Insights from Multigene Panel Sequencing and Comparative Analysis of Metaplastic Carcinoma of the Breast

Background: Metaplastic carcinoma of the breast (MBC) is characterized by resistance to conventional chemotherapy and lack of specific targeted therapy. With this study we sought to define the repertoire of somatic alterations of different subtypes of MBC. Design: TruSight RNA Pan-Cancer Panel (Illumina) was performed to identify somatic variants, novel transcripts, transcript variants and fusions in 7 squamous, 5 matrix-producing and 3 spindle cells MBCs, compared to triple-negative invasive ductal carcinomas of no special type (IDC-NSTs) from The Cancer Genome Atlas (TCGA). Genomic and transcriptomic analyses were performed with OpenCravat and DESeq2. Statistical significance was set at p-values < 0.05. Funding: research project "Tuscany Health Ecosystem" THE – Spoke 6. CUP I53C22000780001. Results: All 15 MBCs harbored recurrent somatic mutations in TP53 and chromatin remodelling genes, including KMT2C and EP300. Compared to triple-negative IDC-NSTs, MBCs more frequently harbored mutations in PI3K/AKT/mTOR and canonical Wnt pathway-related genes, with increased activity in these pathways. Among the different subtypes, TP53, CTNNB1, PIK3R1, EGFR and EP300 mutations were not found in spindle cells MBCs where, instead, NOTCH and ARID1A pathways were activated (Figure A). Druggable ESCAT variants were identified, including PIK3CA hotspot mutations (p.C420R, p.H1047Y) (level I) and ERBB2 hotspot mutations, PTEN alterations, and BRCA1/2 somatic mutations (p.R1699W, p.Q1148Ter) (level II). Notably, RP1-34H18.1-NAV3 gene fusion (47%) was found across all subtypes (Figure B). Interestingly, Volcano plots revealed over 56 differentially expressed genes between spindle cells and matrix-producing MBCs, including CHN1, NTRK1, CMKLR1, CASP7 and TRSP1, FGFR2, EZH2, ERBB3 as upregulated and downregulated genes, respectively. Additionally, more than 20 genes showed distinct expression among the other histological subtypes (Figure C). Conclusions: MBC is a genetically complex and heterogeneous disease, distinct from triple-negative IDC-NST and with differences among subtypes in terms of genomic and transcriptomic profiles. Moreover, our data suggest the rationale for the potential use of therapeutic compounds in case of alterations in ERBB2, PTEN and BRCA1/2 beyond PI3K/AKT/mTOR and Wnt pathways. Finally, the identification of specific fusions never described before in MBC may have potential implications.