Deciphering Epigenetic Regulation of Enhancers in High-Risk Prostate Cancer
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ABSTRACT:
PROVIDER: PRJNA1029062 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Prostate cancer (PCa) is associated with widespread promoter hypermethylation. We hypothesized that aberrant DNA methylation also targets gene enhancers, modulating their activity and contributing to disease etiology. DNA methylation was assessed in a discovery set (n = 37) of primary PCa via the Infinium methylation EPIC array, using high-risk (HR; n=13), low-risk (LR; n=11), and histologically benign (n=13) tissues. A higher proportion of enhancers was hypomethylated in HR (n=385, 15%) than LR (n=105, 10%) PCa, primarily targeting genes involved in development and enriched for oncoprotein binding motifs, including FOXA1. Clinical significance was evaluated by identifying a 17 enhancer differentially methylated probe (DMP) signature using a Least Absolute Shrinkage and Selection Operator model in the discovery set. A logistic regression model was trained using the HR PCa-specific signature in a training set (n=490) and validated in a testing set (n=256). The signature had a 0.81 (95% bootstrapped CI 0.78-0.9) area under the curve, for selective detection of HR PCa, achieving a 0.71 sensitivity and 0.76 specificity (testing set). Array-wide aberrant DNA methylation at enhancers highlighted their epigenetic perturbance in HR disease. A clinically significant enhancer signature from this study could be used for detecting HR PCa.
2025-05-09 | GSE245609 | GEO
Project description:Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations- we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r^2≥0.5. Greater than 88% of the 727 SNPs fall within putative enhancers, many of which alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid in the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancer regions, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium (r^2=0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process. ChIP-seq analysis of H3K27Ac in LNCaP charcoal-stripped serum, H3K27Ac in LNCaP charcoal-stripped serum +DHT, TCF7L2 in LNCaP
2014-01-28 | E-GEOD-51621 | biostudies-arrayexpress
Project description:Neoadjuvant Intense ADT for High Risk Prostate Cancer
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Project description:Neoadjuvant Intense ADT for High Risk Prostate Cancer
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Project description:Parkinson's Disease Risk Enhancers in Microglia
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Project description:Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations- we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r^2≥0.5. Greater than 88% of the 727 SNPs fall within putative enhancers, many of which alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid in the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancer regions, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium (r^2=0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process.
2014-01-28 | GSE51621 | GEO
Project description:miRNA expression of 6 high risk and 8 low risk prostate carcinoma were compared to the expression of 6 benign prostatic hyperplasia. Keywords: expression profile We used microarrays to detail the global programme of miRNA expression underlying tumorigenesis and tumor progression and identified dysregulated genes during this process
2011-07-31 | E-GEOD-18671 | biostudies-arrayexpress
Project description:miRNA expression of 6 high risk and 8 low risk prostate carcinoma were compared to the expression of 6 benign prostatic hyperplasia. Keywords: expression profile
2011-08-01 | GSE18671 | GEO
Project description:Gleason grading is an important prognostic indicator for prostate adenocarcinoma and is crucial for patient treatment decisions. However, intermediate-risk patients diagnosed in Gleason Grade Groups (GG) 2 and GG3 can harbour either aggressive or non-aggressive disease, resulting in under- or over-treatment of a significant number of patients. Here, we performed proteomic, differential expression, machine learning, and survival analyses for 1,348 matched tumour and benign samples from 278 patients. Three proteins (F5, TMEM126B and EARS2) were identified as candidate biomarkers in patients with biochemical recurrence. Multivariate Cox regression yielded 18 proteins, from which a risk score was constructed to dichotomise prostate cancer patients into low- and high-risk groups. This 18-protein signature is prognostic for the risk of biochemical recurrence and completely independent of the intermediate GG. Our results suggest that markers generated by computational proteomic profiling have the potential for clinical applications including integration into prostate cancer management.
2023-11-30 | PXD041005 | Pride
Project description:Background:
Research studies have shown that genetic changes and family history may increase a man s risk for prostate cancer. Researchers want to follow the prostate health of men who have specific genetic changes associated with prostate cancer to help them learn more about which men are at higher risk for prostate cancer.
Objectives:
To study men with specific genetic changes and determine who is at higher risk for getting prostate cancer. To study if certain genetic changes and family history can be used to help prevent or treat prostate cancer.
Eligibility:
Persons assigned male at birth ages 30-75 who have one or more specific genetic changes but without prostate cancer.
Design:
* This study does not perform genetic testing. All participants must have documented genetic changes and able to provide a copy of the report.
* Before enrollment, participants will provide a copy of documented genetic changes and go through a telephone interview to determine eligibility for the study.
* On enrollment, participants will have medical and family history review, medication review, physical exam, blood collection for clinical and research testing, and MRI (magnetic resonance imaging) of the prostate.
* Every year, participants will repeat the physical exam, medical history, family history, medication review, routine blood tests, including PSA and testosterone.
* Every 2 years, participants will repeat all the above plus prostate MRI and blood tests for research.
* If, at any time, the physical exam, blood tests or MRI are abnormal, participants may be asked to do a biopsy.
* If the biopsy results in prostate cancer, participants will be given counseling on next steps, general treatment recommendations, and then followed with a phone call each year.
* Participants may ask to speak with a genetic counselor.
| 2294496 | ecrin-mdr-crc