Decreased copy-neutral loss of heterozygosity in African American colorectal cancers

Abstract

Despite improvements over the past 20 years, African Americans continue to have the highest incidence and mortality rates of colorectal cancer (CRC) in the United States. While previous studies have found that copy number variations (CNVs) occur at similar frequency in African American and White CRCs, copy-neutral loss of heterozygosity (cnLOH) has not been investigated. In the present study, we used publicly available data from The Cancer Genome Atlas (TCGA) as well as data from an African American CRC cohort, the Chicago Colorectal Cancer Consortium (CCCC), to compare frequencies of CNVs and cnLOH events in CRCs in the two racial groups. Using genotype microarray data, we analyzed large-scale CNV and cnLOH events from 166 microsatellite stable CRCs-31 and 39 African American CRCs from TCGA and the CCCC, respectively, and 96 White CRCs from TCGA. As reported previously, the frequencies of CNVs were similar between African American and White CRCs; however, there was a significantly lower frequency of cnLOH events in African American CRCs compared to White CRCs, even after adjusting for demographic and clinical covariates. Although larger differences for chromosome 18 were observed, a lower frequency of cnLOH events in African American CRCs was observed for nearly all chromosomes. These results suggest that mechanistic differences, including differences in the frequency of cnLOH, could contribute to clinicopathological disparities between African Americans and Whites. Additionally, we observed a previously uncharacterized phenomenon we refer to as small interstitial cnLOH, in which segments of chromosomes from 1 to 5 Mb long were affected by cnLOH.

Keywords: African American colorectal cancer; The Cancer Genome Atlas; copy number variation; copy-neutral loss of heterozygosity; genotype and microarray data.

Figure 1.

Model of mechanisms of copy-neutral loss of heterozygosity. (A) After an interhomolog recombination event affecting a given allele (i.e., the B allele, but not the A allele), mitotic segregation can result in either a reduction of homozygosity (from Bb in parental cell to BB or bb in daughter cell) or retention of heterozygosity (Bb in both parental and daughter cell). (B) A non-disjunction event during mitosis can lead to daughter cells with either an extra paternal chromatid or the loss of a paternal chromatid. Subsequent elimination of the single-copy chromosome in the former or duplication of the remaining chromosome in the latter results in cnLOH.

Figure 2.

African American CRCs have a decreased frequency of cnLOH across the genome compared to White CRCs. Frequency of cnLOH by chromosome arm (expressed as the proportion of CRCs affected by cnLOH) is given for each chromosome arm in CCCC African Americans (top, grey), TCGA African Americans (middle, green), and TCGA Whites (bottom, purple).

Figure 3.

African American CRCs have fewer chromosome arms affected by cnLOH than White CRCs. Number of chromosome arms affected by cnLOH in each CRC (expressed as percentage of total chromosome arms) is represented as a dot on the graph, stratified into CCCC African Americans (left, grey), TCGA African Americans (middle, green), and TCGA Whites (right, purple). Boxes represent 25^th, 50^th, and 75^th quartiles, while whiskers represent 1.5 interquartile range for that data series. Note that many samples had no arms affected and that the maximum percentage of arms affected for any individual was < 40%.

Figure 4.

Break-induced DNA replication model for the generation of small-interstitial, copy-neutral loss of heterozygosity (si-cnLOH). (I) DNA replication encounters DNA damage that leads to a replication-associated, single-ended DNA break. The letters variants A and a represent a DNA polymorphism at a locus that is different between the homologous chromosomes. (II) Normally, repair of the replication-associated break is carried out by homologous recombination using the closely apposite sister chromatid; however, on rare occasions, repair is carried out using the homologous chromosome instead (represented by the blue lines). (III) The homologous recombination protein RAD51 catalyzes invasion of the single-stranded DNA with a 3’ end, pairing with the homologous sequence and forming a displacement loop. (IV) The 3’ hydroxyl from the invading DNA strand is available for incorporation by DNA polymerase delta. At the same time as polymerase is extending the invading strand, a DNA helicase displaces the nascent DNA behind polymerase. This generates a moving bubble. As the nascent DNA is displaced, the nascent DNA is replicated by lagging strand synthesis. (V) The break-induced replication mechanism copies variants from the homologous chromosome onto the chromosome that suffered the replication-associated DNA break by conservative DNA synthesis. This copy mechanism maintains copy number and reduces variants to homozygosity. The copy mechanism ends at some point when the invading strand is fully displaced, is recaptured by the sister chromatid, and meets a replication fork that converges upon it from the opposite direction.