Abstract 1383: Evolution of the NCOR1 and NCOR2/SMRT cistromes in prostate cancer progression
Authors: Singh Prashant K. , Long Mark D. , Dhiman Vineet K. , Zhu Qianqian , Sucheston-Campbell Lara , Smiraglia Dominic , Campbell Moray J. 
Published: May 2015

Abstract
The archetypical co-repressors NCOR1 and NCOR2/SMRT exist in large complexes with histone deacetylases and significantly control multiple transcription factors (TFs), including nuclear receptors such as the VDR and AR. NCOR1 and NCOR2/SMRT are altered in cancer by mechanisms, including mutation, but it remains unclear how this disrupts their unique and shared functions either to commission or decommission enhancers through the genome. Previously, we established that altered co-repressor recruitment in prostate cancer (CaP) induces sustained and targeted H3K9me2 at target gene loci that drives increased CpG methylation. We propose that the oncogenic co-repressor cistromes drive CaP progression by inducing repressive histone modifications that in turn trigger methylated CpG regions at selective enhancers leading to stable and heritable changes to the transcriptome.
Using a high throughput micro-fluidic Q-ChIP approach we examined NCOR1, NCOR2/SMRT, H3K9me2, VDR, AR, and RNA POL2 levels at 47 genomic regions distributed over 8 VDR and 10 AR target genes in 5 normal and malignant prostate cell line models, at two time points following either 1α,25(OH)2D3 (D3) or DHT treatment. Binding patterns of NCOR1, NCOR2/SMRT and H3K9me2 distinguished normal, androgen sensitive and castrate recurrent CaP models. Specifically, co-repressor binding was enriched on VDR and AR target genes in a gene-specific manner across the CaP models. For example, PDK2 and BMP2 are AR target genes that had significantly more NCOR2/SMRT binding and gain of CpG methylation in LNCaP C4-2 cells, compared to the isogenic LNCaP. For these targets, and the others examined, gene expression loss and increased CpG methylation was mirrored by the TCGA CaP data, and a more general positive correlation between NCOR2/SMRT and CpG methylation was identified on the genome-wide level in the TCGA CaP data. In LNCaP and LNCaP C4-2 cells genome-wide binding of NCOR1 and NCOR2/SMRT was examined by ChIP-seq to measure the unique and shared cistromes in the emergence of castrate recurrent phenotype. In the first instance, analyses of NCOR1 binding in LNCaP cells revealed very significant enrichment at several TFs including SRF and GATA family members; the most significantly enriched nuclear receptor was RARβ. Subsequent GO term enrichment analyses revealed these genes were involved in metabolic process and chromatin/gene silencing pathways. Finally, we examined NCOR1 and NCOR2/SMRT staining on a TMA of 480 men with CaP who underwent radical prostatectomy. In the first instance, the analysis has revealed that elevated NCOR2/SMRT staining intensity was significantly associated with time to treatment failure.
These findings support the concept that NCOR1 and NCOR2/SMRT recruitment is significantly altered during CaP progression to drive selective, stable and heritable silencing of target genes for multiple transcription factors and is associated with poor outcome in CaP.
Citation Format: Prashant K. Singh, Mark D. Long, Vineet K. Dhiman, Qianqian Zhu, Lara Sucheston-Campbell, Dominic Smiraglia, Moray J. Campbell. Evolution of the NCOR1 and NCOR2/SMRT cistromes in prostate cancer progression. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1383. doi:10.1158/1538-7445.AM2014-1383