Abundant copy-number loss of CYCLOPS and STOP genes in gastric adenocarcinoma

Abstract

Background: Gastric cancer, a leading cause of cancer death worldwide, has been little studied compared with other cancers that impose similar health burdens. Our goal is to assess genomic copy-number loss and the possible functional consequences and therapeutic implications thereof across a large series of gastric adenocarcinomas.

Methods: We used high-density single-nucleotide polymorphism microarrays to determine patterns of copy-number loss and allelic imbalance in 74 gastric adenocarcinomas. We investigated whether suppressor of tumorigenesis and/or proliferation (STOP) genes are associated with genomic copy-number loss. We also analyzed the extent to which copy-number loss affects Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes-genes that may be attractive targets for therapeutic inhibition when partially deleted.

Results: The proportion of the genome subject to copy-number loss varies considerably from tumor to tumor, with a median of 5.5 %, and a mean of 12 % (range 0-58.5 %). On average, 91 STOP genes were subject to copy-number loss per tumor (median 35, range 0-452), and STOP genes tended to have lower copy-number compared with the rest of the genes. Furthermore, on average, 1.6 CYCLOPS genes per tumor were both subject to copy-number loss and downregulated, and 51.4 % of the tumors had at least one such gene.

Conclusions: The enrichment of STOP genes in regions of copy-number loss indicates that their deletion may contribute to gastric carcinogenesis. Furthermore, the presence of several deleted and downregulated CYCLOPS genes in some tumors suggests potential therapeutic targets in these tumors.

Keywords: DNA copy number change; Gastric cancer; Loss of heterozygosity; Tumor suppressor genes.

Fig. 1

Example ASCAT profile and allele-specific copy numbers. The data are from sample 980029. a log₂ R ratio (LRR). Indices of autosomal single-nucleotide polymorphisms (SNPs) that are heterozygous in the nonmalignant sample are plotted along the x-axis. The y-axis indicates LRRs of SNPs in the tumor relative to the nonmalignant sample. Red dots show LRRs for each informative SNP, and green dots show ASCAT’s segmentations. b B-allele frequency (BAF) for the SNPs plotted in a. Red dots show BAFs for each SNP and green dots show ASCAT’s segmentation. c The solution space for the two parameters “ploidy” and “aberrant cell fraction,” with the location of the chosen values marked by a cross. d ASCAT’s model of allele-specific copy numbers. The y-axis indicates the estimated integer chromosomal copy number. Red lines and green lines indicate the higher-copy-number and lower-copy-number chromosomal haplotypes, respectively. The lines are vertically offset slightly to avoid superimposition. e The ASCAT aberration reliability score, a measure of how well the model in d explains the segmented LRRs and BAFs. Regions of copy-number loss according to our definition (total copy number less than 0.7 times the average ploidy) can be found in d by looking for segments that have total copy number (sum of the two allele copy numbers given by the green line and the red line) less than 0.7 × 2.31 = 1.6. Chromosomes 10, 12, and 18 each contain a small segment with total copy number 1 (red line at 1 and green line at 0, indicated by arrows). The region of loss in chromosome 18 is very small, and because of the plotting it is difficult to see the gap in the red line. However the green line at copy number 0 is visible

Fig. 2

Genome-wide overview of frequencies of copy-number loss and loss of heterozygosity across 74 gastric tumors. Copy-number loss is defined as a region where the genomic copy number is less than 0.7 times the average ploidy. See Figs. S7 and S8 for detailed plots across each chromosome

Fig. 3

Regions of copy-number loss across chromosomes 9 and 18. a The proportion of tumors showing copy-number loss at each single-nucleotide polymorphism on chromosome 9, based on ASCAT’s allele-specific copy-number analysis. The locations of Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes (red) and well-established tumor suppressor genes (black) are indicated. b Regions of copy-number loss in specific tumors. c, d Analogous information for chromosome 18. Copy-number loss is defined as a region where the genomic copy number is less than 0.7 times the average ploidy. cen centromere

Fig. 4

Gene Set Enrichment Analysis shows that suppressor of tumorigenesis and/or proliferation (STOP) genes tend to have lower average relative copy number. As discussed in the text, we restricted our attention to genes for which at least four short-hairpin RNAs increased cell proliferation by at least fourfold. a Running enrichment score for the STOP gene set against the list of genes ranked by their average relative copy number across all 74 samples, and then, to break ties, by the correlation coefficient between their average relative copy number and messenger RNA expression level. b Vertical black lines indicate the locations of STOP genes in the ranked list of genes