Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state

Despite the role of the estrogen receptor α (ERα) pathway as a key growth driver for breast cells, the phenotypic consequence of exogenous introduction of ERα into ERα‐negative cells paradoxically has been growth inhibition. We mapped the binding profiles of ERα and its interacting transcription factors (TFs), FOXA1 and GATA3 in MCF‐7 breast carcinoma cells, and observed that these three TFs form a functional enhanceosome that regulates the genes driving core ERα function and cooperatively modulate the transcriptional networks previously ascribed to ERα alone. We demonstrate that these enhanceosome occupied sites are associated with optimal enhancer characteristics with highest p300 co‐activator recruitment, RNA Pol II occupancy, and chromatin opening. Most importantly, we show that the transfection of all three TFs was necessary to reprogramme the ERα‐negative MDA‐MB‐231 and BT‐549 cells to restore the estrogen‐responsive growth resembling estrogen‐treated ERα‐positive MCF‐7 cells. Cumulatively, these results suggest that all the enhanceosome components comprising ERα, FOXA1, and GATA3 are necessary for the full repertoire of cancer‐associated effects of the ERα.

[1]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[2]  Tom Maniatis,et al.  Transcriptional activation: A complex puzzle with few easy pieces , 1994, Cell.

[3]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[4]  G. Bourque,et al.  Transposable elements have rewired the core regulatory network of human embryonic stem cells , 2010, Nature Genetics.

[5]  Brian J. Wilson,et al.  Meta-analysis of human cancer microarrays reveals GATA3 is integral to the estrogen receptor alpha pathway , 2008, Molecular Cancer.

[6]  T. Maniatis,et al.  Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome , 1995, Cell.

[7]  S. Burley,et al.  Binding of the winged‐helix transcription factor HNF3 to a linker histone site on the nucleosome , 1998, The EMBO journal.

[8]  F. Stossi,et al.  Whole-Genome Cartography of Estrogen Receptor α Binding Sites , 2007, PLoS genetics.

[9]  N. D. Clarke,et al.  Integrative model of genomic factors for determining binding site selection by estrogen receptor-α , 2010, Molecular systems biology.

[10]  Frank R. Lin,et al.  Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. , 2002, Molecular cell.

[11]  N. D. Clarke,et al.  Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.

[12]  Harikrishna Nakshatri,et al.  FOXA1 in breast cancer , 2009, Expert Reviews in Molecular Medicine.

[13]  Clifford A. Meyer,et al.  Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. , 2008, Genome research.

[14]  Clifford A. Meyer,et al.  FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription , 2008, Cell.

[15]  H. Rochefort,et al.  Activation of estrogen receptor transfected into a receptor-negative breast cancer cell line decreases the metastatic and invasive potential of the cells. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[16]  K. White,et al.  Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer , 2009, Cell.

[17]  M. Campbell,et al.  PANTHER: a library of protein families and subfamilies indexed by function. , 2003, Genome research.

[18]  Marie-Liesse Asselin-Labat,et al.  Gata-3 is an essential regulator of mammary-gland morphogenesis and luminal-cell differentiation , 2007, Nature Cell Biology.

[19]  Charles M Perou,et al.  FOXA1 Expression in Breast Cancer—Correlation with Luminal Subtype A and Survival , 2007, Clinical Cancer Research.

[20]  E. Liu,et al.  An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.

[21]  P. Farnham Insights from genomic profiling of transcription factors , 2009, Nature Reviews Genetics.

[22]  Klaus H. Kaestner,et al.  FOXA1 is an essential determinant of ERα expression and mammary ductal morphogenesis , 2010, Development.

[23]  C. Osborne,et al.  Forkhead Homologue in Rhabdomyosarcoma Functions as a Bifunctional Nuclear Receptor-interacting Protein with Both Coactivator and Corepressor Functions* , 2001, The Journal of Biological Chemistry.

[24]  K. Kaestner,et al.  The Hepatocyte Nuclear Factor 3 (HNF3 or FOXA) Family in Metabolism , 2000, Trends in Endocrinology & Metabolism.

[25]  J. Eeckhoute,et al.  Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer. , 2007, Cancer research.

[26]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[27]  Barry Komm,et al.  Profiling of estrogen up- and down-regulated gene expression in human breast cancer cells: insights into gene networks and pathways underlying estrogenic control of proliferation and cell phenotype. , 2003, Endocrinology.

[28]  W. Sung,et al.  ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing , 2010, Genome Biology.

[29]  Myles A Brown,et al.  AKT Alters Genome-Wide Estrogen Receptor α Binding and Impacts Estrogen Signaling in Breast Cancer , 2008, Molecular and Cellular Biology.

[30]  Jérôme Eeckhoute,et al.  Positive Cross-Regulatory Loop Ties GATA-3 to Estrogen Receptor α Expression in Breast Cancer , 2007 .

[31]  Debashis Ghosh,et al.  Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis. , 2005, Cancer research.

[32]  Wing-Kin Sung,et al.  CENTDIST: discovery of co-associated factors by motif distribution , 2011, Nucleic Acids Res..

[33]  John D. Minna,et al.  Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery , 2009, PloS one.

[34]  Carl W. Miller,et al.  FOXA1: Growth inhibitor and a favorable prognostic factor in human breast cancer , 2006, International journal of cancer.

[35]  A. Meister,et al.  Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. , 2003, The Plant journal : for cell and molecular biology.

[36]  Clifford A. Meyer,et al.  Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1 , 2005, Cell.

[37]  S. Burley,et al.  Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5 , 1993, Nature.