Lack of APC somatic mutation is associated with early-onset colorectal cancer in African Americans

Abstract

African Americans (AAs) have higher incidence and mortality rates of colorectal cancer (CRC) compared with other US populations. They present with more right-sided, microsatellite stable disease and are diagnosed at earlier ages compared with non-Hispanic Whites (NHWs). To gain insight into these trends, we conducted exome sequencing (n = 45), copy number (n = 33) and methylation analysis (n = 11) of microsatellite stable AA CRCs. Results were compared with data from The Cancer Genome Atlas (TCGA). Two of the 45 tumors contained POLE mutations. In the remaining 43 tumors, only 27 (63%) contained loss-of-function mutations in APC compared with 80% of TCGA NHW CRCs. APC-mutation-negative CRCs were associated with an earlier onset of CRC (P = 0.01). They were also associated with lower overall mutation burden, fewer copy number variants and a DNA methylation signature that was distinct from the CpG island methylator phenotype characterized in microsatellite unstable disease. Three of the APC-mutation-negative CRCs had loss-of-function mutations in BCL9L. Mutations in driver genes identified by TCGA exome analysis were less frequent in AA CRC cases than TCGA NHWs. Genes that regulate the WNT signaling pathway, including SOX9, GATA6, TET1, GLIS1 and FAT1, were differentially hypermethylated in APC-mutation-negative CRCs, suggesting a novel mechanism for cancer development in these tumors. In summary, we have identified a subtype of CRC that is associated with younger age of diagnosis, lack of APC mutation, microsatellite and chromosome stability, lower mutation burden and distinctive methylation changes.

Figure 1.

Candidate driver genes in AA CRCs. The top panel shows the number of SNVs in each of the 43 tumors included in the analysis, coded by mutation type. The bottom panel shows the 32 genes in order of q value rank up to the threshold 0.1, matching the sample to the mutation, coded by mutation type.

Figure 2.

The contribution of known cancer-associated genes to AA CRCs. (A) Underrepresentation of mutations in the most frequently mutated CRC driver genes identified in TCGA. (B) Overrepresentation of cancer-associated genes.

Figure 3.

APC-mutation-negative CRCs exhibit greater chromosome stability. (A) Comparison of copy number changes in APC-mutation-negative versus APC-mutation-positive CRCs. (B) Comparison of copy number changes in AA CCCC versus NHW TCGA CRCs.

Figure 4.

DMRs in APC-mutation-negative tumors cluster with adjacent normal tissue relative to APC-mutation-positive tumors. (A) Heatmap from unsupervised cluster analysis of the top 200 most variable DMRs in the six APC-mutation-positive and five APC-mutation-negative CRCs from the CCCC. (B) Unsupervised cluster analysis using the same 200 most variable DMRs in 15 APC-mutation-positive and 29 APC-mutation-negative CRCs from the TCGA.

Figure 5.

Co-localization of DMRs in APC-mutation-positive and mutation-negative tumors with seven chromatin states based on Reference Epigenome Mapping Consortium’s ChIP-seq data. (A) Comparison of 11 CRCs to adjacent normal tissue demonstrates global hypomethylation with focal hypermethylation. (B) Comparison of five APC-mutation-negative tumors with adjacent normal tissue demonstrates increased methylation in the absence of global hypomethylation.