Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer

Abstract

Colorectal cancer (CRC) is characterized by specific patterns of copy number alterations (CNAs), which helped with the identification of driver oncogenes and tumor suppressor genes (TSGs). More recently, the usage of single nucleotide polymorphism arrays provided information of copy number neutral loss of heterozygosity, thus suggesting the occurrence of somatic uniparental disomy (UPD) and uniparental polysomy (UPP) events. The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs and CNAs in sporadic CRC. Our results indicate that regions showing high frequencies of UPD/UPP mostly coincide with regions typically involved in genomic losses. Among them, chromosome arms 3p, 5q, 9q, 10q, 14q, 17p, 17q, 20p, 21q and 22q preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. Several regions affected by recurrent UPDs/UPPs contain well-known TSGs, as well as novel candidates such as ARID1A, DLC1, TCF7L2 and DMBT1. In addition, VCAN, FLT4, SFRP1 and GAS7 were also frequently involved in regions of UPD/UPP and displayed high levels of methylation. Finally, sequencing and fluorescence in situ hybridization analysis of the gene APC underlined that a somatic UPD event might represent the second hit to achieve biallelic inactivation of this TSG in colorectal tumors. In summary, our data define a profile of somatic UPDs/UPPs in sporadic CRC and highlights the importance of these events as a mechanism to achieve the inactivation of TSGs.

Figure 1.

Profile of CNAs and UPDs/UPPs from our study (A) and from the TCGA cohort (B). Chromosomes are represented in the outer ring of the circos plot. In the middle, gained regions are in green and lost regions in red. The inner ring shows frequency of UPDs/UPPs in blue. To note, regions with high frequency of UPD/UPP matched with regions with high frequency of copy number loss.

Figure 2.

Distribution of the length of UPD/UPP events and genomic losses. The interquartile range is represented by the black box inside the violin plots. The median is represented by the white dot. Events smaller than 2.5Mb have been discarded.

Figure 3.

UPD of chromosome 5 accompanied by a homozygous nonsense mutation of sample 33. (A) Tumor-matched normal PSCBS profiling of SNP array data showing total copy number (panel 1), decrease of heterozygosity (panel 2) and allele-specific copy number (panel 3). Dotted horizontal lines represent specific thresholds for each parameter. As illustrated, APC is located in a region with cnLOH. (B) Sanger sequencing of the gene APC showing the existence of a nonsense mutation (c.4360A>T) in the tumor. The minority allele could represent intratumoral heterogeneity and/or infiltration of normal cells. (C) Microscopic assessment of FISH signals using fluorescent probes covering the gene APC (red) and a control probe at 5q31.2 (green). Single isolated nuclei displaying two copies of APC and the control probe confirmed that most tumor population showed a disomic chromosome 5q within this sample. Scale bar = 5 µm.