Whole-exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry

Abstract

In this study, we used whole-exome sequencing of a cohort of 45 advanced-stage, treatment-naïve Nigerian (NG) primary prostate cancer tumors and 11 unmatched nontumor tissues to compare genomic mutations with African American (AA) and European American (EA) The Cancer Genome Atlas (TCGA) prostate cancer. NG samples were collected from six sites in central and southwest Nigeria. After whole-exome sequencing, samples were processed using GATK best practices. BRCA1 (100%), BARD1 (45%), BRCA2 (27%), and PMS2(18%) had germline alterations in at least two NG nontumor samples. Across 111 germline variants, the AA cohort reflected a pattern [BRCA1 (68%), BARD1 (34%), BRCA2 (28%), and PMS2 (16%)] similar to NG samples. Of the most frequently mutated genes, BRCA1 showed a statistically (P ≤ 0.05) higher germline mutation frequency in men of African ancestry (MAA) and increasing variant frequency with increased African ancestry. Disaggregating gene-level mutation frequencies by variants revealed both ancestry-linked and NG-specific germline variant patterns. Driven by rs799917 (T>C), BRCA1 showed an increasing mutation frequency as African ancestry increased. BRCA2_rs11571831 was present only in MAA, and BRCA2_rs766173 was elevated in NG men. A total of 133 somatic variants were present in 26 prostate cancer-associated genes within the NG tumor cohort. BRCA2 (27%), APC (20%), ATM (20%), BRCA1 (13%), DNAJC6 (13%), EGFR (13%), MAD1L1 (13%), MLH1 (11%), and PMS2 (11%) showed mutation frequencies >10%. Compared with TCGA cohorts, NG tumors showed statistically significant elevated frequencies of BRCA2, APC, and BRCA1. The NG cohort variant pattern shared similarities (cosign similarities ≥0.734) with Catalogue of Somatic Mutations in Cancer signatures 5 and 6, and mutated genes showed significant (q < 0.001) gene ontology (GO) and functional enrichment in mismatch repair and non-homologous repair deficiency pathways. Here, we showed that mutations in DNA damage response genes were higher in NG prostate cancer samples and that a portion of those mutations correlate with African ancestry. Moreover, we identified variants of unknown significance that may contribute to population-specific routes of tumorigenesis and treatment. These results present the most comprehensive characterization of the NG prostate cancer exome to date and highlight the need to increase diversity of study populations.

Significance: MAA have higher rates of prostate cancer incidence and mortality, however, are severely underrepresented in genomic studies. This is the first study utilizing whole-exome sequencing in NG men to identify West African ancestry-linked variant patterns that impact DNA damage repair pathways.

FIGURE 1

Sample collection sites and genetic admixture analysis. A, At clinical sites across Nigeria, 45 samples were collected. B, Admixture v1.3.0 was used to estimate ancestry proportions, based on reference populations from the 1000 Genomes Project phase III superpopulations. Prior to analysis, rare variants (i.e., <5% across all phase III 1000 genomes), all indels, and any SNPs that were not biallelic were removed. Samples within the CaPTC cohort had an average African proportion of 99.1%. TCGA Samples (n = 50) with >70% African ancestry were classified as AA; 402 TCGA samples contained >60% European admixture. Those samples were sorted by European proportion, and the top 50 samples were classified as EA and utilized in this study. The average European proportion of this group was 99.996%. C, Germline variants within the NG and TCGA cohorts were compared with phase III 1000 Genomes superpopulations using principal component analysis. NG samples strongly clustered with the African superpopulation. AAs samples clustered with the African superpopulation; European samples clustered with the European superpopulation.

FIGURE 2

Prostate cancer germline variant oncoplot. A, NG germline variants detected across 11 normal samples were filtered against known ClinVar cancer variants. In at least two tumor samples, four genes known to harbor cancer-related variants were mutated. These genes included BRCA1 (BRCA1 DNA repair associated)—100%, BARD1—45%, BRCA2 (DNA repair associated)—27%, and PMS2 (PMS1 homolog 2, mismatch repair system component)—18%. As a comparison with NG prostate cancer exome samples, TCGA prostate cancer samples (n = 50 AA and n = 50 EA) were downloaded through dbGAP and analyzed for genetic variants. B, In the AA cohort. eight genes showed germline mutations in at least two samples. C, In the EA cohort, 10 genes showed germline mutations in at least two samples.

FIGURE 3

NG prostate cancer cohort germline mutations comparison with TCGA prostate cancer cohorts and lollipop plots. A, Prostate cancer of NG and AA men showed more BRCA1 germline mutations (P ≤ 0.001 and P ≤ 0.01, respectively) compared with European men. In addition, prostate cancer of NG men showed more (P ≤ 0.036) BRCA1 mutations relative to AA men. In prostate cancer of EA men, BARD1 was mutated at a higher rate (P ≤ 0.048). BRCA2 showed no significant difference in cohort mutation rates. AA men with greater than 90% African ancestry (n = 19) show a statistically significant (P ≤ 0.021) increase in BRCA1 germline mutations when compared with those with lower amounts of African ancestry (n = 29). In addition, AA men with 90% African ancestry have a statistically higher (P = 0.012) frequency of the BRCA1 variant rs799917. B, To disaggregate mutation rates down to specific variants, lollipop plots revealed a finer variation in cohort patterns. The ancestry-linked pattern of BRCA1 is driven by rs799917, which was more frequent (P ≤ 0.001) for men of African ancestry. rs16941 and rs16942 were elevated in prostate cancer of European men, but that difference was not statistically significant. BARD1 germline variants showed no significant difference in variant rates; however, the patterns appeared to be specific to NG men. Compared with AA and EA cohorts, rs2070096 was lower and rs2070094 was higher. BRCA2 germline variants displayed no statistically different variant rates, but both ancestry-linked and NG-specific patterns were discernable. rs11571831 was present only in prostate cancer of men of African ancestry, and rs766173 was elevated in prostate cancer of NG Men. P values were produced via two-sided Fisher exact test groupwise comparison.

FIGURE 4

Prostate cancer somatic variants within known prostate cancer–associated genes. A, Variant calling within the NG cohort (n = 45) produced 1,168,250 variants. A total of 25 genes were known to be associated with prostate cancer harbored variants in at least two tumor samples. The most frequently mutated of these included BRCA2 (BRCA2 DNA repair associated)—27%, APC (APC regulator of WNT signaling pathway)—20%, ATM (ATM serine/threonine kinase)—20%, BRCA1 (BRCA1 DNA repair associated)—13%, and DNAJC6 [DnaJ heatshock protein family (Hsp40) member C6]—13%. As a comparison with NG prostate cancer exome samples, TCGA prostate cancer samples (n = 50 AA and n = 50 EA) were downloaded through dbGAP and analyzed for genetic variants. B, Prostate cancer of NG men showed a significant (P ≤ 0.01) elevation in BRCA2 somatic mutations compared with African and EA men. A significant increase was also evident for APC (P ≤ 0.05) and BRCA1 (P ≤ 0.05). Compared with NG men, prostate cancer of AAs were elevated (P ≤ 0.05). NG and AA men also showed higher, but not significant, mutation frequencies of ATM, MED12, and BRAF. C, Somatic mutations for NGs and AAs were distributed across the amino acid sequence of the most mutated genes. None of the variants were shared across or within cohorts. D and E, SNPs in the NG prostate cancer cohort were compared with known cancer-related mutation signatures within the COSMIC. A total of 89% of NG prostate cancer mutation patterns were similar (cosign similarity ≥0.796) with COSMIC signatures 6. The remaining 11% were more like COSMIC 5. F, Mutated genes (n = 83) present in at least two NG prostate cancer tumor samples (n = 45) were imported into Cytoscape to assess functional gene ontology enrichment and visualize the GO term interaction network, using Kyoto Encyclopedia of Genes and Genomes pathways. Variants showed significant (q ≤ 0.000538) GO and functional enrichment across multiple GO groups, including mismatch repair, homologous recombination, prostate cancer, and several cancer-related signaling pathways.