Naixia Ren, Qingqing Liu, Lingjie Yan, Qilai Huang
Functional characterization of cancer risk-associated single nucleotide polymorphism (SNP) identified by genome-wide association studies (GWAS) has become a big challenge. To identify the regulatory risk SNPs that can lead to transcriptional misregulation, we performed parallel reporter gene assays with both alleles of 213 prostate cancer risk-associated GWAS SNPs in 22Rv1 cells. We disclosed 32 regulatory SNPs that exhibited different regulatory activities with two alleles. For one of the regulatory SNPs, rs684232, we found that the variation altered chromatin binding of transcription factor FOXA1 on the DNA region and led to aberrant gene expression of VPS53, FAM57A, and GEMIN4, which play vital roles in prostate cancer malignancy. Our findings reveal the roles and underlying mechanism of rs684232 in prostate cancer progression and hold great promise in benefiting prostate cancer patients with prognostic prediction and target therapies.
Naixia Ren, Qingqing Liu, Lingjie Yan, Qilai Huang. Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer Predisposition. 2021-08-16. https://doi.org/10.3390/ijms22168792
The GEO series linked to this publication contains a companion episomal DiR-seq MPRA run in human PC-3 prostate cancer cells using the same 55-bp allele-specific risk-SNP library. Three RNA/cDNA reporter libraries were compared with two shared plasmid-input libraries.
Episomal DiR-seq MPRA of 55-bp allele-specific oligos centered on prostate-cancer risk SNPs, transfected into human 22Rv1 prostate cancer cells. Three RNA/cDNA reporter libraries were compared with two plasmid-input libraries.
The GEO series linked to this publication contains a companion episomal DiR-seq MPRA run in human LNCaP prostate cancer cells using the same 55-bp allele-specific risk-SNP library. Three RNA/cDNA reporter libraries were compared with two LNCaP-specific plasmid-input libraries.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 8 files (ZIP)GSE165765_raw_counts.tar.gzGSE165765_sample-to-library_relationships.txt.gzGSE165765_series.txtGSE165765_SNP_barcode_id.txt.gzijms-22-08792-s001.zipsource_manifest.txtSupplementary figures.pdfSupplementary Tables.xlsx