Novel targetable biomarkers in clear cell carcinoma of the breast uncovered by molecular profiling: A study of nine cases

Genetic Alterations in Invasive Breast Carcinoma with a Glycogen-Rich Clear Cell Pattern: A Case Report

Invasive carcinoma with a glycogen-rich clear cell pattern (IC-GRCCP) is a rare and understudied subtype of invasive breast carcinoma of no special type (IBC-NST). Here we report the molecular characteristics of a mammary IC-GRCCP diagnosed in a 69-year-old woman. Next-generation sequencing of the tumor revealed an inv(1)(p36.12,q32.1) leading to loss-of-function of ARID1A gene, a MAP2K4 truncating mutation (p.E376), MYC amplification, a variant of uncertain significance of PTPRB gene (p.D1848N) and deep deletions of NCKAP5, CCNT2, MAP3K19, LRP1B, and KMT2A. The analysis of the involved pathways shows close resemblance to the ovarian clear cell carcinoma and indicates similarities in the molecular mechanisms of development of glycogen-rich clear cell carcinomas in different organs. Our findings and the literature review suggest new potential strategies for treatment of mammary IC-GRCCP, including epigenetic therapies, checkpoint inhibitors, radiation, or other double-strand DNA breaks-inducing agents. Nevertheless, larger studies are needed to substantiate those ideas.

Novel targetable biomarkers in clear cell carcinoma of the breast uncovered by molecular profiling: A study of nine cases

We profiled nine pure clear cell carcinomas of the breast using massively parallel DNA and RNA sequencing (NGS), in situ hybridization (ISH), and immunohistochemistry (IHC). All cases were primary mammary clear cell carcinomas that were diagnosed in female patients (mean age: 53.4 years; range: 31‐69 years). Based on our findings, we conclude that the majority of clear cell carcinomas are ER/PR positive and consequently amenable to anti‐ER treatment modalities. A subset of clear cell carcinomas also harbored alterations in PIK3CA/PTEN/AKT pathway, particularly PTEN, indicating a potential benefit of PI3K/Akt/mTOR inhibitors. The status of I‐O biomarkers in clear cell carcinomas indicates a limited therapeutic benefit of immune checkpoint inhibitors (against PD‐1/PD‐L1).