ARv7 splice variant. None of the cases was HER2 positive. Pathogenic mutations were found in PIK3R1 and BRCA2 (#1), TP53, PTEN and CDKN2A (#2), TP53 and BCOR1 (#3). PTEN protein loss was confirmed by IHC in PTEN mutated cases as well as in two additional cases without detectable PTEN gene mutation. No gene fusion was seen in any of the cases. Low PD-L1 expression (1-10%) was exclusively seen in immune cells (n=3/8). All tested cases (n=8) were MSI stable and had low TMB (3-7 mutations/mb) (n=3). Conclusion: Clear cell carcinomas are predominantly ER and AR-positive and consequently amenable for endocrine treatment regimes. Frequent AR over-expression without ARv7 may support trials with anti-AR therapies. A proportion of clear cell carcinomas harbors alterations in the PIK3CA/PTEN pathway indicating a potential benefit of PI3K/Akt/mTOR inhibitors while the presence of PD-L1 on immune cells warrants the trials with immune checkpoint inhibitors.Caris Life Sciences, Phoenix, Arizona, US