Ovarian clear cell carcinoma (CCC) is one of the most malignant types of ovarian carcinomas, particularly at advanced stages. Unlike the more common type of ovarian cancer, high-grade serous carcinoma, ovarian CCC is often resistant to platinum-based chemotherapy, and therefore an effective treatment for this tumor type at advanced stages is urgently needed. In this study, we analyzed 97 ovarian CCCs for sequence mutations in KRAS, BRAF, PIK3CA, TP53, PTEN, and CTNNB1 as these mutations frequently occur in other major types of ovarian carcinomas. The samples included 18 CCCs for which affinity-purified tumor cells from fresh specimens were available, 69 microdissected tumors from paraffin tissues, and 10 tumor cell lines. Sequence mutations of PIK3CA, TP53, KRAS, PTEN, CTNNB1, and BRAF occurred in 33%, 15%, 7%, 5%, 3%, and 1% of CCC cases, respectively. Sequence analysis of PIK3CA in 28 affinity-purified CCCs and CCC cell lines showed a mutation frequency of 46%. Samples with PIK3CA mutations showed intense phosphorylated AKT immunoreactivity. These findings demonstrate that ovarian CCCs have a high frequency of activating PIK3CA mutations. We therefore suggest that the use of PIK3CA-targeting drugs may offer a more effective therapeutic approach compared with current chemotherapeutic agents for patients with advanced-stage and recurrent CCC.

Molecular genetic aberrations involving the p53, cyclin E-FBXW7, and PI3K pathways represent major mechanisms in the development of uterine serous carcinoma.

Dedifferentiated endometrial carcinoma is an aggressive type of endometrial cancer that contains a mix of low grade endometrioid and undifferentiated carcinoma components. We performed targeted sequencing of 8 dedifferentiated endometrial carcinomas and identified somatic frameshift/nonsense mutations in SMARCA4, a core member of the switch/sucrose non-fermenting (SWI/SNF) complex, in the undifferentiated components of 4 tumors. Immunohistochemical analysis confirmed the loss of SMARCA4 in the undifferentiated component of these 4 SMARCA4-mutated cases while the corresponding low grade endometrioid component showed retained SMARCA4 expression. An expanded survey of another member of the SWI/SNF complex showed SMARCB1 loss in the undifferentiated component of 2 SMARCA4-intact tumors. Subsequent immunohistochemical analysis of SMARCA4 and SMARCB1 was done in an additional set of 22 centrally reviewed dedifferentiated endometrial carcinomas and 31 grade 3 endometrioid carcinomas. Combining the results from the index and the expansion set, 15 of 30 (50%) of the dedifferentiated endometrial carcinomas examined showed either SMARCA4 loss (37%) or SMARCB1 loss (13%). The loss of SMARCA4 or SMARCB1 was mutually exclusive and occurred only in the undifferentiated component. All 31 grade 3 endometrioid carcinomas showed intact SMARCA4/SMARCB1 expression. The majority (73%) of the SMARCA4-deficient and half of SMARCB1-deficient undifferentiated component developed in a mismatch repair protein (MMR)-deficient molecular context. The observed spatial association between SMARCA4/SMARCB1 loss and histologic dedifferentiation suggests that loss of these SWI/SNF complex proteins may contribute to the development of dedifferentiated endometrial carcinoma.

Ovarian serous carcinoma, the most common and lethal type of ovarian cancer, is thought to develop from two distinct molecular pathways. High-grade (HG) serous carcinomas contain frequent TP53 mutations, whereas low-grade (LG) carcinomas arise from serous borderline tumors (SBT) and harbor mutations in KRAS/BRAF/ERBB2 pathway. However, the molecular alterations involved in the progression from SBT to LG carcinoma remain unknown. In addition, the extent of deletion of tumor suppressors in ovarian serous carcinomas has not been well studied. To further address these two issues, we assessed DNA copy number changes among affinity-purified tumor cells from 37 ovarian serous neoplasms including SBT, LG, and HG tumors using highdensity 250K single nucleotide polymorphism arrays. Chromosomal instability index as measured by changes in DNA copy number was significantly higher in HG than in LG serous carcinomas. Hemizygous ch1p36 deletion was common in LG serous carcinomas but was rarely seen in SBT. This region contains several candidate tumor suppressors including miR34a. In contrast, in HG serous carcinomas, significant numbers of amplifications and deletions, including homozygous deletions, were identified. Among homozygous deletions, loci containing Rb1, CDKN2A/B, CSMD1, and DOCK4 were most common, being present in 10.6%, 6.4%, 6.4%, and 4.3%, respectively, in independent 47 affinity-purified HG serous carcinomas. Except for the CDKN2A/B region, these homozygous deletions were not present in either SBT or LG tumors. Our study provides a genome-wide homozygous deletion profile in HG serous carcinomas, which can serve as a molecular foundation to study tumor suppressors in ovarian cancer.