The FOXN3-NEAT1-SIN3A repressor complex promotes progression of hormonally responsive breast cancer
Wanjin Li, … , Jing Liang, Yongfeng Shang
Wanjin Li, … , Jing Liang, Yongfeng Shang
Published August 14, 2017
Citation Information: J Clin Invest. 2017;127(9):3421-3440. https://doi.org/10.1172/JCI94233.
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Research Article Cell biology Endocrinology

The FOXN3-NEAT1-SIN3A repressor complex promotes progression of hormonally responsive breast cancer

Abstract

The pathophysiological function of the forkhead transcription factor FOXN3 remains to be explored. Here we report that FOXN3 is a transcriptional repressor that is physically associated with the SIN3A repressor complex in estrogen receptor–positive (ER+) cells. RNA immunoprecipitation–coupled high-throughput sequencing identified that NEAT1, an estrogen-inducible long noncoding RNA, is required for FOXN3 interactions with the SIN3A complex. ChIP-Seq and deep sequencing of RNA genomic targets revealed that the FOXN3-NEAT1-SIN3A complex represses genes including GATA3 that are critically involved in epithelial-to-mesenchymal transition (EMT). We demonstrated that the FOXN3-NEAT1-SIN3A complex promotes EMT and invasion of breast cancer cells in vitro as well as dissemination and metastasis of breast cancer in vivo. Interestingly, the FOXN3-NEAT1-SIN3A complex transrepresses ER itself, forming a negative-feedback loop in transcription regulation. Elevation of both FOXN3 and NEAT1 expression during breast cancer progression corresponded to diminished GATA3 expression, and high levels of FOXN3 and NEAT1 strongly correlated with higher histological grades and poor prognosis. Our experiments uncovered that NEAT1 is a facultative component of the SIN3A complex, shedding light on the mechanistic actions of NEAT1 and the SIN3A complex. Further, our study identified the ERα-NEAT1-FOXN3/NEAT1/SIN3A-GATA3 axis that is implicated in breast cancer metastasis, providing a mechanistic insight into the pathophysiological function of FOXN3.

Authors

Wanjin Li, Zihan Zhang, Xinhua Liu, Xiao Cheng, Yi Zhang, Xiao Han, Yu Zhang, Shumeng Liu, Jianguo Yang, Bosen Xu, Lin He, Luyang Sun, Jing Liang, Yongfeng Shang

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Figure 3

Genome-wide analysis of the transcriptional targets of the FOXN3-NEAT1-SIN3A complex.

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Genome-wide analysis of the transcriptional targets of the FOXN3-NEAT1-S...
(A) Genomic distribution of the transcriptional targets of FOXN3 and SIN3A based on ChIP-Seq data (left). Venn diagrams of overlapping genes targeted by FOXN3 and SIN3A in MCF-7 cells (right). (B) MEME-ChIP analysis of the DNA binding motifs of FOXN3 and SIN3A (left). The binding profiles of FOXN3 and SIN3A on NCOA2 and TJP1 are shown (right). (C) MEME-ChIP analysis of the DNA binding motifs of NEAT1. Venn diagrams of overlapping genes targeted by FOXN3, SIN3A, and NEAT1 in MCF-7 cells based on FOXN3-SIN3A ChIP-Seq data and NEAT1 CHART-Seq data (left). Density distributions (read count per million of mapped reads) of SIN3A, NEAT1, and MALAT1 peaks on the transcription start site (TSS) of FOXN3-enriched genes were analyzed by ngs.plot (right). (D) qPCR measurement of the expression of the indicated genes in MCF-7 cells under FOXN3 depletion. Error bars represent mean ± SD for triplicate experiments (*P < 0.05, **P < 0.01; t test). (E) qChIP verification of the ChIP-Seq results on the promoter of the indicated genes with antibodies against the indicated proteins in MCF-7 cells. Error bars represent mean ± SD for triplicate experiments (**P < 0.01, 2-way ANOVA).