Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A prostate cancer risk element functions as a repressive loop that regulates HOXA13

ABSTRACT: Prostate cancer (PCa) is the leading cancer among men in the United States, with genetic factors contributing to ~42% of the susceptibility to PCa. To understand the causal genetic factors associated with PCa, we have focused on a PCa risk region located at 7p15.2. We performed Hi-C analysis and demonstrated that this region has long range interactions with the HOXA locus, located ~873 kb away. Using the CRISPR/Cas9 system, we deleted a 4 kb region encompassing several prostate cancer risk-associated SNPs and performed RNA-seq to investigate transcriptomic changes in RWPE1 prostate cells lacking the regulatory element. Our results suggest that the risk element affects the expression of HOXA13 and HOTTIP, but not other genes in the HOXA locus, via a repressive loop. Forced expression of HOXA13 was also performed to gain insight into the mechanisms by which this risk element affects prostate cancer risk.

ORGANISM(S): Homo sapiens

PROVIDER: GSE98898 | GEO | 2017/11/01

SECONDARY ACCESSION(S): PRJNA386902

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Homo sapiens

Project description:A prostate cancer risk element functions as a repressive loop that regulates HOXA13

| PRJNA386902 | ENA

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

Project description:Background: Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the function of these non-coding risk loci is critical to elucidate the genetic susceptibility to prostate cancer. Results: We generated genome-wide regulatory element maps and performed genome-wide chromosome confirmation capture assays (in situ Hi-C) in normal and tumorigenic prostate cells. Using this information, we annotated the regulatory potential of 2,181 fine-mapped PCa risk-associated SNPs and predicted a set of target genes that are regulated by PCa risk-related H3K27Ac-mediated loops. We next identified PCa risk-associated CTCF sites involved in long-range chromatin loops. We used CRISPR-mediated deletion to remove PCa risk-associated CTCF anchor regions and the CTCF anchor regions looped to the PCa risk-associated CTCF sites; we observed up to 100 fold increases in expression of genes within the loops when the PCa risk-associated CTCF anchor regions were deleted. Conclusions: We have identified GWAS risk loci involved in long-range loops that function to repress gene expression within chromatin loops. Our studies provide new insights into the genetic susceptibility to prostate cancer.

2018-08-15 | GSE118514 | GEO

Methylation profiling of normal and cancerous breast cells from human patients and cell lines in a 125 kB region of the HOXA cluster

Project description:To evaluate DNA methylation profile associated with breast cancer in 125 kB region of HOXA cluster we analyzed DNA from normal cancerous breast specimens and cell lines. Analysis was performed on the tiling array covering entire HOXA region with 500bp resolution. Immunoprecipitation with anti-methylcytosine antibody was for target preparation. Cy3 labeling was used for inmmunoprecipitated DNA, Cy5 labeling was used for reference input DNA.

2006-11-03 | E-MEXP-880 | biostudies-arrayexpress

Prostate Cancer Risk SNPs in Androgen Receptor Target Sites

Project description:We profiled androgen receptor (AR) genomic targets using high-throughput sequencing of chromatin-immunoprecipitated (ChIP) DNA from TMPRSS2-ERG fusion gene positive DUCaP prostate cancer cells. ChIp-seq and microarray gene expression profiling datasets were integrated with the NHGRI GWAS PCa risk SNPs catalog to identify disease susceptibility SNPs localized within functional androgen receptor binding sites (ARBSs). Eighty GWAS index or linked SNPs were found to be localized in ARBSs. Among these rs11891426:T>G in the 7th intron of the melanophilin gene was found located within a novel putative auxiliary AR binding motif, which we found enriched in the neighborhood of canonical androgen responsive elements. T→G exchange attenuated the transcriptional activity of the ARBS in an AR reporter gene assay of prostate cancer cell models. It went also in line with decreased melanophilin protein level in primary prostate tumors with G allele.These results unravel a hidden link between androgen receptor and a functional PCa risk SNP, whose allele alteration affects androgen regulation of its host gene melanophilin . Genomic profile of androgen receptor binding sites of androgen or vehicle treated DUCaP cells using ChIP-seq. IgG precipiated DNAs from both treatments served as controls.

2015-07-10 | E-GEOD-70679 | biostudies-arrayexpress

CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia

Project description:We analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that CTCF binding site located between HOXA7 and HOXA9 genes (CBS7/9) is critical for establishing and maintaining aberrant HOXA9-HOXA13 gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active HOXA chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and disrupted ectopic long-range interactions among the posterior HOXA genes. Consistent with the role of the CBS7/9 boundary in HOXA locus chromatin organization, attenuation of the CBS7/9 boundary function reduced posterior HOTTIP lincRNA and HOXA gene expression and altered myeloid specific transcriptome profiles important for pathogenesis of myeloid malignancies.

2018-05-17 | GSE113191 | GEO

MicroRNA expression profiling of the prostate biopsy samples from African American and European American prostate cancer patients

Project description:Prostate cancer (PCa) tends to be more aggressive and lethal in African Americans (AA) compared to European Americans (EA). To further understand the thebiological risk factors associated with PCa disparities observed in AA and EA patients, we performed microRNA profiling using Agilent Human miRNA arrays to identify the differentially expressed microRNAs beween: 1) AA and EA PCa patients; 2) AA PCa vs. AA normal; and 3) EA PCa vs. EA normal. 54 prostate biopsy specimens (tumor and adjacent normal tissues) were collected from 14 African American and 13 European American prostate cancer patients. 54 RNA samples, purified from the collected biopy specimens using Qiagen miRNeasy kit, were process and applied to Agilent human miRNA arrays. Array data was normalized and analyzed using Agilent GeneSpring program.

2015-07-27 | E-GEOD-64318 | biostudies-arrayexpress

Opposite response of hTERT expression by androgen dose: Androgen-mediated inhibition of hTERT is mediated by the ING1 and ING2 tumor suppressors in prostate cancer cells

Project description:The catalytic subunit of the human telomerase (hTERT) is activated during tumorigenesis in many cancers including prostate cancer (PCa). Androgens mediate their effect through the androgen receptor (AR), a key factor controlling PCa growth. hTERT expression is known to be regulated by androgens, however contrarily observed to be inhibited or activated. Here, we reveal that androgens repress or activate hTERT expression in a concentration-dependent manner. Low physiological androgen levels activate while supraphysiological androgen levels (SAL) repress hTERT expression. We confirmed SAL-mediated gene repression of hTERT in native human PCa samples derived from patients treated ex vivo as well as in cancer spheroids derived from androgen-dependent and castration resistant PCa (CRPC) cells. Interestingly, based on chromatin immunoprecipitation (ChIP) data both a positive androgen response element (pARE) at -4kb distal and a negative response element (nARE) at the proximal -0.1kb promoter region were identified. Focusing on the nARE it was narrowed down to -121 to -58 bp in the core promoter region. ChIP experiments confirmed an androgen-dependent recruitment of AR and the tumor suppressors inhibitor of growth 1 and 2 (ING1 and ING2), recently identified as AR co-repressors. Mechanistically, the knockdown of either ING1 or ING2 reduced androgen-mediated repression of hTERT indicating that ING1 and ING2 mediate AR-regulated transrepression on the hTERT expression. Thus, our data suggest a dual, biphasic function of AR to control hTERT expression by transactivation and transrepression. The inhibition of hTERT by androgens by a nARE located in the proximal promoter region is mediated at least in part by the AR co-repressors ING1 and ING2.

2022-03-04 | GSE155528 | GEO

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

Project description:Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The rs1859962 single nucleotide polymorphism (SNP) part of the 17q24.3 locus is a risk factor for prostate cancer (PCa). It defines a 130kb linkage disequilibrium (LD) block that lies in a ~2Mb gene desert area. Despite a role for the proximal SOX9 gene in PCa development, the functional biology driving the risk of this 17q24.3 risk locus is unknown. In the present study, we integrate genome-wide chromatin landscape datasets, namely epigenomes and chromatin openness from diverse cell-types to identify one PCa specific enhancer within the rs1859962 risk LD block. We reveal that this enhancer is part of a 1Mb chromatin loop with the SOX9 gene in PCa cells. The rs8072254 and rs1859961 SNPs part of this LD block map to this enhancer and impose allele-specific gene expression. The variant allele of rs1859961 directly decreases FoxA1 binding while increasing AP-1 binding compared to the reference allele. This latter is key in driving allele-specific gene expression. Together, our results demonstrate the risk associated with the PCa rs1859962 risk LD block is accounted for by multiple genetic variants mapping to a unique enhancer looping to the SOX9 oncogene. Allele-specific recruitment of the transcription factor AP-1 accounts in part for the increased enhancer activity ascribed to this PCa risk LD block. This further demonstrates that an integrative genomics approach can identify the functional biology disrupted by genetic risk-variants. Examination of histone modification H3K36me3 in the prostate cancer LNCaP cell line under DHT treatment.

2012-06-03 | E-GEOD-35829 | biostudies-arrayexpress

CRISPRi screen of prostate cancer associated risk cis-regulatory elements [RNA-seq]

Project description:Prostate cancer (PCa) associated risk SNPs are enriched in cis-regulatory elements (CREs). In this study, we screened 260 CREs that contain at least one PCa risk SNP for essentiality in V16A, 22Rv1 and A549 cells. We tiled the CREs and 14 control regions using 5,873 sgRNAs.

2020-12-16 | GSE142809 | GEO

CRISPRi screen of prostate cancer associated risk cis-regulatory elements [Hi-C]

2020-12-16 | GSE143370 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data