Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden

Abstract

Bladder cancers are a leading cause of death from malignancy. Molecular markers might predict disease progression and behaviour more accurately than the available prognostic factors. Here we use whole-genome sequencing to identify somatic mutations and chromosomal changes in 14 bladder cancers of different grades and stages. As well as detecting the known bladder cancer driver mutations, we report the identification of recurrent protein-inactivating mutations in CDKN1A and FAT1. The former are not mutually exclusive with TP53 mutations or MDM2 amplification, showing that CDKN1A dysfunction is not simply an alternative mechanism for p53 pathway inactivation. We find strong positive associations between higher tumour stage/grade and greater clonal diversity, the number of somatic mutations and the burden of copy number changes. In principle, the identification of sub-clones with greater diversity and/or mutation burden within early-stage or low-grade tumours could identify lesions with a high risk of invasive progression.

Figure 1. Somatic SNV spectrum genome-wide.

The proportions of somatic SNVs of each type are shown for each of our cancers (whole genome or exome) in comparison with the TCGA bladder cancer data (exomes).

Figure 2. Summary of known and putative somatic-driver mutations after filtering in each cancer.

MDM2 amplification is included in the figure for comparison with TP53 and CDKN1A. The established driver mutations PIK3CA and MLL3 are included despite being present in only one tumour to allow comparison with the presence of other mutations. Note that only mutations passing our filtering criteria are shown here, and that other potentially pathogenic mutations of lesser predicted functional effects may exist in these cancers.

Figure 3. The MDM2 amplicon.

SNV allele frequencies (left-hand y axis) across each of the amplicons in the four cancers (#615, #635, #709 and #745) with copy number gain around MDM2 are shown. The red dots correspond to variants present in the constitutional DNA, green to the same variants in the tumours and blue to somatic SNVs. Estimated copy number in each region (right-hand y axis) is shown as a black line for guidance, although close inspection of the allelic frequency changes suggests that the level of amplicon complexity is not fully captured. A tumour without MDM2 region amplification (#4101) is shown for comparison. The position of MDM2 (chr12:69,201,971–69,239,320) is shown below the plots.

Figure 4. Clonality across the tumours.

Summary of the frequency distributions of the key somatic mutations plus 50 random SNVs (y axis) for each tumour. The x axis shows the frequency of each mutant between 0 and 1. See Supplementary Data 3 for more details.