Recurrent SMARCA4 mutations in small cell carcinoma of the ovary

Abstract

Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, highly aggressive form of ovarian cancer primarily diagnosed in young women. We identified inactivating biallelic SMARCA4 mutations in 100% of the 12 SCCOHT tumors examined. Protein studies confirmed loss of SMARCA4 expression, suggesting a key role for the SWI/SNF chromatin-remodeling complex in SCCOHT.

Figure 1. SMARCA4 mutations in SCCOHT and TCGA samples

(a) Domain structure of the SMARCA4 protein (UniProt, SMCA4_HUMAN) overlaid with the alterations identified in 11 of the 12 SCCOHT cases in this study (case numbers in parentheses; case 103 with exon deletion is not shown). SNF2_N, SNF2 family N-terminal domain; helicase, helicase-conserved C-terminal domain; SnAC, Snf2-ATP coupling, chromatin- remodeling complex; bromo, bromodomain. Genomic coordinates for splice-site mutations can be found in Supplementary Table 5. (b) Percentages of samples with nonsynonymous SMARCA4 mutations in SCCOHT and TCGA non-hypermutated samples (numbers of samples per study in parentheses). Blue bars represent samples with missense-only mutations, and orange bars represent samples with non-missense (including nonsense, frameshift, splice-site and indel) mutations. GBM, glioblastoma multiforme; AML, acute myeloid leukemia.

Figure 2. Analyses of the splice-site mutation in case 102

(a) Immunoblotting with antibody to the N terminus of SMARCA4. A high-grade serous ovarian cancer cell line (PEO4) and frozen tumor samples from two individuals with high-grade serous ovarian cancer (HGOC) were used as positive controls and retain protein expression. Protein extracted from H1299 non-small-cell lung cancer cells, deficient in SMARCA4, served as a negative control (Supplementary Fig. 6). Protein extracted from SCCOHT cases 101 and 102, both with donor-site splice-site mutations, show loss of SMARCA4 protein expression. (b) Loss of protein expression in archival tissue stained with a polyclonal antibody to SMARCA4. Note the intense staining of blood vessels and stromal cell nuclei as internal controls. Scale bar, 10 μm.