Identification of Susceptibility Loci and Genes for Colorectal Cancer Risk

Abstract

Background & aims: Known genetic factors explain only a small fraction of genetic variation in colorectal cancer (CRC). We conducted a genome-wide association study to identify risk loci for CRC.

Methods: This discovery stage included 8027 cases and 22,577 controls of East-Asian ancestry. Promising variants were evaluated in studies including as many as 11,044 cases and 12,047 controls. Tumor-adjacent normal tissues from 188 patients were analyzed to evaluate correlations of risk variants with expression levels of nearby genes. Potential functionality of risk variants were evaluated using public genomic and epigenomic databases.

Results: We identified 4 loci associated with CRC risk; P values for the most significant variant in each locus ranged from 3.92 × 10(-8) to 1.24 × 10(-12): 6p21.1 (rs4711689), 8q23.3 (rs2450115, rs6469656), 10q24.3 (rs4919687), and 12p13.3 (rs11064437). We also identified 2 risk variants at loci previously associated with CRC: 10q25.2 (rs10506868) and 20q13.3 (rs6061231). These risk variants, conferring an approximate 10%-18% increase in risk per allele, are located either inside or near protein-coding genes that include transcription factor EB (lysosome biogenesis and autophagy), eukaryotic translation initiation factor 3, subunit H (initiation of translation), cytochrome P450, family 17, subfamily A, polypeptide 1 (steroidogenesis), splA/ryanodine receptor domain and SOCS box containing 2 (proteasome degradation), and ribosomal protein S2 (ribosome biogenesis). Gene expression analyses showed a significant association (P < .05) for rs4711689 with transcription factor EB, rs6469656 with eukaryotic translation initiation factor 3, subunit H, rs11064437 with splA/ryanodine receptor domain and SOCS box containing 2, and rs6061231 with ribosomal protein S2.

Conclusions: We identified susceptibility loci and genes associated with CRC risk, linking CRC predisposition to steroid hormone, protein synthesis and degradation, and autophagy pathways and providing added insight into the mechanism of CRC pathogenesis.

Keywords: Colon Cancer; Epidemiology; Single Nucleotide Polymorphisms; eQTL.

Figure 1. Forest plots for newly identified CRC risk variants (a) rs4711689, (b) rs2450115, (c) rs6469656, (d) rs4919687, (e) rs11064437, (f) rs6061231

Per-allele OR estimates are presented as boxes with the area proportional to the inverse variance of the estimates. Horizontal lines represent the coverage of 95% confidence intervals (CIs).

Figure 2. Expression quantitative trait locus (eQTL) analyses in samples of normal colorectal mucosa adjacent to the tumor obtained from 188 CRC patients of East Asian ancestry

a. TFEB relative expression and genotypes of rs4711689; b. EIF3H relative expression and genotypes of rs6469656; c. SPSB2 relative expression and genotypes of rs11064437; d. RPS21 relative expression and genotypes of rs6061231.

Figure 3. Regional association plots of the risk loci (a) rs4711689 at 6p21.1ⁱ;(b) rs2450115 at 8q23.3;(c) rs6469656 at 8q23.3; (d) rs4919687 at 10q24.3; (e) rs11064437 at 12p13.3; (f) rs6061231 at 20q13.3

In each plot, the log₁₀ (P-values) (y axis) for the association of SNPs with CRC risk are shown according to their chromosomal positions (x axis) in NCBI Build 37. Blue lines represent the estimated recombination rates from the 1000 Genomes Project (Phase 3). Arrows indicate genomic locations of genes within the 1Mb regions centered on the newly-identified risk variants. The color of the SNP represents its LD (r²) with the index SNP at each locus. Only results from the GWAS studies (4,508 cases /16,588 controls in total) are shown. The plots were generated using the online tool LocusZoom.