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Henry WS, Hendrickson DG, Beca F, Glass B, Lindahl-Allen M, He L, Ji Z, Struhl K, Beck AH, Rinn JL, Toker A. LINC00520 is induced by Src, STAT3, and PI3K and plays a functional role in breast cancer. Oncotarget 2018; 7:81981-81994. [PMID: 27626181 PMCID: PMC5347668 DOI: 10.18632/oncotarget.11962] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/02/2016] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in normal cellular homeostasis as well as pathophysiological conditions, including cancer. Here we performed global gene expression profiling of mammary epithelial cells transformed by oncogenic v-Src, and identified a large subset of uncharacterized lncRNAs potentially involved in breast cancer development. Specifically, our analysis revealed a novel lncRNA, LINC00520 that is upregulated upon ectopic expression of oncogenic v-Src, in a manner that is dependent on the transcription factor STAT3. Similarly, LINC00520 is also increased in mammary epithelial cells transformed by oncogenic PI3K and its expression is decreased upon knockdown of mutant PIK3CA. Additional expression profiling highlight that LINC00520 is elevated in a subset of human breast carcinomas, with preferential enrichment in the basal-like molecular subtype. ShRNA-mediated depletion of LINC00520 results in decreased cell migration and loss of invasive structures in 3D. RNA sequencing analysis uncovers several genes that are differentially expressed upon ectopic expression of LINC00520, a significant subset of which are also induced in v-Src-transformed MCF10A cells. Together, these findings characterize LINC00520 as a lncRNA that is regulated by oncogenic Src, PIK3CA and STAT3, and which may contribute to the molecular etiology of breast cancer.
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Affiliation(s)
- Whitney S Henry
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - David G Hendrickson
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francisco Beca
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Benjamin Glass
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Marianne Lindahl-Allen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lizhi He
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zhe Ji
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Andrew H Beck
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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Fleming JD, Giresi PG, Lindahl-Allen M, Krall EB, Lieb JD, Struhl K. STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer. Epigenetics Chromatin 2015; 8:7. [PMID: 25784959 PMCID: PMC4362815 DOI: 10.1186/1756-8935-8-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/21/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Transient induction of the Src oncoprotein in a non-transformed breast cell line can initiate an epigenetic switch to a cancer cell via a positive feedback loop that involves activation of the signal transducer and activator of transcription 3 protein (STAT3) and NF-κB transcription factors. RESULTS We show that during the transformation process, nucleosome-depleted regions (defined by formaldehyde-assisted isolation of regulatory elements (FAIRE)) are largely unchanged and that both before and during transformation, STAT3 binds almost exclusively to previously open chromatin regions. Roughly, a third of the transformation-inducible genes require STAT3 for the induction. STAT3 and NF-κB appear to drive the regulation of different gene sets during the transformation process. Interestingly, STAT3 directly regulates the expression of NFKB1, which encodes a subunit of NF-κB, and IL6, a cytokine that stimulates STAT3 activity. Lastly, many STAT3 binding sites are also bound by FOS and the expression of several AP-1 factors is altered during transformation in a STAT3-dependent manner, suggesting that STAT3 may cooperate with AP-1 proteins. CONCLUSIONS These observations uncover additional complexities to the inflammatory feedback loop that are likely to contribute to the epigenetic switch. In addition, gene expression changes during transformation, whether driven by pre-existing or induced transcription factors, occur largely through pre-existing nucleosome-depleted regions.
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Affiliation(s)
- Joseph D Fleming
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Paul G Giresi
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637 USA
| | - Marianne Lindahl-Allen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Elsa B Krall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Jason D Lieb
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637 USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
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Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell 2011; 44:410-423. [PMID: 22055187 DOI: 10.1016/j.molcel.2011.08.037] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 05/30/2011] [Accepted: 08/15/2011] [Indexed: 11/17/2022]
Abstract
Histone acetyltransferase (HAT) complexes are coactivators that are important for transcriptional activation by modifying chromatin. Metazoan SAGA and ATAC are distinct multisubunits complexes that share the same catalytic HAT subunit (GCN5 or PCAF). Here, we show that these human HAT complexes are targeted to different genomic loci representing functionally distinct regulatory elements both at broadly expressed and tissue-specific genes. While SAGA can principally be found at promoters, ATAC is recruited to promoters and enhancers, yet only its enhancer binding is cell-type specific. Furthermore, we show that ATAC functions at a set of enhancers that are not bound by p300, revealing a class of enhancers not yet identified. These findings demonstrate important functional differences between SAGA and ATAC coactivator complexes at the level of the genome and define a role for the ATAC complex in the regulation of a set of enhancers.
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Affiliation(s)
- Arnaud R Krebs
- Program of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
| | - Krishanpal Karmodiya
- Program of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
| | - Marianne Lindahl-Allen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, C-315240 Longwood Avenue, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, C-315240 Longwood Avenue, Boston, MA 02115, USA
| | - Làszlò Tora
- Program of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
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Iliopoulos D, Lindahl-Allen M, Polytarchou C, Hirsch HA, Tsichlis PN, Struhl K. Loss of miR-200 inhibition of Suz12 leads to polycomb-mediated repression required for the formation and maintenance of cancer stem cells. Mol Cell 2010; 39:761-72. [PMID: 20832727 DOI: 10.1016/j.molcel.2010.08.013] [Citation(s) in RCA: 319] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 05/10/2010] [Accepted: 06/28/2010] [Indexed: 12/19/2022]
Abstract
In an inducible oncogenesis model, the miR-200 family is inhibited during CSC formation but not transformation, and inhibition of miR-200b increases CSC formation. Interestingly, miR-200b directly targets Suz12, a subunit of a polycomb repressor complex (PRC2). Loss of miR-200 during CSC formation increases Suz12 expression, Suz12 binding, H3-K27 trimethylation, and Polycomb-mediated repression of the E-cadherin gene. miR-200b expression or Suz12 depletion blocks the formation and maintenance of mammospheres, and in combination with chemotherapy suppresses tumor growth and prolongs remission in mouse xenografts. Conversely, ectopic expression of Suz12 in transformed cells is sufficient to generate CSCs. The miR-200b-Suz12-cadherin pathway is important for CSC growth and invasive ability in genetically distinct breast cancer cells, and its transcriptional signature is observed in metastatic breast tumors. The interaction between miR-200 and Suz12 is highly conserved, suggesting that it represents an ancient regulatory mechanism to control the growth and function of stem cells.
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Affiliation(s)
- Dimitrios Iliopoulos
- Department Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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