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Genomic profiling of H3K27ac and transcription factor binding in ERG-overexpressing prostate cancer

ABSTRACT: Structural rearrangements leading to the TMPRSS2:ERG (T2E) fusion typify ~50% of prostate tumors and result in overexpression of the ERG transcription factor. Using T2E and non-T2E primary prostate tumors, we assessed the impact of ERG overexpression on chromatin by integrating ChIP-seq against H3K27ac, a chromatin modification found at active cis-regulatory elements, with paired genomic and expression data. We show that T2E tumors have a consistent and distinct cis-regulatory landscape to non-T2E tumors which drives their unique transcriptional profile. The T2E-specific cis-regulatory landscape is driven by ERG-mediated co-option of prostate master transcription factors HOXB13 and FOXA1 and is typified by Cluster Of Regulatory Elements (COREs) including one spreading into the ERG locus of the structurally rearranged allele. This gives rise to a cis-regulatory element within the rearranged ERG gene that contributes to ERG overexpression. The unique cis-regulatory landscape in T2E primary prostate tumors also reveals the activation of the NOTCH signalling pathway. Accordingly, chemical NOTCH pathway inhibition limited the invasive nature of T2E prostate cancer cells, revealing an actionable vulnerability against T2E prostate tumors. Taken together, our work delineates the role of ERG over-expression in co-opting master transcription factors to deploy a unique cis-regulatory landscape inducing a dependency on NOTCH signaling in T2E prostate tumors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE96652 | GEO | 2017/07/25

SECONDARY ACCESSION(S): PRJNA379295

REPOSITORIES: GEO

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H3K27ac ChIP-seq in TMPRSS2:ERG positive and negative prostate cancer tissue samples

Project description:The TMPRSS2:ERG (T2E) structural rearrangements typifies ~50% of prostate tumors and results in overexpression of the ERG transcription factor. Using chromatin data collected in T2E and non-T2E primary prostate tumors, we show a distinct cis-regulatory landscape between T2E and non-T2E, inclusive of Cluster Of Regulatory Elements (COREs). This is mediated by ERG co-option of HOXB13 and FOXA1 implementing a T2E-specific transcriptional profile. We also report a T2E-specific CORE on the structurally rearranged ERG locus arising from spreading of the TMPRSS2 locus pre-existing CORE, assisting in its overexpression. Finally, we show that the T2E-specific cis-regulatory landscape reveals a vulnerability against the NOTCH pathway. Taken together, our work shows that overexpressed ERG co-opts master transcription factors to deploy a unique cis-regulatory landscape inducing a druggable dependency on NOTCH signaling in T2E prostate tumors.

| EGAS00001002496 | EGA

Co-expression of genes with ERG in prostate cancers

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Co-expression of genes with ERG in prostate cancer cell lines

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Co-expression of genes with ERG in prostate cancer cell lines

Project description:ERG overexpression is the most frequent molecular alteration in prostate cancer. We analyzed different stages of prostate cancer to identify genes that were coexpressed with ERG overexpression. In primary prostate tumors, it was shown that TDRD1 expression was the strongest correlated gene with ERG overexpression and we suggest TDRD1 as a direct ERG target gene. 6 Prostate cancer cell lines and 11 prostate cancer xenografts are included in this study. Each sample was analyzed once.

2013-02-11 | E-GEOD-41407 | biostudies-arrayexpress

Co-expression of genes with ERG in prostate cancers

Project description:ERG overexpression is the most frequent molecular alteration in prostate cancer. We analyzed different stages of prostate cancer to identify genes that were coexpressed with ERG overexpression. In primary prostate tumors, it was shown that TDRD1 expression was the strongest correlated gene with ERG overexpression and we suggest TDRD1 as a direct ERG target gene. 48 Prostate cancer samples from radical prostatectomies were included in this study. These samples contained more than 70% cancer and less than 30% stromal tissue. Each sample was analyzed once.

2013-02-11 | E-GEOD-41408 | biostudies-arrayexpress

sci-ATAC-seq identifies unique neuronal adhesion molecules and common transcription factor networks in high-grade localized prostate cancers

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Integration of ERG gene mapping and gene expression profiling identifies distinct categories of human prostate cancer

Project description:OBJECTIVE: Previous expression microarray analyses have failed to take into consideration the genetic heterogeneity and complex patterns of ERG gene alteration frequently found in cancerous prostates. The objective of this study is for the first time, to integrate the mapping of ERG gene alterations with the collection of expression microarray data. PATIENTS AND METHODS: We have deterimined genome-wide expression levels with Affymetrix GeneChip Human Exon 1.0 ST arrays using RNA prepared from 35 specimens of prostate cancer from 28 prostates. RESULTS: The expression profiles exhibit clustering, in unsupervised hierarchical analyses, into two distinct prostate cancer categories, with one group strongly associated with indicators of poor clinical outcome. The two categories are not tightly linked to ERG gene status. Through analysis of the data we identify a subgoup of cancers lacking ERG gene rearrangements that exhibit an outlier pattern of SPINK1 mRNA expression. We also show that a major distinction between ERG gene rearranged and non-rearranged cancers involves the levels of expression of genes linked to exposure to beta-estradiol, and to retinoic acid. CONCLUSIONS: Our studies show that expression profiling of prostate cancer samples containing single patterns of ERG alterations can provide novel insights into the mechanism of prostate cancer development, and support the view that factors other than ERG gene status are the major determinants of poor clinical outcome. Keywords: disease state analysis

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Development of peptidomimetic inhibitors of the ERG gene fusion product in prostate cancer (expression)

Project description:Transcription factors play a key role in the development of diverse cancers, and therapeutically targeting them has remained a challenge. In prostate cancer, the gene encoding the transcription factor ERG is recurrently rearranged and plays a critical role in prostate oncogenesis. Here, we identified a series of peptides that interact specifically with the DNA binding domain of ERG. The most prevalent consensus peptide series matched the tumor suppressor Deleted in Liver Cancer 1 (DLC1). ERG inhibitory peptides and derived peptidomimetics (EIPs) bound with high affinity and specificity leading to proteolytic degradation of ERG. The EIPs attenuated ERG-mediated transcription, chromatin recruitment, protein-protein interactions, cell invasion, and tumor growth. Thus, peptidomimetic targeting of transcription factor fusion products may provide a promising therapeutic strategy for prostate cancer as well as other cancers.

2014-07-15 | GSE58940 | GEO

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ERG is a critical regulator of Wnt/LEF1 signaling in prostate cancer

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2013-05-29 | E-GEOD-47423 | biostudies-arrayexpress

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