Theranostic molecular profiling of pleomorphic ductal carcinoma of the breast

Pleomorphic ductal carcinoma (PDC) is a very rare subtype of invasive ductal carcinoma of no‐special type (NST), characterized by the presence of highly atypical/bizarre (>6‐fold variation in nuclear size) and multinucleated (giant) neoplastic cells comprising >50% of the tumor cell population (Figure 1A). PDC is typically triple‐negative breast cancer (TNBC), associated with an aggressive clinical course and a poor outcome.2–4 So far, no single study explored novel predictive biomarkers for the precision medicine purposes in the patients with PDC. Formalin‐fixed paraffin‐embedded tissue samples of the six PDC patients (four primary and two metastatic cases) were sequenced for 592‐genes using NextSeq platform (Illumina, La Jolla, CA, USA). Tumor mutational load (TML) was calculated using only somatic nonsynonymous missense mutations; high TML was considered when it was ≥17 mutations/Mb. Microsatellite instability (MSI) status was explored by the direct analysis of known MSI loci in the target regions of the sequenced genes. Cases were considered microsatellite instable (MSI‐H) if they exhibited ≥46 altered microsatellite loci (the threshold was established by comparing to the PCR‐based MSI FA result from ~2100 cases). Copy number variations (CNVs) were determined by comparing the depth of sequencing of genomic loci with a diploid control. Calculated gains ≥6 copies were considered amplified. ArcherDx FusionPlex Assay was used to detect gene fusions (52 gene targets). Immunohistochemistry was used to detect expression of PD‐L1 (SP142 antibody, Ventana) in tumor cells (TC) and immune cells (IC). PD‐L1 positivity in TC was defined as 2+ intensity in ≥5% of tumor cells. PD‐L1 status