The long tail of oncogenic drivers in prostate cancer

Abstract

Comprehensive genomic characterization of prostate cancer has identified recurrent alterations in genes involved in androgen signaling, DNA repair, and PI3K signaling, among others. However, larger and uniform genomic analysis may identify additional recurrently mutated genes at lower frequencies. Here we aggregate and uniformly analyze exome sequencing data from 1,013 prostate cancers. We identify and validate a new class of E26 transformation-specific (ETS)-fusion-negative tumors defined by mutations in epigenetic regulators, as well as alterations in pathways not previously implicated in prostate cancer, such as the spliceosome pathway. We find that the incidence of significantly mutated genes (SMGs) follows a long-tail distribution, with many genes mutated in less than 3% of cases. We identify a total of 97 SMGs, including 70 not previously implicated in prostate cancer, such as the ubiquitin ligase CUL3 and the transcription factor SPEN. Finally, comparing primary and metastatic prostate cancer identifies a set of genomic markers that may inform risk stratification.

Figure 1

Mutational significance in 1013 prostate cancers. (a) Uniform alignment, mutation calling, and significance analysis. (b) Recurrently mutated genes (n = 97). Genes are ordered by frequency, and mutations are stratified by mutation type and, for missense mutation, by recurrence. Recurrence is defined via cancerhotspots.org, OncoKB.org, and COSMIC; truncating mutations are defined as frameshift, nonsense, splice, nonstop. (c) Mutations in epigenetic regulators and chromatin remodelers are significantly enriched in ETS-negative tumors. p-values are calculated using a two-tailed Fisher’s exact test and shown for ETS fusions compared to all epigenetic mutations (including those co-occurring with SPOP and CUL3) and for ETS fusions compared to non-overlapping mutations in epigenetic modifiers only. (d) Cohort-wide view of mutations in epigenetic regulators and chromatin remodelers, which affect 20% of samples. Samples are shown from left to right (only the 202 tumors with alterations are shown, out of 1013), and gene alterations are color-coded by mutation type and, for missense mutations, by assumed driver status; mutations are assumed to be drivers if they have been previously reported and entered into COSMIC or annotated in OncoKB or variants of unknown significance (VUS).

Figure 2

Ubiquitin and splicing pathways in prostate cancer. (a) Mutations in CUL3 are exclusively missense mutations, and five tumors show the recurrent p.Met299Arg mutation. CUL3 mutations are mutually exclusive with SPOP mutations, and including USP28, USP7, 12% of tumors harbor alterations in members of the ubiquitin pathway. (b) CUL3-mutant tumors show copy-number profile similar to those of SPOP-mutant tumors. Chromosomes are shown from left to right, samples from top to bottom. Regions of loss are indicated by shades of blue, and gains are indicated by shades of red. (c) Mutations in members of the splicing pathway are found in 4% of tumors, including oncogenic mutations in SF3B1 and U2AF1.

Figure 3

SPEN mutations and WNT pathway alterations. (a) The majority of SPEN mutations are truncating and clonal in metastatic samples. (b) Oncoprint highlighting the distributions of SPEN mutations with alterations in members of the AR signaling. (c) Alterations in WNT/CTNNB1 pathway are found in 10% of tumors, primarily with loss of function mutations in APC and missense mutations in CTNNB1. (d) CTNNB1 mutations cluster primarily in hotspots in the N-terminal domain. (e) 3D structure of CTNNB1 showing novel mutations clustered around the CTNNB1-interacting domain of AXIN (highlighted in light gray).

Figure 4

Enrichment of genomic alterations in metastatic tumors. (a) Most genomic alterations are enriched in metastatic disease. Alteration percentages in metastatic samples (n=333) are shown on the x-axis, primary samples (n=680) on the y-axis. The significance of enrichment (two-sided Fisher’s test q-value or weighted permutation test) is shown by the size of the dots. Genes in bold have a significant enrichment of mutations using Fisher’s test and weighted permutation test correcting for mutation burden. (b) Pathway alteration frequencies in metastatic disease compared to primary disease. A sample was considered altered in a given pathway if at least a single gene in the pathway had a genomic alteration. p-values indicate the level of significance (two-sided Fisher’s exact test).