Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi, Michelle C. Barton, W. Lee Kraus, Wei Li, Sharon Y.R. Dent

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy. Results: To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells. Discussion: Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway. Conclusions: Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment.

Original languageEnglish (US)
Article number150
JournalBMC Genomics
Volume19
Issue number1
DOIs
StatePublished - Feb 20 2018

Fingerprint

Histone Code
Epigenomics
Chromatin
Breast Neoplasms
Cell Line
Triple Negative Breast Neoplasms
Epithelial-Mesenchymal Transition
Neoplasm Genes
Androgen Receptors
Transcriptome
Vitamin D
Breast
Biomarkers
Epithelial Cells
Cell Proliferation
RNA
Gene Expression
Neoplasms
Therapeutics

Keywords

  • Breast cancer subtypes
  • Chromatin states
  • Epigenetics
  • Histone modifications

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Xi, Y., Shi, J., Li, W., Tanaka, K., Allton, K. L., Richardson, D., ... Dent, S. Y. R. (2018). Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. BMC Genomics, 19(1), [150]. https://doi.org/10.1186/s12864-018-4533-0

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. / Xi, Yuanxin; Shi, Jiejun; Li, Wenqian; Tanaka, Kaori; Allton, Kendra L.; Richardson, Dana; Li, Jing; Franco, Hector L.; Nagari, Anusha; Malladi, Venkat S.; Coletta, Luis Della; Simper, Melissa S.; Keyomarsi, Khandan; Shen, Jianjun; Bedford, Mark T.; Shi, Xiaobing; Barton, Michelle C.; Lee Kraus, W.; Li, Wei; Dent, Sharon Y.R.

In: BMC Genomics, Vol. 19, No. 1, 150, 20.02.2018.

Research output: Contribution to journalArticle

Xi, Y, Shi, J, Li, W, Tanaka, K, Allton, KL, Richardson, D, Li, J, Franco, HL, Nagari, A, Malladi, VS, Coletta, LD, Simper, MS, Keyomarsi, K, Shen, J, Bedford, MT, Shi, X, Barton, MC, Lee Kraus, W, Li, W & Dent, SYR 2018, 'Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes', BMC Genomics, vol. 19, no. 1, 150. https://doi.org/10.1186/s12864-018-4533-0
Xi, Yuanxin ; Shi, Jiejun ; Li, Wenqian ; Tanaka, Kaori ; Allton, Kendra L. ; Richardson, Dana ; Li, Jing ; Franco, Hector L. ; Nagari, Anusha ; Malladi, Venkat S. ; Coletta, Luis Della ; Simper, Melissa S. ; Keyomarsi, Khandan ; Shen, Jianjun ; Bedford, Mark T. ; Shi, Xiaobing ; Barton, Michelle C. ; Lee Kraus, W. ; Li, Wei ; Dent, Sharon Y.R. / Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes. In: BMC Genomics. 2018 ; Vol. 19, No. 1.
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