scholarly journals Validation of prostate cancer risk variants by CRISPR/Cas9 mediated genome editing

2018 ◽  
Author(s):  
Xing Wang ◽  
James E. Hayes ◽  
Xing Xu ◽  
Xiaoni Gao ◽  
Dipti Mehta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cancer Risk ◽  
Association Studies ◽  
Prostate Cancer Risk ◽  
Genome Wide Association Studies ◽  
Single Nucleotide ◽  
Cancer Pathogenesis ◽  
Risk Variants ◽  
Specific Manner

AbstractGWAS have identified numerous SNPs associated with prostate cancer risk. One such SNP is rs10993994. It is located in the MSMB promoter, associates with MSMB encoded β-microseminoprotein prostate secretion levels, and is associated with mRNA expression changes in MSMB and the adjacent gene NCOA4. In addition, our previous work showed a second SNP, rs7098889, is in LD with rs10993994 and associated with MSMB expression independent of rs10993994. Here, we generate a series of clones with single alleles removed by double guide RNA (gRNA) mediated CRISPR/Cas9 deletions, through which we demonstrate that each of these SNPs independently and greatly alters MSMB expression in an allele-specific manner. We further show that these SNPs have no substantial effect on the expression of NCOA4. These data demonstrate that a single SNP can have a large effect on gene expression and illustrate the importance of functional validation to deconvolute observed correlations. The method we have developed is generally applicable to test any SNP for which a relevant heterozygous cell line is available.Author summaryIn pursuing the underlying biological mechanism of prostate cancer pathogenesis, scientists utilized the existence of common single nucleotide polymorphisms (SNPs) in human genome as genetic markers to perform large scale genome wide association studies (GWAS) and have so far identified more than a hundred prostate cancer risk variants. Such variants provide an unbiased and systematic new venue to study the disease mechanism, and the next big challenge is to translate these genetic associations to the causal role of altered gene function in oncogenesis. The majority of these variants are waiting to be studied and lots of them may act in oncogenesis through gene expression regulation. To prove the concept, we took rs10993994 and its linked rs7098889 as an example and engineered single cell clones by allelic-specific CRISPR/Cas9 deletion to separate the effect of each allele. We observed that a single nucleotide difference would lead to surprisingly high level of MSMB gene expression change in a gene specific and tissue specific manner. Our study strongly supports the notion that differential level of gene expression caused by risk variants and their associated genetic locus play a major role in oncogenesis and also highlights the importance of studying the function of MSMB encoded β-MSP in prostate cancer pathogenesis.

scholarly journals Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer Predisposition

2021 ◽  
Vol 22 (16) ◽  
pp. 8792
Author(s):  
Naixia Ren ◽  
Qingqing Liu ◽  
Lingjie Yan ◽  
Qilai Huang
Keyword(s):  
Prostate Cancer ◽  
Cancer Risk ◽  
Cancer Progression ◽  
Association Studies ◽  
Functional Characterization ◽  
Prostate Cancer Risk ◽  
Underlying Mechanism ◽  
Great Promise ◽  
Genome Wide Association Studies ◽  
Regulatory Snps

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.

scholarly journals Post genome-wide association studies functional characterization of prostate cancer risk loci

BMC Genomics ◽  
2013 ◽  
Vol 14 (Suppl 8) ◽  
pp. S9 ◽  
Author(s):  
Junfeng Jiang ◽  
Weirong Cui ◽  
Wanwipa Vongsangnak ◽  
Guang Hu ◽  
Bairong Shen
Keyword(s):  
Prostate Cancer ◽  
Cancer Risk ◽  
Association Studies ◽  
Functional Characterization ◽  
Prostate Cancer Risk ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Association of Prostate Cancer Risk Variants with Gene Expression in Normal and Tumor Tissue

2014 ◽  
Vol 24 (1) ◽  
pp. 255-260 ◽  
Author(s):  
Kathryn L. Penney ◽  
Jennifer A. Sinnott ◽  
Svitlana Tyekucheva ◽  
Travis Gerke ◽  
Irene M. Shui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cancer Risk ◽  
Tumor Tissue ◽  
Prostate Cancer Risk ◽  
Risk Variants

scholarly journals Allele-specific epigenetic activity in prostate cancer and normal prostate tissue implicates prostate cancer risk mechanisms

2021 ◽  
Author(s):  
Anamay Shetty ◽  
Ji-Heui Seo ◽  
Connor A Bell ◽  
Edward P O'Connor ◽  
Mark Pomerantz ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Risk ◽  
Association Studies ◽  
Significant Risk ◽  
Prostate Cancer Risk ◽  
Regulatory Elements ◽  
Genome Wide Association Studies ◽  
Normal Prostate ◽  
Allele Specificity ◽  
Specific Regulation

Background: Genome-wide association studies of prostate cancer have identified >250 significant risk loci, but the causal variants and mechanisms for these loci remain largely unknown. Here, we sought to identify and characterize risk harboring regulatory elements by integrating epigenomes from primary prostate tumor and normal tissues of 27 patients across the H3K27ac, H3K4me3, and H3K4me2 histone marks and FOXA1 and HOXB13 transcription factors. Results: We identified 7,371 peaks with significant allele-specificity (asQTL peaks). Showcasing their relevance to prostate cancer risk, H3K27ac T-asQTL peaks were the single annotation most enriched for prostate cancer GWAS heritability (40x), significantly higher than corresponding non-asQTL H3K27ac peaks (14x) or coding regions (14x). Surprisingly, fine-mapped GWAS risk variants were most significantly enriched for asQTL peaks observed in tumors, including asQTL peaks that were differentially imbalanced with respect to tumor-normal states. These data pinpointed putative causal regulatory elements at 20 GWAS loci, of which 11 were detected only in the tumor samples. More broadly, tumor-specific asQTLs were enriched for expression QTLs in benign tissues as well as accessible regions found in stem cells, supporting a hypothesis where some germline variants become reactivated during/after transformation and can be captured by epigenomic profiling of the tumor. Conclusion: Our study demonstrates the power of allele-specificity in chromatin signals to uncover GWAS mechanisms, highlights the relevance of tumor-specific regulation in the context of cancer risk, and prioritizes multiple loci for experimental follow-up.

Association between RNASEL, MSR1, and ELAC2 single nucleotide polymorphisms and gene expression in prostate cancer risk

2016 ◽  
Vol 34 (10) ◽  
pp. 431.e1-431.e8 ◽  
Author(s):  
Maria Jesus Alvarez-Cubero ◽  
Manrique Pascual-Geler ◽  
Luis Javier Martinez-Gonzalez ◽  
Manuela Expósito Ruiz ◽  
Maria Saiz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cancer Risk ◽  
Single Nucleotide Polymorphisms ◽  
Prostate Cancer Risk ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Association between single nucleotide polymorphisms, gene expression and prostate cancer risk at the moment of diagnosis

2017 ◽  
Vol 16 (3) ◽  
pp. e613-e614
Author(s):  
I. Puche Sanz ◽  
I. Robles-Fernández ◽  
M. Pascual-Geler ◽  
L. Martínez-Gonzalez ◽  
J.A. Lorente ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cancer Risk ◽  
Single Nucleotide Polymorphisms ◽  
Prostate Cancer Risk ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
The Moment

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

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 547 ◽  
Author(s):  
Peng Zhang ◽  
Lori S. Tillmans ◽  
Stephen N. Thibodeau ◽  
Liang Wang
Keyword(s):  
Prostate Cancer ◽  
Cancer Risk ◽  
Single Nucleotide Polymorphisms ◽  
Protein Binding ◽  
Prostate Cancer Risk ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Functional Variants ◽  
Dependent Protein

Genome-wide association studies have identified over 150 risk loci that increase prostate cancer risk. However, few causal variants and their regulatory mechanisms have been characterized. In this study, we utilized our previously developed single-nucleotide polymorphisms sequencing (SNPs-seq) technology to test allele-dependent protein binding at 903 SNP sites covering 28 genomic regions. All selected SNPs have shown significant cis-association with at least one nearby gene. After preparing nuclear extract using LNCaP cell line, we first mixed the extract with dsDNA oligo pool for protein–DNA binding incubation. We then performed sequencing analysis on protein-bound oligos. SNPs-seq analysis showed protein-binding differences (>1.5-fold) between reference and variant alleles in 380 (42%) of 903 SNPs with androgen treatment and 403 (45%) of 903 SNPs without treatment. From these significant SNPs, we performed a database search and further narrowed down to 74 promising SNPs. To validate this initial finding, we performed electrophoretic mobility shift assay in two SNPs (rs12246440 and rs7077275) at CTBP2 locus and one SNP (rs113082846) at NCOA4 locus. This analysis showed that all three SNPs demonstrated allele-dependent protein-binding differences that were consistent with the SNPs-seq. Finally, clinical association analysis of the two candidate genes showed that CTBP2 was upregulated, while NCOA4 was downregulated in prostate cancer (p < 0.02). Lower expression of CTBP2 was associated with poor recurrence-free survival in prostate cancer. Utilizing our experimental data along with bioinformatic tools provides a strategy for identifying candidate functional elements at prostate cancer susceptibility loci to help guide subsequent laboratory studies.

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