Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci

Abstract

Background: Estimates suggest that up to 30% of colorectal cancers (CRC) may develop due to an increased genetic risk. The mean age at diagnosis for CRC is about 70 years. Time of disease onset 20 years younger than the mean age is assumed to be indicative of genetic susceptibility. We have compared high resolution tumor genome copy number variation (CNV) (Roche NimbleGen, 385 000 oligo CGH array) in microsatellite stable (MSS) tumors from two age groups, including 23 young at onset patients without known hereditary syndromes and with a median age of 44 years (range: 28-53) and 17 elderly patients with median age 79 years (range: 69-87). Our aim was to identify differences in the tumor genomes between these groups and pinpoint potential susceptibility loci. Integration analysis of CNV and genome wide mRNA expression data, available for the same tumors, was performed to identify a restricted candidate gene list.

Results: The total fraction of the genome with aberrant copy number, the overall genomic profile and the TP53 mutation spectrum were similar between the two age groups. However, both the number of chromosomal aberrations and the number of breakpoints differed significantly between the groups. Gains of 2q35, 10q21.3-22.1, 10q22.3 and 19q13.2-13.31 and losses from 1p31.3, 1q21.1, 2q21.2, 4p16.1-q28.3, 10p11.1 and 19p12, positions that in total contain more than 500 genes, were found significantly more often in the early onset group as compared to the late onset group. Integration analysis revealed a covariation of DNA copy number at these sites and mRNA expression for 107 of the genes. Seven of these genes, CLC, EIF4E, LTBP4, PLA2G12A, PPAT, RG9MTD2, and ZNF574, had significantly different mRNA expression comparing median expression levels across the transcriptome between the two groups.

Conclusions: Ten genomic loci, containing more than 500 protein coding genes, are identified as more often altered in tumors from early onset versus late onset CRC. Integration of genome and transcriptome data identifies seven novel candidate genes with the potential to identify an increased risk for CRC.

Figure 1

Study design comparing the tumor genomes of early onset and late onset colorectal cancer patients. Tumor samples from early onset and late onset CRC patients were analyzed with aCGH (DNA/genome level) and the data were integrated with the mRNA expression (RNA/transcriptome level) of the same samples. About 10 000 genes show corresponding DNA and RNA level. Exclusion of genes located outside chromosomal regions with statistically significant difference between the two patient groups resulted in 107 genes, summarized in Additional file 6. Further, exclusion of genes whose mRNA expression levels were not statistically significant between patients groups resulted in a short list of seven potential predisposing genes, as summarized in Table 3.

Figure 2

Genomic profile across all chromosomes from 40 tumor samples. A) Copy number profile across all 40 colorectal carcinomas, including early onset (n = 23) and late onset (n = 17) tumors. Percentage of samples with gains is shown in red and losses in green. Gains and losses in the short arm of acrocentric chromosomes are not considered and further discussed. The centromere positions are indicated by dashed lines, and changes recorded at the p-arms and q-arms are shown to the left and right of the dashed lines, respectively. B) Copy number profiles of early onset (solid) as compared to late onset (line) colorectal carcinomas.

Figure 3

Genes mapping to the chromosome bands with copy number aberrations associated with early onset CRC. Chromosomal sites gained or lost with statistical significance in the early compared to the late onset tumor group are shown in red or green boxes, respectively. Chromosomes with no aberrations or aberrations in centromere regions only, are shaded. Genes which have expression levels corresponding to chromosomal aberration, and concurrently located within the statistically significant regions are indicated within the boxes. Genes which also have significantly different expression level between early onset and late onset groups are further marked with green or red background.

Figure 4

mRNA expression levels of a short list of seven candidate genes for early onset CRC. Log transformed mRNA expression values plotted against age. Red bullets indicate copy number gain, green bullets indicate loss and grey bullets indicate normal copy number. Box plots for each of the patient groups are indicated for each gene.