Genetic analysis of low-grade adenosquamous carcinoma of the breast that progressed to high-grade metaplastic carcinoma

Low-grade adenosquamous carcinoma (LGASC) is a rare type of metaplastic carcinoma of the breast (MBC) with an indolent clinical course. A few cases with high-grade transformation have been reported; however, their genetic alterations remain unclear. This study was designed to explore the somatic genetic characteristics of LGASC with transformation to high-grade MBC. Whole-genome sequencing analysis was performed on five MBCs from four patients, including one case with matching primary LGASC and lymph node metastatic tumor consisting of high-grade MBC with a predominant metaplastic squamous cell carcinoma pattern (MSC) that has progressed from LGASC, and three de novo MSC. Both LGASC and its associated MSC, unlike de novo MSC, had no TP53 mutation and tended to have fewer structural variants than de novo MSC. Both LGASC and its associated MSC had common mutations and copy number alterations, including GNAS R844C, which shows an increase in its allele frequency in MSC. These results indicated that LGASC and its associated MSC were ancestry clonal and that clonal selection occurred during progression. MSC associated with LGASC had additional pathogenic deletions of multiple tumor suppressor genes caused by, for example, SMAD4–DCC fusion. Reverse transcription polymerase chain reaction, followed by Sanger sequencing, confirmed this fusion transcript in both LGASC and its associated MSC; however, chimera proteins were not detected by Western blotting. SMAD4 protein expression had already decreased at the stage of LGASC, which may have contributed to the tumorigenesis of LGASC. In conclusion, not only LGASC but also its associated high-grade MBC may be genetically different from de novo high-grade MBC. The progression from LGASC to high-grade MBC may concern the concentration of the driver mutation caused by clonal selection and inactivation of tumor suppressor genes.