Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer

Abstract

Background: Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear.

Results: We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner.

Conclusions: We conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis.

Figure 1

Rearrangements in colorectal tumors detected by long mate-pair sequencing. (a) Circos plots displaying rearrangements and their chromosomal locations in primary and metastatic colorectal tumor samples. Rearrangement fusion points and orientations are indicated by colored links: red, head-head; blue, tail-head; green, head-tail; orange, tail-tail (low coordinate to high coordinate). Chromosome ideograms are shown on the outer ring. The inner two rings show copy number profiles based on log R ratios derived from SNP array analysis. Red copy number plots correspond to the liver metastasis and blue plots correspond to the primary tumor. Copy number variation for matching normal colon and liver tissue are plotted in black. (b) Classes of rearrangements identified in tumors of the four patients. Deletion-type rearrangements have tail-head orientation, tandem duplication type rearrangements have head-tail orientation and inverted rearrangements have head-head or tail-tail orientation. (c) Lesion-specific presence of rearrangements in primary and metastatic tumors as based on PCR genotyping of DNA samples from primary tumor, metastasis and control tissue.

Figure 2

Examples of clusters of rearrangements in primary and metastatic tumor genomes. (a) A cluster of rearrangements involving chromosomes 3 and 6 specific for the primary tumor of patient 4. (b) A cluster of rearrangements on chromosome 13, which could be found in both the primary tumor and the liver metastasis of patient 1. (c) A metastasis-specific cluster of rearrangements involving chromosomes 17 and 21 of patient 4. Orientations of fusions are colored as in Figure 1. Red copy number plots and B allele frequencies correspond to the liver metastasis and blue plots correspond to the primary tumor. Copy number variation and B allele frequencies for matching normal colon and liver tissue are plotted in black. (d) Breakpoints and copy number changes involving a cluster of rearrangements on chromosomes 15 and 20 in the primary tumor genome of patient 3. The upper panel shows a nucleotide-resolution map of fusion points for this cluster. Lines indicate fusions between chromosomal fragments. Genomic coordinates indicate positions of breakpoints. Chromosomal fragments with both head and tail side connected to other fragments are retained, while fragments that lack any link (fusion) are supposed to be deleted. This expected pattern of retained and deleted fragments is reflected by the copy number profile for chromosome 15 (lower panel). BAF, B allele frequency.

Figure 3

Cancer-related genes affected by rearrangements breakpoints. (a) Disruption of EXO1 and FH (fumarate hydratase) by rearrangement breakpoints in a metastasis-specific cluster on chromosome 1 in patient 3. (b) Disruption of MYCBP2 by a rearrangement breakpoint in a cluster on chromosome 13 in patient 1. Genes from the Cancer Genome Census are also depicted for this cluster. (c) Disruption of SORBS2 by metastasis-specific deletions in patients 2 and 4. (d) Disruption of CSMD1 by a metastasis-specific deletion in patient 2.