Dataset Information

Single-minded homolog 2 resides in the chromatin protein network of androgen receptor and modulates gene expression in prostate cancer cells Single-minded homolog 2 resides in the chromatin protein network of androgen receptor and modulates gene expression in prostate cancer cells

ABSTRACT: We investigated the composition of chromatin protein network around endogenous androgen receptor (AR) in VCaP castration resistant prostate cancer cells using recently developed chromatin-directed proteomic approach called ChIP-SICAP . The androgen-induced AR chromatin protein network contained expected TFs, e.g. HOXB13, chromatin remodeling proteins, e.g. SMARCA4, and several novel candidates not previously associated with AR, e.g. prostate cancer biomarker SIM2. Based on these findings, the role of SMARCA4 and SIM2 was further characterized at AR chromatin domains . Silencing of SIM2 altered chromatin accessibility at a similar number of AR-binding sites as SMARCA4, an established ATPase subunit of the BAF chromatin remodeling complex, often aberrantly expressed in prostate cancer. Despite the wide co-occurrence on chromatin of SMARCA4 and AR, depletion of SMARCA4 influenced chromatin accessibility and expression of a restricted set of AR target genes, in particular those involved in cell morphogenetic changes in epithelial-mesenchymal transition. Silencing of SIM2, in turn, affected the expression of a much larger group of androgen-regulated genes, e.g. those involved in cellular responses to external stimuli and steroid hormone stimulus. The silencing also reduced proliferation of VCaP cells and tumor size in chick embryo chorioallantoic membrane assay, further suggesting the importance of SIM2 in the regulation prostate cancer cells.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Gianluca Sigismondo

LAB HEAD: Jorma J Palvimo

PROVIDER: PXD025193 | Pride | 2021-06-17

REPOSITORIES: Pride

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Publications

Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells.

Launonen Kaisa-Mari KM Paakinaho Ville V Sigismondo Gianluca G Malinen Marjo M Sironen Reijo R Hartikainen Jaana M JM Laakso Hanna H Visakorpi Tapio T Krijgsveld Jeroen J Niskanen Einari A EA Palvimo Jorma J JJ

Oncogene 20210614 27

Treatment of prostate cancer confronts resistance to androgen receptor (AR)-targeted therapies. AR-associated coregulators and chromatin proteins hold a great potential for novel therapy targets. Here, we employed a powerful chromatin-directed proteomics approach termed ChIP-SICAP to uncover the composition of chromatin protein network, the chromatome, around endogenous AR in castration resistant prostate cancer (CRPC) cells. In addition to several expected AR coregulators, the chromatome contai ...[more]

PMID: 34127815

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Project description:Androgen receptor (AR) is a transcription factor that plays a central role in the growth and development of the normal prostate and its malignant transformation. More recently, a majority of prostate cancers have been shown to harbor recurrent gene fusions of the androgen-regulated gene, TMPRSS2, to the oncogenic ETS transcription factor ERG. Here we employed chromatin immunoprecipitation coupled to massively parallel sequencing (ChIP-Seq) to explore the genome-wide localization of these transcription factors in human prostate cancer cell lines as well as tissues. Unexpectedly, transcriptional networks emanating from AR and ERG were found to be highly overlapping. Furthermore, AR was found to regulate known 5’ fusion partners in prostate cancer including TMPRSS2, as well as negatively regulating its own expression. While induced by androgen through fusion to TMPRSS2, ERG itself was shown to inhibit AR expression and positively regulate the genomic locus of wild-type ERG, thus revealing multiple levels of molecular cross-talk between AR and ERG. Importantly, androgen-sensitive prostate cancer cells in which ERG is overexpressed are able to proliferate and invade in the absence of androgen. Thus, we dissected the intertwined genomic landscape of two master transcriptional regulators of prostate cancer and suggest a role for ERG in maintaining transcriptional networks necessary for androgen-independent prostate cancer growth. These studies may suggest that future therapies against prostate cancer should target both AR and ERG, rather than AR alone, in order to achieve maximum effectiveness. ChIP_Seq examination of histone modifications and key transcription factors in LNCaP and VCaP prostate cancer cell lines in un-treated, vehicle treated or 10nM R1881 treated conditions. LNCaP ChIP-Seq experiments include samples GSM353609-GSM353618, GSM353625-GSM353628, GSM353633-GSM353635, GSM353641-GSM353644, and GSM353648. VCaP ChIP-Seq experiments include samples GSM353601-GSM353608, GSM353619-GSM353624, GSM353629-GSM353632, and GSM353645-GSM353647. In addition, we performed re-ChIP of AR and ERG in VCaP cells (GSM356767), and examined the effect of ERG knockdown on AR and ERG binding (samples GSM353636-GSM353639). To study ectopic ERG binding we performed ERG ChIP-Seq in stable RWPE+ERG or control cells (samples GSM353649-GSM353650). AR ChIP-Seq was also done in the AR-positive but ETS fusion-negative 22RV1 cells (GSM353640). To further study transcription factor binding and chromatin state we performed ChIP-Seq of AR, ERG, H3K4me3, H3K9me3, H3K27me3 and RNA Pol II in a metastatic prostate tumor tissue (samples GSM353651-GSM353656). To couple the ChIP-Seq experiments with gene expression, we have also done Illumian SAGE-tag profiling in LNCaP cells following androgen treatment for 0, 24 and 48hrs. These DGE experiments correspond to samples GSM353657-GSM353659.

Project description:The androgen receptor (AR) is an androgen-activated nuclear receptor. The androgen signaling axis is critical in all stages of prostate cancer, although the mechanism by which it contributes to tumorigenesis remains unclear. Mutations in the AR have been detected in prostate tumors; one such mutant, E231G, exhibits increased ligand sensitivity in the presence of specific cofactors. Mice with prostate-specific expression of AR-E231G invariably develop prostatic intraepithelial neoplasia (PIN) by 12 weeks, and metastatic prostate cancer by 52 weeks. To determine a potential mechanism of AR-driven tumorigenesis in AR-E231G mice, we compared gene expression profiles in prostates of 12 week old AR-E231G mice with another AR-variant mouse strain (AR-T857A) that does not develop tumors. Pathway classification of the 132 candidate genes differentially expressed in AR-E231G mouse prostates compared to AR-T857A mouse prostates revealed enrichment for groups important in prostate cancer, including “cancer,” “fatty acid metabolism” and “cell cycle” pathways. Two genes significantly upregulated in the AR-E231G model were Adm and Cited1. siRNA suppression of ADM and CITED1 expression by up to 63% and 79%, respectively, in LNCaP human prostate cancer cells, resulted in an approximate 1.8-fold increase in cell death. Cell proliferation was reduced by 35% when CITED1 mRNA expression was suppressed, but not significantly altered by ADM suppression. A gene signature set derived from this model was able to distinguish between primary Gleason grade 3 and Gleason grade 4 tumors (p=0.04237), and between human non-malignant and cancerous prostate in a test (p=0.02352) and validation cohort (p=7.53x10-9), highlighting the relevance of the AR-E231G model to the human disease. RNA was extracted from ventral prostate tissue from 12-week old AR-E231G and AR-T857A mice in FVB background. Pooled RNA from 3 mice per genotype were extracted using the RNeasy kit (Qiagen, Germantown, MD, USA), and 10 µg RNA was hybridized to a total of 2 Affymetrix Mouse Genome 430 2.0 chip® microarrays. Microarray data was normalized by Robust Multiarray Averaging. Probes with expression changes were identified using a fold-change cut-off of log1.5. Normalized microarray data was analysed using Ingenuity Pathways Analysis (IPA, Redwood City, CA, USA).

Dataset Information

Single-minded homolog 2 resides in the chromatin protein network of androgen receptor and modulates gene expression in prostate cancer cells Single-minded homolog 2 resides in the chromatin protein network of androgen receptor and modulates gene expression in prostate cancer cells

Publications

Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells.

Similar Datasets

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