Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Wenqian Li, Yuanxin Xi, Dana Richardson, Kendra L. Allton, Kaori Tanaka, Jing Li, Shino Murakami, Khandan Keyomarsi, Mark T. Bedford, Xiaobing Shi, Wei Li, Michelle C. Barton, Sharon Y.R. Dent, W. Lee Kraus

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer cell lines representing five major molecular subtypes of breast cancer, as well as two immortalized ("normal") human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif P-values, and enrichment of H3K4me1 and H3K27ac. When applied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis.

Original languageEnglish (US)
Pages (from-to)159-170
Number of pages12
JournalGenome Research
Volume28
Issue number2
DOIs
StatePublished - Feb 2018

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Breast Neoplasms
Gene Expression
Triple Negative Breast Neoplasms
Transcription Factors
Cell Line
Gene Regulatory Networks
Transcriptome
Breast
RNA
Messenger RNA
Growth

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Franco, H. L., Nagari, A., Malladi, V. S., Li, W., Xi, Y., Richardson, D., ... Kraus, W. L. (2018). Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Research, 28(2), 159-170. https://doi.org/10.1101/gr.226019.117

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. / Franco, Hector L.; Nagari, Anusha; Malladi, Venkat S.; Li, Wenqian; Xi, Yuanxin; Richardson, Dana; Allton, Kendra L.; Tanaka, Kaori; Li, Jing; Murakami, Shino; Keyomarsi, Khandan; Bedford, Mark T.; Shi, Xiaobing; Li, Wei; Barton, Michelle C.; Dent, Sharon Y.R.; Kraus, W. Lee.

In: Genome Research, Vol. 28, No. 2, 02.2018, p. 159-170.

Research output: Contribution to journalArticle

Franco, HL, Nagari, A, Malladi, VS, Li, W, Xi, Y, Richardson, D, Allton, KL, Tanaka, K, Li, J, Murakami, S, Keyomarsi, K, Bedford, MT, Shi, X, Li, W, Barton, MC, Dent, SYR & Kraus, WL 2018, 'Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis', Genome Research, vol. 28, no. 2, pp. 159-170. https://doi.org/10.1101/gr.226019.117
Franco, Hector L. ; Nagari, Anusha ; Malladi, Venkat S. ; Li, Wenqian ; Xi, Yuanxin ; Richardson, Dana ; Allton, Kendra L. ; Tanaka, Kaori ; Li, Jing ; Murakami, Shino ; Keyomarsi, Khandan ; Bedford, Mark T. ; Shi, Xiaobing ; Li, Wei ; Barton, Michelle C. ; Dent, Sharon Y.R. ; Kraus, W. Lee. / Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. In: Genome Research. 2018 ; Vol. 28, No. 2. pp. 159-170.
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