ArticleOncotarget2016
Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer.
Article in Oncotarget, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it, 53 citations in OpenAlex.
- Pooled it
- Identification of novel protein markers and therapeutic targets for common urological cancers by integrating large-scale human plasma proteome with the genome.Scientific reports · 2026Article
- ZG16B: A key regulator of tumor progression and immune microenvironment modulation in cancer (Review).International journal of molecular medicine · 2026Review
- Genome mining and characterisation of biosynthetic clusters in Aspergillus japonicus isolated from the Amazon rainforest.Memorias do Instituto Oswaldo Cruz · 2026Article
- Proteomic Profiling of Pre- and Post-Surgery Saliva of Glioblastoma Patients II: A Preliminary Investigation of the Complementary Low Molecular Mass Fraction.International journal of molecular sciences · 2025Article
- Combining tissue biomarkers with mpMRI to diagnose clinically significant prostate cancer. Analysis of 21 biomarkers in the PICTURE study.Prostate cancer and prostatic diseases · 2025Article
- Inferring cell-type-specific causal gene regulatory networks during human neurogenesis.Genome biology · 2023Article
- Genomic and transcriptomic profiling reveal molecular characteristics of parathyroid carcinoma.Experimental & molecular medicine · 2023Article
- Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique.Frontiers in cellular and infection microbiology · 2023Article
- LPS-Induced Liver Injury of Magang Geese through Toll-like Receptor and MAPK Signaling Pathway.Animals : an open access journal from MDPI · 2022Article
- Precision intervention for prostate cancer: Re-evaluating who is at risk.Cancer letters · 2022Review
- Article
- Identification of Novel Diagnostic Biomarkers in Prostate Adenocarcinoma Based on the Stromal-Immune Score and Analysis of the WGCNA and ceRNA Network.Disease markers · 2022Article
- Integrating Multimorbidity into a Whole-Body Understanding of Disease Using Spatial Genomics.Results and problems in cell differentiation · 2022Article
- Discrimination between 34 of 36 Possible Combinations of Three C>T SNP Genotypes in theInternational journal of molecular sciences · 2021Article
- The oncological relevance of fragile sites in cancer.Communications biology · 2021Review
- Epigenetics, microRNA and Metabolic Syndrome: A Comprehensive Review.International journal of molecular sciences · 2021Review
- Human Mitoribosome Biogenesis and Its Emerging Links to Disease.International journal of molecular sciences · 2021Review
- A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility.Cancer research · 2021Article
- Role of GTPases in Driving Mitoribosome Assembly.Trends in cell biology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Prostate cancer (PCa) is the second most common solid tumor for cancer related deaths in American men. Genome wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with the increased risk of PCa. Because most of the susceptibility SNPs are located in noncoding regions, little is known about their functional mechanisms. We hypothesize that functional SNPs reside in cell type-specific regulatory elements that mediate the binding of critical transcription factors (TFs), which in turn result in changes in target gene expression. Using PCa-specific functional genomics data, here we identify 38 regulatory candidate SNPs and their target genes in PCa. Through risk analysis by incorporating gene expression and clinical data, we identify 6 target genes (ZG16B, ANKRD5, RERE, FAM96B, NAALADL2 and GTPBP10) as significant predictors of PCa biochemical recurrence. In addition, 5 SNPs (rs2659051, rs10936845, rs9925556, rs6057110 and rs2742624) are selected for experimental validation using Chromatin immunoprecipitation (ChIP), dual-luciferase reporter assay in LNCaP cells, showing allele-specific enhancer activity. Furthermore, we delete the rs2742624-containing region using CRISPR/Cas9 genome editing and observe the drastic downregulation of its target gene UPK3A. Taken together, our results illustrate that this new methodology can be applied to identify regulatory SNPs and their target genes that likely impact PCa risk. We suggest that similar studies can be performed to characterize regulatory variants in other diseases.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.