Landscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma

Abstract

Uterine serous carcinoma (USC) is a biologically aggressive subtype of endometrial cancer. We analyzed the mutational landscape of USC by whole-exome sequencing of 57 cancers, most of which were matched to normal DNA from the same patients. The distribution of the number of protein-altering somatic mutations revealed that 52 USC tumors had fewer than 100 (median 36), whereas 5 had more than 3,000 somatic mutations. The mutations in these latter tumors showed hallmarks of defects in DNA mismatch repair. Among the remainder, we found a significantly increased burden of mutation in 14 genes. In addition to well-known cancer genes (i.e., TP53, PIK3CA, PPP2R1A, KRAS, FBXW7), there were frequent mutations in CHD4/Mi2b, a member of the NuRD-chromatin-remodeling complex, and TAF1, an element of the core TFIID transcriptional machinery. Additionally, somatic copy-number variation was found to play an important role in USC, with 13 copy-number gains and 12 copy-number losses that occurred more often than expected by chance. In addition to loss of TP53, we found frequent deletion of a small segment of chromosome 19 containing MBD3, also a member of the NuRD-chromatin-modification complex, and frequent amplification of chromosome segments containing PIK3CA, ERBB2 (an upstream activator of PIK3CA), and CCNE1 (a target of FBXW7-mediated ubiquitination). These findings identify frequent mutation of DNA damage, chromatin remodeling, cell cycle, and cell proliferation pathways in USC and suggest potential targets for treatment of this lethal variant of endometrial cancer.

Fig. 1.

Somatic variation pattern underlying USC. (A) Distribution of the number of protein-altering somatic mutations in 34 normal-tumor USC pairs. Subplot left, mutation spectrum in four hypermutator phenotype samples; subplot right, mutation spectrum in 30 moderately mutated samples. (B and C) Thirty tumors with moderate somatic burden are arranged by the total number of somatic point mutations from left to right. The four hypermutator phenotype tumors are excluded in this analysis. (B) Significantly mutated genes are listed vertically by the order of damaging or conserved P values shown in Table 1. (C) Genes with significant CNVs and genes of interest are listed. Copy neutral status is shown as lavender rectangles. Five samples without CNV information are marked by crosses.

Fig. 2.

Mapping of USC mutations onto the crystal structure of CHD4. (A) Schematic representation of somatic mutations found in CHD4. The horizontal bar represents full-length CHD4 protein with functional domains shown as boxes. Somatic mutations found in USC are marked in red text. All mutations are missense mutations except E1628X, which is a nonsense mutation. (B) C464 locates in the second PHD finger, which binds directly to histone H3 methylated at K9. An NMR structure of the second PHD domain of CHD4 (blue ribbon plot) has been determined [Protein Data Bank (PDB) ID: 2L75] (17). Red dot represents C464Y mutation. (Lower) A close-up view of the zinc–C464 interaction. (C) Somatic mutations in catalytic core of CHD4 mapped to the crystal structure of a related protein, human CHD1 (sequence identity of the ATPase lobes is 42%, homology is 57% over 572 residues; PDB ID: 3MWY) (18). Blue, ATPase lobe 1; light purple, ATPase lobe 2; cyan, chromodomains; green, C-terminal bridge. Three mutations (red dots) in CHD4 fall within known conserved motifs (motifs B, V, VI) (19); three mutations were found in unknown helicase motif i, and two mutations were found in unknown motif ii. (D) A close-up view of mutations in five motifs in C. Somatic mutations are labeled in red text; amino acid positions in parentheses represent homologous positions in CHD1.

Fig. 3.

Schematic representation of TAF1 functional domains and mutation conservation analysis. (A) Functional domains in TAF1 are represented by colored boxes with domain names noted below (23). HAT domain, histone acetyltransferase domain. Mutations found in USC are labeled at the top by red text. (B) Multiple sequence alignment across vertebrate and invertebrate species around the seven mutations found in USC. Mutation positions in human TAF1 are labeled in red at the top. Sequence aligned by Clustal W 2.0 (24).

Fig. 4.

Copy-number profile of 25 USC tumors. Frequency of copy-number gain (red) and copy-number loss (blue) are plotted along the genome. Horizontal dotted line, genome-wide significance level for CNV gain (red) and CNV loss (blue). Genes of interest in significant CNV peak regions are labeled.

Fig. 5.

Major altered pathways in USC. The altered percentages shown for genes and pathways come from the 25 matched tumors with CNV information. Genes are colored based on their activity in the pathway diagram. Pink, predicted activated; blue, predicted inactivated; gray, uncertain at this stage; lines with blunt end, inhibiting effect; lines with pointed end, promoting effect; dotted line, uncertain. Mutation and CNV status for each gene across the 25 samples are shown at the bottom following the pathway diagram.