Abstract SY43-03: Long-range epigenetic control of estrogen-responsive transcription
Authors: Lin Chun-Lin , Huang Tim Hui-Ming 
Published: August 2019

Estrogen stimulation triggers ERα binding to distant estrogen response elements (DEREs) through intra- or inter-chromatin interactions (Hsu et al. 2013; Hsu et al. 2015). Prolonged or repetitive stimulation causes alterations of histone marks and DNA methylation patterns in neighboring regions of DEREs, establishing three-dimensional structures for concordant transcription of estrogen-responsive genes. DEREs from multiple chromosome regions can be mobilized to form transcription depots for synchronized transcription of neighboring target genes. Heterochromatin protein 1 (HP1) acts as an anchor in regulating chromatin movement of DERE-mediated transcription assemblages in the nucleus (Hsu et al. 2015). Although HP1 is a fundamental unit of heterochromatin and acts a transcriptional repressor, we found that this protein may serve as a lamina buttress to support free movement of flexible chromatin in assembling transcription factories (Beisel and Paro 2011; Hsu et al. 2015). Neutralizing HP1 function deregulates the formation of DERE depots for concordant transcription of target genes. Furthermore, deletion of DEREs using the CRISPR/Cas9 genomic editing system alters transcription profiles of proliferation-associated networks, resulting in reduced cellular growth of luminal breast cancer cells. The epigenetic control of DERE-related chromatin movement has profoundly geographic influences on local genomic structures of gene clusters. Frequent chromatin interactions increase DNA breaks at or nearby looping sites, contributing to genomic instability in cancer cells (Kaiser and Semple 2018). Inappropriate DNA repair leads to genomic fusion and duplication of DEREs and target promoters. Amplified DEREs potentially cooperate with epigenetic machineries for long-range transcription regulation, leading to intensification of gene activation and repression for advanced development of luminal breast cancer. Specifically, we have identified DEREs on chromosome 20q13 frequently amplified and translocated to other chromosomes in this cancer subtype (Hsu et al. 2015).

Genome-wide survey of The Cancer Genomic Atlas (TCGA) breast cancer cohort identified 17 contiguous chromosome regions that contain gene clusters (n=16 to 33 genes) with high correlation coefficients between their amplification and expression levels. Five of these identified regions were from chromosome 17q, and, moreover, upregulation of their gene expression was linked to luminal breast cancer with adverse clinical outcomes. Specifically, we found that six genes BCAS3, BRIP1, INTS2, MED13, METTL2A and TLK2 displayed concordantly high expression are located on the active or open topologically associating domains of 17q23 enriched with permissive chromatin marks H3K36me3 and H3K4me3. Complex translocation patterns between 17q23 and 20q13 were detected in breast tumors. The expression of these genes was increased in breast cancer cells after estrogen stimulation. However, this synchronized regulatory function was abolished in breast cancer cells harboring CRISPR/Cas9-knockout of 20q13 DEREs. These findings further establish that the 17q23 region can serve as an estrogen-driven transcriptional hub to promote ERα-mediated gene regulation and also extend previously published results showing that 17q23 genes are indeed DERE-bound ERα target genes.

One of these DERE-regulated loci is Tousled Like Kinase 2 (TLK2), known to participate in checkpoint regulation and DNA damage response (Bruinsma et al. 2016), is an actionable target. Amplification-associated upregulation of TLK2 can be suppressed in breast cancer cells treated with phenothiazine antipsychotics, thioridazine, perphenazine and trifluoperazine (Sudeshna and Parimal 2010). Antiproliferative effects of phenothiazines were prominent especially in high TLK2-expressing cells, compared to those low TLK2-expressing cells that were relatively insensitive to phenothiazines. To further extend the potential use of TLK2 inhibition, we determined the efficacy of phenothiazine treatment on ex vivo cultures of patient-derived circulating tumor cells (CTCs). Enriched populations of CTCs were obtained from blood samples of breast cancer patients with metastatic disease. CTCs derived from patients with ERα-positive breast cancer appeared to be more sensitive to TLK2 inhibition compared to those of ERα-negative patients. Therefore, these antipsychotics can potentially be used as an adjunct for treating breast cancer tumors carrying DERE-mediated 17q23 amplification.

Citations:

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Bruinsma W, van den Berg J, Aprelia M, Medema RH. 2016. Tousled-like kinase 2 regulates recovery from a DNA damage-induced G2 arrest. EMBO reports doi:10.15252/embr.201540767: e201540767.

Hsu P-Y, Hsu H-K, Lan X, Juan L, Yan Pearlly S, Labanowska J, Heerema N, Hsiao T-H, Chiu Y-C, Chen Y et al. 2013. Amplification of Distant Estrogen Response Elements Deregulates Target Genes Associated with Tamoxifen Resistance in Breast Cancer. Cancer Cell 24: 197-212.

Hsu PY, Hsu HK, Hsiao TH, Ye Z, Wang E, Profit AL, Jatoi I, Chen Y, Kirma NB, Jin VX et al. 2015. Spatiotemporal control of estrogen-responsive transcription in ERα-positive breast cancer cells. Oncogene 35: 2379.

Kaiser VB, Semple CA. 2018. Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline. Genome biology 19: 101-101.

Sudeshna G, Parimal K. 2010. Multiple non-psychiatric effects of phenothiazines: A review. European Journal of Pharmacology 648: 6-14.

Citation Format: Chun-Lin Lin, Tim Hui-Ming Huang. Long-range epigenetic control of estrogen-responsive transcription [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY43-03.