Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells
Abstract
Estrogen (E2) and Progesterone (Pg), via their specific receptors (ERalpha and PR), are major determinants in the development and progression of endometrial carcinomas, However, their precise mechanism of action and the role of other transcription factors involved are not entirely clear. Using Ishikawa endometrial cancer cells, we report that E2 treatment exposes a set of progestin-dependent PR binding sites which include both E2 and progestin target genes. ChIP-seq results from hormone-treated cells revealed a non-random distribution of PAX2 binding in the vicinity of these estrogen-promoted PR sites. Altered expression of hormone regulated genes in PAX2 knockdown cells suggests a role for PAX2 in fine-tuning ERalpha and PR interplay in transcriptional regulation. Analysis of long-range interactions by Hi-C coupled with ATAC-seq data showed that these regions, that we call 'progestin control regions' (PgCRs), exhibited an open chromatin state even before hormone exposure and were non-randomly associated with regulated genes. Nearly 20% of genes potentially influenced by PgCRs were found to be altered during progression of endometrial cancer. Our findings suggest that endometrial response to progestins in differentiated endometrial tumor cells results in part from binding of PR together with PAX2 to accessible chromatin regions. What maintains these regions open remains to be studied.
Data availability
All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus under accession number GSE139398 (reviewer access: ergbqgaebbmjrmt).Source data file has been provided for Figure 6.T47D ChIPseq data is available under GEO accession number GSE41466 (Ballare et al, 2013) and Hi-C data in GEO accession GSE53463 (Le-Dily et al, 2014). RNAseq datasets from proliferative (GSM3890623, GSM3890624, GSM3890625 and GSM3890626) and mid-secretory (GSM3890627, GSM3890628, GSM3890629, GSM3890630 and GSM3890631) human endometrium were obtained from GEO accession GSE132711 (SuperSeries GSE132713) (Chi et al, 2020). ChIPseq coverage data of proliferative and secretory normal endometrium were downloaded from GEO accession GSE132712 (SuperSeries GSE132713) (Chi et al, 2020). Human endometrial cancer RNAseq samples (n=575) were downloaded from The Cancer Genome Atlas (TCGA), project TCGA-UCEC. Additional normal and endometrial cancer samples (n=109) were accessed through CPTAC program in the National Cancer Institute using cptac platform installed with python (Dou et al, 2020).
-
Endometrial transcriptome and PGR cistrome in cycling fertile womenNCBI Gene Expression Omnibus, GSE132713.
-
Hormone induced repression of genes requires BRG1-mediated H1.2 deposition at target promotersNCBI Gene Expression Omnibus, GSE83785.
-
Nucleosome driven transcription factor binding and gene regulationNCBI Gene Expression Omnibus, GSE41466.
Article and author information
Author details
Funding
Consejo Nacional de Investigaciones Científicas y Técnicas (PIP 2015-682)
- Patricia Saragüeta
Fondo para la Investigación Científica y Tecnológica (PICT 2015-3426)
- Patricia Saragüeta
H2020 European Research Council (FP7/2007-2013 grant agreement 609989)
- Miguel Beato
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Inez Rogatsky, Hospital for Special Surgery, United States
Version history
- Preprint posted: August 20, 2019 (view preprint)
- Received: December 22, 2020
- Accepted: January 11, 2022
- Accepted Manuscript published: January 12, 2022 (version 1)
- Version of Record published: March 1, 2022 (version 2)
Copyright
© 2022, La Greca et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 1,767
- views
-
- 280
- downloads
-
- 15
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Cancer Biology
Diffuse midline gliomas (DMGs) are aggressive and fatal pediatric tumors of the central nervous system that are highly resistant to treatments. Lysine to methionine substitution of residue 27 on histone H3 (H3-K27M) is a driver mutation in DMGs, reshaping the epigenetic landscape of these cells to promote tumorigenesis. H3-K27M gliomas are characterized by deregulation of histone acetylation and methylation pathways, as well as the oncogenic MYC pathway. In search of effective treatment, we examined the therapeutic potential of dual targeting of histone deacetylases (HDACs) and MYC in these tumors. Treatment of H3-K27M patient-derived cells with Sulfopin, an inhibitor shown to block MYC-driven tumors in vivo, in combination with the HDAC inhibitor Vorinostat, resulted in substantial decrease in cell viability. Moreover, transcriptome and epigenome profiling revealed synergistic effect of this drug combination in downregulation of prominent oncogenic pathways such as mTOR. Finally, in vivo studies of patient-derived orthotopic xenograft models showed significant tumor growth reduction in mice treated with the drug combination. These results highlight the combined treatment with PIN1 and HDAC inhibitors as a promising therapeutic approach for these aggressive tumors.
-
- Cancer Biology
- Cell Biology
High-throughput vertebrate animal model systems for the study of patient-specific biology and new therapeutic approaches for aggressive brain tumors are currently lacking, and new approaches are urgently needed. Therefore, to build a patient-relevant in vivo model of human glioblastoma, we expressed common oncogenic variants including activated human EGFRvIII and PI3KCAH1047R under the control of the radial glial-specific promoter her4.1 in syngeneic tp53 loss-of-function mutant zebrafish. Robust tumor formation was observed prior to 45 days of life, and tumors had a gene expression signature similar to human glioblastoma of the mesenchymal subtype, with a strong inflammatory component. Within early stage tumor lesions, and in an in vivo and endogenous tumor microenvironment, we visualized infiltration of phagocytic cells, as well as internalization of tumor cells by mpeg1.1:EGFP+ microglia/macrophages, suggesting negative regulatory pressure by pro-inflammatory cell types on tumor growth at early stages of glioblastoma initiation. Furthermore, CRISPR/Cas9-mediated gene targeting of master inflammatory transcription factors irf7 or irf8 led to increased tumor formation in the primary context, while suppression of phagocyte activity led to enhanced tumor cell engraftment following transplantation into otherwise immune-competent zebrafish hosts. Altogether, we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging, high-throughput genetic and chemical manipulations to highlight important tumor-suppressive roles for the innate immune system on glioblastoma initiation, with important future opportunities for therapeutic discovery and optimizations.