rs2294008T, a risk allele for gastric and gallbladder cancers, suppresses the PSCA promoter by recruiting the transcription factor YY1

Abstract

Previous genomewide association studies identified prostate stem cell antigen (PSCA) as a gastric cancer (GC) susceptibility gene and showed an association between GC and the T allele of the single nucleotide polymorphism rs2294008 (C/T) in this gene. The protein product of this gene inhibits cell growth, and the T allele significantly suppresses the transcriptional activity of the À3.2 kb PSCA upstream region. However, the mechanism remains unknown. In this study, we conducted reporter assays using the PSCA upstream region containing the C allele and identified the region from À200 to +38 bp of the transcription initiation site of the gene as a critical region of the À3.2 kb PSCA upstream region. We found that introducing the T allele at rs2294008 generated a consensus binding sequence for the Polycomb group transcription factor Yin Yang 1 (YY1) and that disruption of the consensus sequence restored the transcriptional activity to the À3.2 kb PSCA upstream region. These findings imply that the T allele significantly suppresses PSCA expression in vivo by recruiting YY1 to its promoter, which eventually predisposes gastric epithelial cells to GC development.

Functional annotation of high-quality SNP biomarkers of gastric cancer susceptibility: the Yin Yang ofPSCArs2294008

“…Intriguingly, increased expression of YY15 and decreased expression of PSCA3 in GC tissues compared with normal have been previously reported, and confirmed by our own mRNA data (tumour:normal fold change (fc)=1.32, p=4.1E-23 for YY1 ; fc=0.10, p=2.7E-43 for PSCA : figure 1). Moreover, GC risk associated with rs2294008 has been attributed to PSCA silencing by rs2294008T via recruitment of abnormally expressed YY1 at the beginning of malignancy 3. Taken together, we propose that rs2294008T has opposing effects on PSCA expression in normal compared with neoplastic gastric epithelium determined by protein expression, binding affinity and the repressive influence of YY1 in gastric epithelia.…”

“…The risk alleles of both SNPs were associated with increased PSCA mRNA (figure 1). This result appears to be at odds with previous in vitro findings in GC cell lines where rs2294008T showed transcriptional repression of PSCA and inhibition of tumour suppressor functions,2 3 and PSCA was down-regulated in GC in vitro and in vivo 4. However, PSCA rs2294008T can create a low-affinity DNA binding site for the transcriptional repressor CTCF (HaploReg V.2) consistent with our observation of a positive influence of rs2294008T on PSCA mRNA in normal gastric tissues.…”

“…RNA-seq analysis of normal gastric tissue (NIH Roadmap Project). Motifs: basic illustration of transcription factor DNA binding motifs identified using position weight matrices from HaploReg V.2 and reported data (Saeki et al ;3 PubMed PMID: 25727947). Open chromatin: DNase I hypersensitivity clusters in 125 cell types from ENCODE.…”

“…However, PSCA rs2294008T can create a low-affinity DNA binding site for the transcriptional repressor CTCF (HaploReg V.2) consistent with our observation of a positive influence of rs2294008T on PSCA mRNA in normal gastric tissues. Additionally, rs2294008T generates a strong consensus binding motif for the polycomb group transcriptional repressor, Yin Yang 1 (YY1), which is not coexpressed in the same cells/region of normal gastric epithelium as PSCA 3. Intriguingly, increased expression of YY15 and decreased expression of PSCA3 in GC tissues compared with normal have been previously reported, and confirmed by our own mRNA data (tumour:normal fold change (fc)=1.32, p=4.1E-23 for YY1 ; fc=0.10, p=2.7E-43 for PSCA : figure 1).…”

“…Additionally, rs2294008T generates a strong consensus binding motif for the polycomb group transcriptional repressor, Yin Yang 1 (YY1), which is not coexpressed in the same cells/region of normal gastric epithelium as PSCA 3. Intriguingly, increased expression of YY15 and decreased expression of PSCA3 in GC tissues compared with normal have been previously reported, and confirmed by our own mRNA data (tumour:normal fold change (fc)=1.32, p=4.1E-23 for YY1 ; fc=0.10, p=2.7E-43 for PSCA : figure 1). Moreover, GC risk associated with rs2294008 has been attributed to PSCA silencing by rs2294008T via recruitment of abnormally expressed YY1 at the beginning of malignancy 3.…”