Single-Nucleotide Polymorphisms Sequencing Identifies Candidate Functional Variants at Prostate Cancer Risk Loci

Area of Science:

• Genetics
• Molecular Biology
• Oncology

Background:

• Genome-wide association studies have identified numerous prostate cancer risk loci, but causal variants and regulatory mechanisms remain largely uncharacterized.
• Understanding these genetic underpinnings is crucial for developing targeted therapies and improving risk prediction for prostate cancer.

Purpose of the Study:

• To develop and apply a novel sequencing technology (SNPs-seq) for identifying allele-dependent protein-DNA binding at prostate cancer risk loci.
• To characterize the functional impact of single-nucleotide polymorphisms (SNPs) associated with prostate cancer susceptibility.
• To identify candidate genes and regulatory elements involved in prostate cancer development and progression.

Main Methods:

• Utilized single-nucleotide polymorphisms sequencing (SNPs-seq) to assess allele-dependent protein binding at 903 prostate cancer risk SNPs in LNCaP cells, with and without androgen treatment.
• Performed electrophoretic mobility shift assays (EMSA) to validate allele-specific binding for selected SNPs at the CTBP2 and NCOA4 loci.
• Conducted clinical association analysis of candidate genes CTBP2 and NCOA4 in prostate cancer patient data.

Main Results:

• SNPs-seq identified significant allele-dependent protein binding in 42-45% of tested SNPs, with 74 promising candidates identified.
• EMSA validated allele-specific protein binding for rs12246440, rs7077275 (CTBP2 locus), and rs113082846 (NCOA4 locus).
• CTBP2 was upregulated and NCOA4 downregulated in prostate cancer; lower CTBP2 expression correlated with poorer recurrence-free survival.

Conclusions:

• The SNPs-seq technology is effective for identifying functional genetic variants at prostate cancer susceptibility loci.
• CTBP2 and NCOA4 are identified as candidate genes with allele-dependent regulatory mechanisms influencing prostate cancer.
• This approach provides a valuable strategy for prioritizing functional elements for further investigation in prostate cancer research.