Molecular characterization of ovarian squamous cell carcinoma originating from mature teratoma

Squamous cell carcinoma (SCC) of the ovary, an uncommon form of gynecologic cancer, typically originates from the malignant transformation of a pre-existing mature ovarian teratoma (MOT). However, due to its rarity, the molecular pathways driving its development are not well understood. To address this knowledge gap, we performed molecular inversion probe (MIP) array analysis and targeted sequencing of 275 cancer susceptibility genes on 11 ovarian SCC samples derived from MOTs. Additionally, we conducted the same molecular tests on two samples of ovarian metastases of SCCs that originated from primary sites outside the ovary, specifically, one from endometrial cancer and one from cervical SCC. Utilizing MIP arrays, we identified failures in meiosis I and II, as well as instances of endoreduplication within haploid ova, in five, two, and four samples of ovarian SCCs arising from MOTs, respectively. Notably, such alterations were absent in samples of ovarian metastases, implying that primary ovarian SCCs may derive from teratoma cells. Targeted sequencing identified TP53 as the most frequently mutated gene in ovarian SCCs, occurring in 82% of cases. This was followed by mutations in PIK3CA (36%), PTEN (27%), and KMT2D (27%). Furthermore, mutations in CDKN2A and copy number loss of 9p21.3 were observed in 54.5% of the cohort. In summary, our study elucidates the germ cell origin of ovarian SCC and provides a comprehensive analysis of its genomic landscape, which may assist in differential diagnosis and inform the development of targeted therapies with potential clinical benefits. KEY MESSAGES: Failures in meiosis I/II and endoreduplication found in primary ovarian SCCs.  Ovarian SCCs may derive from germ cells in mature teratomas.  Alterations absent in ovarian metastases from SCC aid differential diagnosis. TP53 mutations found in 82% of ovarian SCC cases. CDKN2A mutations and 9p21.3 loss observed in 54.5% of ovarian SCC cohort.