High-throughput profiling of histone post-translational modifications and chromatin modifying proteins by reverse phase protein array

被引：11

作者：

Wang, Xuan ^{[1
]}

Shi, Zhongcheng ^{[1
]}

Lu, Hsin-Yi ^{[1
]}

Kim, Jean J. ^{[1
,2
,3
]}

Bu, Wen ^{[2
,4
]}

Villalobos, Jose A. ^{[5
]}

Perera, Dimuthu N. ^{[1
]}

Jung, Sung Yun ^{[5
]}

Wang, Tao ^{[5
]}

Grimm, Sandra L. ^{[1
,3
]}

Taylor, Bethany C. ^{[5
]}

Rajapakshe, Kimal ^{[1
,2
]}

Park, Hyekyung ^{[1
]}

Wulfkuhle, Julia ^{[6
]}

Young, Nicolas L. ^{[2
,3
,5
]}

Li, Yi ^{[2
,4
]}

Coarfa, Cristian ^{[2
,3
]}

Edwards, Dean P. ^{[2
,3
]}

Huang, Shixia ^{[1
,2
,3
,7
]}

机构：

[1] Baylor Coll Med, Adv Technol Cores, Houston, TX 77030 USA

[2] Baylor Coll Med, Dept Mol & Cellular Biol, Houston, TX USA

[3] Baylor Coll Med, Dan L Duncan Comprehens Canc Ctr, Houston, TX USA

[4] Baylor Coll Med, Lester & Sue Smith Breast Ctr, Houston, TX USA

[5] Baylor Coll Med, Verna & Marrs McLean Dept Biochem & Mol Biol, Houston, TX USA

[6] George Mason Univ, Ctr Appl Prote & Mol Med, Fairfax, VA USA

[7] Baylor Coll Med, Dept Educ, Innovat & Technol, Houston, TX USA

来源：

JOURNAL OF PROTEOMICS | 2022年 / 262卷

关键词：

Epigenetics; RPPA; High-throughput; Post-translational modifications; Induced pluripotent stem cells; Breast cancer; PLURIPOTENT STEM-CELLS; TRANSGENIC MICE; METHYLATION; EPIGENETICS; DISCOVERY; ACETYLATION; INDUCTION; MUTATION; CANCERS; TARGET;

D O I：

10.1016/j.jprot.2022.104596

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Epigenetic variation plays a significant role in normal development and human diseases including cancer, in part through post-translational modifications (PTMs) of histones. Identification and profiling of changes in histone PTMs, and in proteins regulating PTMs, are crucial to understanding diseases, and for discovery of epigenetic therapeutic agents. In this study, we have adapted and validated an antibody-based reverse phase protein array (RPPA) platform for profiling 20 histone PTMs and expression of 40 proteins that modify histones and other epigenomic regulators. The specificity of the RPPA assay for histone PTMs was validated with synthetic peptides corresponding to histone PTMs and by detection of histone PTM changes in response to inhibitors of histone modifier proteins in cell cultures. The useful application of the RPPA platform was demonstrated with two models: induction of pluripotent stem cells and a mouse mammary tumor progression model. Described here is a robust platform that includes a rapid microscale method for histone isolation and partially automated workflows for analysis of histone PTMs and histone modifiers that can be performed in a high-throughput manner with hundreds of samples. This RPPA platform has potential for translational applications through the discovery and validation of epigenetic states as therapeutic targets and biomarkers.Significance: Our study has established an antibody-based reverse phase protein array platform for global profiling of a wide range of post-translational modifications of histones and histone modifier proteins. The high throughput platform provides comprehensive analyses of epigenetics for biological research and disease studies and may serve as screening assay for diagnostic purpose or therapy development.

引用

页数：15

共 77 条

[1] The diverse functions of Dot1 and H3K79 methylation [J].

Anh Tram Nguyen ;

Zhang, Yi .

GENES & DEVELOPMENT, 2011, 25 (13) :1345-1358

[2]

Barbarotta L M., 2015, JADPRO, V6, DOI DOI 10.6004/JADPRO.2015.6.1.3

[3]

Boellner Stefanie, 2015, Microarrays (Basel), V4, P98, DOI 10.3390/microarrays4020098

[4] Mammary Precancerous Stem and Non-Stem Cells Evolve into Cancers of Distinct Subtypes [J].

Bu, Wen ;

Liu, Zhenyu ;

Jiang, Weiyu ;

Nagi, Chandandeep ;

Huang, Shixia ;

Edwards, Dean P. ;

Jo, Eunji ;

Mo, Qianxing ;

Creighton, Chad J. ;

Hilsenbeck, Susan G. ;

Leavitt, Andrew D. ;

Lewis, Michael T. ;

Wong, Stephen T. C. ;

Li, Yi .

CANCER RESEARCH, 2019, 79 (01) :61-71

[5] Lentivirus Vectors for Stably Introducing Genes into Mammary Epithelial Cells in Vivo [J].

Bu, Wen ;

Xin, Li ;

Toneff, Michael ;

Li, Lei ;

Li, Yi .

JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA, 2009, 14 (04) :401-404

[6]

Buenrostro Jason D, 2015, Curr Protoc Mol Biol, V109, DOI 10.1002/0471142727.mb2129s109

[7] Integrative analysis of multi-platform reverse-phase protein array data for the pharmacodynamic assessment of response to targeted therapies [J].

Byron, Adam ;

Bernhardt, Stephan ;

Ouine, Berengere ;

Cartier, Aurelie ;

Macleod, Kenneth G. ;

Carragher, Neil O. ;

Sibut, Vonick ;

Korf, Ulrike ;

Serrels, Bryan ;

de Koning, Leanne .

SCIENTIFIC REPORTS, 2020, 10 (01)

[8] The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression [J].

Chan, Kui-Ming ;

Fang, Dong ;

Gan, Haiyun ;

Hashizume, Rintaro ;

Yu, Chuanhe ;

Schroeder, Mark ;

Gupta, Nalin ;

Mueller, Sabine ;

James, C. David ;

Jenkins, Robert ;

Sarkaria, Jann ;

Zhang, Zhiguo .

GENES & DEVELOPMENT, 2013, 27 (09) :985-990

[9] Mammary Stem Cells and Tumor-Initiating Cells Are More Resistant to Apoptosis and Exhibit Increased DNA Repair Activity in Response to DNA Damage [J].

Chang, Chi-Hsuan ;

Zhang, Mei ;

Rajapakshe, Kimal ;

Coarfa, Cristian ;

Edwards, Dean ;

Huang, Shixia ;

Rosen, Jeffrey M. .

STEM CELL REPORTS, 2015, 5 (03) :378-391

[10] H3K9 Histone Methyltransferase G9a Promotes Lung Cancer Invasion and Metastasis by Silencing the Cell Adhesion Molecule Ep-CAM [J].

Chen, Min-Wei ;

Hua, Kuo-Tai ;

Kao, Hsin-Jung ;

Chi, Chia-Chun ;

Wei, Lin-Hung ;

Johansson, Gunnar ;

Shiah, Shine-Gwo ;

Chen, Pai-Sheng ;

Jeng, Yung-Ming ;

Cheng, Tsu-Yao ;

Lai, Tsung-Ching ;

Chang, Jeng-Shou ;

Jan, Yi-Hua ;

Chien, Ming-Hsien ;

Yang, Chih-Jen ;

Huang, Ming-Shyan ;

Hsiao, Michael ;

Kuo, Min-Liang .

CANCER RESEARCH, 2010, 70 (20) :7830-7840

← 1 2 3 4 5 6 7 8 →