Mapping of genetic abnormalities of primary tumours from metastatic CRC by high-resolution SNP arrays

Abstract

Background: For years, the genetics of metastatic colorectal cancer (CRC) have been studied using a variety of techniques. However, most of the approaches employed so far have a relatively limited resolution which hampers detailed characterization of the common recurrent chromosomal breakpoints as well as the identification of small regions carrying genetic changes and the genes involved in them.

Methodology/principal findings: Here we applied 500K SNP arrays to map the most common chromosomal lesions present at diagnosis in a series of 23 primary tumours from sporadic CRC patients who had developed liver metastasis. Overall our results confirm that the genetic profile of metastatic CRC is defined by imbalanced gains of chromosomes 7, 8q, 11q, 13q, 20q and X together with losses of the 1p, 8p, 17p and 18q chromosome regions. In addition, SNP-array studies allowed the identification of small (<1.3 Mb) and extensive/large (>1.5 Mb) altered DNA sequences, many of which contain cancer genes known to be involved in CRC and the metastatic process. Detailed characterization of the breakpoint regions for the altered chromosomes showed four recurrent breakpoints at chromosomes 1p12, 8p12, 17p11.2 and 20p12.1; interestingly, the most frequently observed recurrent chromosomal breakpoint was localized at 17p11.2 and systematically targeted the FAM27L gene, whose role in CRC deserves further investigations.

Conclusions/significance: In summary, in the present study we provide a detailed map of the genetic abnormalities of primary tumours from metastatic CRC patients, which confirm and extend on previous observations as regards the identification of genes potentially involved in development of CRC and the metastatic process.

Figure 1. Metastatic colorectal cancer genome for the 23 CRC patients studied.

In panel A an overall view of both the gained (blue areas) and lost (red areas) chromosome regions across the genome are shown for the 23 patients genotyped on the Affymetrix 500k SNP array platform. In panel B a summary plot showing the frequency of CN gains (plotted above zero values in the x-axis) and losses (plotted below zero values the x-axis) detected for each individual chromosome, is displayed. Those chromosome regions most frequently showing recurrent losses and gains by SNP arrays were localized in chromosomes 1p, 8p, 17p and 18, and involved the whole chromosome 7 and the 8q, 13q and 20q chromosome regions, respectively.

Figure 2. Representative karyotype of a primary metastatic colorectal tumor as determined by the Affymetrix 500K SNP array genotyping platform, showing summary results for those chromosome gains/losses more frequently detected in the colorectal tumor samples analyzed (n = 23).

Figure 3. Expression levels of MYC, MAP4K and BIRC7 mRNA as assessed by RQ-PCR in metastatic CRC tumors and their corresponding paired normal tissue (n = 18).

Note that MYC and BIRC7 mRNA levels from metastatic CRC tumours samples are significantly higher than in their paired normal tissues (p<0.0001). By contrast, MAP4K mRNA levels in metastatic CRC tumors are significantly lower than normal (p<0.0001).