Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-seq data

Kathryn J. Huber-Keener, Xiuping Liu, Zhong Wang, Yaqun Wang, Willard Freeman, Song Wu, Maricarmen D. Planas-Silva, Xingcong Ren, Yan Cheng, Yi Zhang, Kent Vrana, Chang Gong Liu, Jin-Ming Yang, Rongling Wu

Research output: Contribution to journalArticle

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Abstract

Resistance to tamoxifen (Tam), a widely used antagonist of the estrogen receptor (ER), is a common obstacle to successful breast cancer treatment. While adjuvant therapy with Tam has been shown to significantly decrease the rate of disease recurrence and mortality, recurrent disease occurs in one third of patients treated with Tam within 5 years of therapy. A better understanding of gene expression alterations associated with Tam resistance will facilitate circumventing this problem. Using a next generation sequencing approach and a new bioinformatics model, we compared the transcriptomes of Tam-sensitive and Tam-resistant breast cancer cells for identification of genes involved in the development of Tam resistance. We identified differential expression of 1215 mRNA and 513 small RNA transcripts clustered into ERα functions, cell cycle regulation, transcription/translation, and mitochondrial dysfunction. The extent of alterations found at multiple levels of gene regulation highlights the ability of the Tam-resistant cells to modulate global gene expression. Alterations of small nucleolar RNA, oxidative phosphorylation, and proliferation processes in Tam-resistant cells present areas for diagnostic and therapeutic tool development for combating resistance to this anti-estrogen agent.

Original languageEnglish (US)
Article numbere41333
JournalPloS one
Volume7
Issue number7
DOIs
StatePublished - Jul 23 2012

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tamoxifen
Tamoxifen
Gene expression
breast neoplasms
Analytical models
Cells
RNA
Breast Neoplasms
Gene Expression
gene expression
therapeutics
Small Nucleolar RNA
neoplasm cells
Oncology
oxidative phosphorylation
Oxidative Phosphorylation
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Transcription
Therapeutics
Bioinformatics

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Huber-Keener, Kathryn J. ; Liu, Xiuping ; Wang, Zhong ; Wang, Yaqun ; Freeman, Willard ; Wu, Song ; Planas-Silva, Maricarmen D. ; Ren, Xingcong ; Cheng, Yan ; Zhang, Yi ; Vrana, Kent ; Liu, Chang Gong ; Yang, Jin-Ming ; Wu, Rongling. / Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-seq data. In: PloS one. 2012 ; Vol. 7, No. 7.
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abstract = "Resistance to tamoxifen (Tam), a widely used antagonist of the estrogen receptor (ER), is a common obstacle to successful breast cancer treatment. While adjuvant therapy with Tam has been shown to significantly decrease the rate of disease recurrence and mortality, recurrent disease occurs in one third of patients treated with Tam within 5 years of therapy. A better understanding of gene expression alterations associated with Tam resistance will facilitate circumventing this problem. Using a next generation sequencing approach and a new bioinformatics model, we compared the transcriptomes of Tam-sensitive and Tam-resistant breast cancer cells for identification of genes involved in the development of Tam resistance. We identified differential expression of 1215 mRNA and 513 small RNA transcripts clustered into ERα functions, cell cycle regulation, transcription/translation, and mitochondrial dysfunction. The extent of alterations found at multiple levels of gene regulation highlights the ability of the Tam-resistant cells to modulate global gene expression. Alterations of small nucleolar RNA, oxidative phosphorylation, and proliferation processes in Tam-resistant cells present areas for diagnostic and therapeutic tool development for combating resistance to this anti-estrogen agent.",
author = "Huber-Keener, {Kathryn J.} and Xiuping Liu and Zhong Wang and Yaqun Wang and Willard Freeman and Song Wu and Planas-Silva, {Maricarmen D.} and Xingcong Ren and Yan Cheng and Yi Zhang and Kent Vrana and Liu, {Chang Gong} and Jin-Ming Yang and Rongling Wu",
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Huber-Keener, KJ, Liu, X, Wang, Z, Wang, Y, Freeman, W, Wu, S, Planas-Silva, MD, Ren, X, Cheng, Y, Zhang, Y, Vrana, K, Liu, CG, Yang, J-M & Wu, R 2012, 'Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-seq data', PloS one, vol. 7, no. 7, e41333. https://doi.org/10.1371/journal.pone.0041333

Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-seq data. / Huber-Keener, Kathryn J.; Liu, Xiuping; Wang, Zhong; Wang, Yaqun; Freeman, Willard; Wu, Song; Planas-Silva, Maricarmen D.; Ren, Xingcong; Cheng, Yan; Zhang, Yi; Vrana, Kent; Liu, Chang Gong; Yang, Jin-Ming; Wu, Rongling.

In: PloS one, Vol. 7, No. 7, e41333, 23.07.2012.

Research output: Contribution to journalArticle

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T1 - Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-seq data

AU - Huber-Keener, Kathryn J.

AU - Liu, Xiuping

AU - Wang, Zhong

AU - Wang, Yaqun

AU - Freeman, Willard

AU - Wu, Song

AU - Planas-Silva, Maricarmen D.

AU - Ren, Xingcong

AU - Cheng, Yan

AU - Zhang, Yi

AU - Vrana, Kent

AU - Liu, Chang Gong

AU - Yang, Jin-Ming

AU - Wu, Rongling

PY - 2012/7/23

Y1 - 2012/7/23

N2 - Resistance to tamoxifen (Tam), a widely used antagonist of the estrogen receptor (ER), is a common obstacle to successful breast cancer treatment. While adjuvant therapy with Tam has been shown to significantly decrease the rate of disease recurrence and mortality, recurrent disease occurs in one third of patients treated with Tam within 5 years of therapy. A better understanding of gene expression alterations associated with Tam resistance will facilitate circumventing this problem. Using a next generation sequencing approach and a new bioinformatics model, we compared the transcriptomes of Tam-sensitive and Tam-resistant breast cancer cells for identification of genes involved in the development of Tam resistance. We identified differential expression of 1215 mRNA and 513 small RNA transcripts clustered into ERα functions, cell cycle regulation, transcription/translation, and mitochondrial dysfunction. The extent of alterations found at multiple levels of gene regulation highlights the ability of the Tam-resistant cells to modulate global gene expression. Alterations of small nucleolar RNA, oxidative phosphorylation, and proliferation processes in Tam-resistant cells present areas for diagnostic and therapeutic tool development for combating resistance to this anti-estrogen agent.

AB - Resistance to tamoxifen (Tam), a widely used antagonist of the estrogen receptor (ER), is a common obstacle to successful breast cancer treatment. While adjuvant therapy with Tam has been shown to significantly decrease the rate of disease recurrence and mortality, recurrent disease occurs in one third of patients treated with Tam within 5 years of therapy. A better understanding of gene expression alterations associated with Tam resistance will facilitate circumventing this problem. Using a next generation sequencing approach and a new bioinformatics model, we compared the transcriptomes of Tam-sensitive and Tam-resistant breast cancer cells for identification of genes involved in the development of Tam resistance. We identified differential expression of 1215 mRNA and 513 small RNA transcripts clustered into ERα functions, cell cycle regulation, transcription/translation, and mitochondrial dysfunction. The extent of alterations found at multiple levels of gene regulation highlights the ability of the Tam-resistant cells to modulate global gene expression. Alterations of small nucleolar RNA, oxidative phosphorylation, and proliferation processes in Tam-resistant cells present areas for diagnostic and therapeutic tool development for combating resistance to this anti-estrogen agent.

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