Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial-mesenchymal transition

Abstract

Carcinosarcomas (CSs) of the uterus and ovary are highly aggressive neoplasms containing both carcinomatous and sarcomatous elements. We analyzed the mutational landscape of 68 uterine and ovarian CSs by whole-exome sequencing. We also performed multiregion whole-exome sequencing comprising two carcinoma and sarcoma samples from six tumors to resolve their evolutionary histories. The results demonstrated that carcinomatous and sarcomatous elements derive from a common precursor having mutations typical of carcinomas. In addition to mutations in cancer genes previously identified in uterine and ovarian carcinomas such as TP53, PIK3CA, PPP2R1A, KRAS, PTEN, CHD4, and BCOR, we found an excess of mutations in genes encoding histone H2A and H2B, as well as significant amplification of the segment of chromosome 6p harboring the histone gene cluster containing these genes. We also found frequent deletions of the genes TP53 and MBD3 (a member with CHD4 of the nucleosome remodeling deacetylase complex) and frequent amplification of chromosome segments containing the genes PIK3CA, TERT, and MYC Stable transgenic expression of H2A and H2B in a uterine serous carcinoma cell line demonstrated that mutant, but not wild-type, histones increased expression of markers of epithelial-mesenchymal transition (EMT) as well as tumor migratory and invasive properties, suggesting a role in sarcomatous transformation. Comparison of the phylogenetic relationships of carcinomatous and sarcomatous elements of the same tumors demonstrated separate lineages leading to these two components. These findings define the genetic landscape of CSs and suggest therapeutic targets for these highly aggressive neoplasms.

Keywords: exome sequencing; ovarian carcinosarcoma; uterine carcinosarcoma.

Fig. 1.

Mutational landscape across 41 CS samples. Mutation spectra for each sample are shown. Samples are grouped based on origin and histology of the carcinomatous component. The CNV fraction is the fraction of the genome that is affected by copy number gain or loss. (Lower) Mutations found in genes with a burden q value less than 0.2 are shown.

Fig. 2.

Structural analysis of histone mutations. (Left) Identified mutations in H2A and H2B are mapped onto the crystal structures of the core nucleosome particle (PDB ID codes 1AOI and 1XK5). (Right) Zoomed-in view of four representative mutations predicted to have large impacts on normal histone functions.

Fig. 3.

Evolution paths of six CSs. (A–F) Each panel shows the phylogenetic tree for one CS tumor that has undergone multiregion sequencing. The tumor name and number of root mutations are indicated at the top of the phylogenetic tree. Ca1 and Ca2 are samples dissected from carcinoma areas, Sa1 and Sa2 are samples dissected from sarcoma areas, root mutations are mutations shared by all samples from the same tumor, sarcomatous (carcinomatous) trunk mutations are mutations shared by all sarcomatous (carcinomatous) samples but never in the carcinomatous (sarcomatous) samples, and sarcomatous (carcinomatous) are private mutations [mutations found in sarcomatous (carcinomatous) samples besides trunk mutations]. Branch length is proportional to the number of nonsynonymous mutations. Driver genes are significantly mutated histone genes, and LOH events are highlighted.