Comprehensive Profiling of Metaplastic Breast Carcinoma Reveals Frequent Over-Expression of PD-L1

Background: Metaplastic breast carcinoma (MBC) is a rare subtype of breast carcinoma less responsive to conventional chemotherapy relative to usual breast carcinomas such as ductal and lobular subtype. In molecular terms, MBC usually clusters with triple negative breast cancers (TNBC), but MBCs portray a worse prognosis in comparison with TNBC. Published studies investigating MBCs for specific biomarkers of therapy response are rare and limited by the methodological approaches. Methods: 297 samples [MBC (n=75), triple-negative breast cancer of no-special-type (TNBC-NOS, n=106), HER2-positive breast cancers (n=32) and luminal breast cancers (n=84)] were profiled using direct sequencing analysis [Illumina MiSeq Next Generation Sequencing (NGS)]. Immunohistochemistry for PD-L1 (SP142, Spring Bioscience) and PD-1 (NAT105, Ventana) was performed using automated procedures. Results: 89% MBCs exhibited triple-negative immunophenotype (ER-/PR-/HER2-). The most common mutations in MBCs included TP53 (67%) and PIK3CA mutations (23%). Other mutations were rare including HRAS mutations (7%), STK11 (5%), FBXW7, PTEN, c-MET and JAK3 (4%, respectively). PD-L1 expression on cancer cells was detected in significantly higher proportion of MBCs (46%) than in other molecular subtypes (6% in luminal and HER2+ breast cancers, respectively and 9% in TNBC-NOS, p\u3c0.001). PD-1 positive tumors infiltrating lymphocytes (TILs) varied greatly in MBCs (0 to \u3e50/mm2). Conclusion: Comprehensive profiling of a large cohort of this rare carcinoma highlighted predominance of TP53 mutations, wild type EGFR gene expression, a distinct increase in proportion of PD-L1 expression in carcinoma cells, and PD-1 expression in TILs. The latter propert