Comprehensive analysis of copy number aberrations in microsatellite stable colon cancer in view of stromal component

Abstract

Background: Somatic copy number aberrations (CNAs) are common acquired changes in cancer cells having an important role in the progression of colon cancer (colorectal cancer, CRC). This study aimed to perform a characterisation of CNA and their impact in gene expression.

Methods: Copy number aberrations were inferred from SNP array data in a series of 99 CRC. Copy number aberration events were calculated and used to assess the association between copy number dosage, clinical and molecular characteristics of the tumours, and gene expression changes. All analyses were adjusted for the quantity of stroma in each sample, which was inferred from gene expression data.

Results: High heterogeneity among samples was observed; the proportion of altered genome ranged between 0.04 and 26.6%. Recurrent CNA regions with gains were frequent in chromosomes 7p, 8q, 13q, and 20, whereas 8p, 17p, and 18 cumulated losses. A significant positive correlation was observed between the number of somatic mutations and total CNA (Spearman's r=0.42, P=0.006). Approximately 37% of genes located in CNA regions changed their level of expression and the average partial correlation (adjusted for stromal content) with copy number was 0.54 (interquartile range 0.20 to 0.81). Altered genes showed enrichment in pathways relevant for CRC. Tumours classified as CMS2 and CMS4 by the consensus molecular subtyping showed higher frequency of CNA. Losses of one small region in 1p36.33, with gene CDK11B, were associated with poor prognosis. More than 66% of the recurrent CNA were validated in the The Cancer Genome Atlas (TCGA) data when analysed with the same procedure. Furthermore, 79% of the genes with altered expression in our data were validated in the TCGA.

Conclusions: Although CNA are frequent events in microsatellite stable CRC, few focal recurrent regions were found. These aberrations have strong effects on gene expression and contribute to deregulate relevant cancer pathways. Owing to the diploid nature of stromal cells, it is important to consider the purity of tumour samples to accurately calculate CNA events in CRC.

Figure 1

Distribution of clinical characteristics according to the proportion of altered genome. The histogram represents the proportion of altered genome by sample (purple: gains, red: losses). In the lower part, the clinical characteristics of the individuals are represented: sex (blue: female, red: male), age (sliding scale from white: minimum to brown: maximum), tumour location (light green: left, dark green: right), development of metastases (light pink: no, dark pink: yes), CIMP (white: no, green: CIMP low, blue: CIMP high), number of mutations (sliding scale from white: 0 to dark blue: maximum), proportion of stroma (light green: low, dark green: high), molecular subtype (yellow: CMS1, blue: CMS2, plink: CMS3, green: CMS4). (A) All CNA. (B) Gains. (C) Losses.

Figure 2

Frequency of CNA by chromosome. Each graph represents a chromosome with chromosomal position in the X-axis. Y-axis displays the percentage of tumour with gains (>0, purple) or losses (<0, red). The height of the bar is proportional to the number of samples showing the CNA change. Dashed lines represent the frequency (black: 5%, green: 20% red: 50%).

Figure 3

Relationship between gene expression and CNA. (A–D) Boxplots showing examples of gene expression changes based on CNA levels. Spearman’s correlation and FDR P-value are shown. ‘L’ indicates number of individuals losing the region, whereas ‘G’ indicates number of individuals gaining the region. (E) Circus plot of CNA recurrent regions and their association with changes in gene expression. Outer circle shows ideograms of the chromosomes. Inner circles show, in order, focal regions (gains in purple, losses in red), broad events, and genomic location of significant associations between CNA and the difference in expression between tumour and adjacent normal (blue) in cis analysis. The central arcs indicate genomic locations with significant trans associations between CNA and changes of gene expression.