1. Cancer Biology
  2. Cell Biology
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Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells

  1. Alejandro La Greca
  2. Nicolás Bellora
  3. François Le Dily
  4. Rodrigo Jara
  5. Ana Silvina Nacht
  6. Javier Quilez Oliete
  7. José Luis Villanueva
  8. Enrique Vidal
  9. Gabriela Merino
  10. Cristóbal Fresno
  11. Inti Tarifa Reischle
  12. Griselda Vallejo
  13. Guillermo Pablo Vicent
  14. Elmer Fernández
  15. Miguel Beato
  16. Patricia Saragüeta  Is a corresponding author
  1. Biology and Experimental Medicine Institute, Argentina
  2. Institute of Nuclear Technologies for Health, Argentina
  3. Centre for Genomic Regulation, Spain
  4. Córdoba University, Argentina
Research Article
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Cite this article as: eLife 2022;11:e66034 doi: 10.7554/eLife.66034

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).

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Alejandro La Greca

    Biology and Experimental Medicine Institute, Buenos Aires, Argentina
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0309-7683
  2. Nicolás Bellora

    National Scientific and Technical Research Council (CONICET), Institute of Nuclear Technologies for Health, Bariloche, Argentina
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6637-3465
  3. François Le Dily

    Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  4. Rodrigo Jara

    Biology and Experimental Medicine Institute, Buenos Aires, Argentina
    Competing interests
    The authors declare that no competing interests exist.
  5. Ana Silvina Nacht

    Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  6. Javier Quilez Oliete

    Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  7. José Luis Villanueva

    Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  8. Enrique Vidal

    Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  9. Gabriela Merino

    Bioscience Data Mining Group, Córdoba University, Córdoba, Argentina
    Competing interests
    The authors declare that no competing interests exist.
  10. Cristóbal Fresno

    Bioscience Data Mining Group, Córdoba University, Córdoba, Argentina
    Competing interests
    The authors declare that no competing interests exist.
  11. Inti Tarifa Reischle

    Biology and Experimental Medicine Institute, Buenos Aires, Argentina
    Competing interests
    The authors declare that no competing interests exist.
  12. Griselda Vallejo

    Biology and Experimental Medicine Institute, Buenos Aires, Argentina
    Competing interests
    The authors declare that no competing interests exist.
  13. Guillermo Pablo Vicent

    Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  14. Elmer Fernández

    Bioscience Data Mining Group, Córdoba University, Córdoba, Argentina
    Competing interests
    The authors declare that no competing interests exist.
  15. Miguel Beato

    Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  16. Patricia Saragüeta

    Biology and Experimental Medicine Institute, Buenos Aires, Argentina
    For correspondence
    patriciasaragueta2@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8222-9690

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

  1. Inez Rogatsky, Hospital for Special Surgery, United States

Publication history

  1. Received: December 22, 2020
  2. Accepted: January 11, 2022
  3. Accepted Manuscript published: January 12, 2022 (version 1)

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.

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