Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes
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 cance...
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| Format: | Article |
| Language: | English |
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BMC
2018-02-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4533-0 |
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doaj-b6b28abd82404ab384f6ee9983f4d6f1 |
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Article |
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DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
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 |
| spellingShingle |
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 Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes BMC Genomics Breast cancer subtypes Epigenetics Histone modifications Chromatin states |
| author_facet |
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 |
| author_sort |
Yuanxin Xi |
| title |
Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes |
| title_short |
Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes |
| title_full |
Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes |
| title_fullStr |
Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes |
| title_full_unstemmed |
Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes |
| title_sort |
histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes |
| publisher |
BMC |
| series |
BMC Genomics |
| issn |
1471-2164 |
| publishDate |
2018-02-01 |
| description |
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. |
| topic |
Breast cancer subtypes Epigenetics Histone modifications Chromatin states |
| url |
http://link.springer.com/article/10.1186/s12864-018-4533-0 |
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doaj-b6b28abd82404ab384f6ee9983f4d6f12020-11-25T01:00:56ZengBMCBMC Genomics1471-21642018-02-0119111110.1186/s12864-018-4533-0Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypesYuanxin Xi0Jiejun Shi1Wenqian Li2Kaori Tanaka3Kendra L. Allton4Dana Richardson5Jing Li6Hector L. Franco7Anusha Nagari8Venkat S. Malladi9Luis Della Coletta10Melissa S. Simper11Khandan Keyomarsi12Jianjun Shen13Mark T. Bedford14Xiaobing Shi15Michelle C. Barton16W. Lee Kraus17Wei Li18Sharon Y. R. Dent19Department of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of MedicineDepartment of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of MedicineThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterThe Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterLaboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterLaboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterLaboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterThe Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterLaboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDepartment of Molecular and Cellular Biology and Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of MedicineThe Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer CenterAbstract 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.http://link.springer.com/article/10.1186/s12864-018-4533-0Breast cancer subtypesEpigeneticsHistone modificationsChromatin states |