Quantitative proteomic analysis of histone modifications in decitabine sensitive and resistant leukemia cell lines

Chunchao Zhang,Samir Hanash,Guillermo Garcia-Manero,Yue Wei,Jinfeng Suo,Hiroyuki Katayama

doi:10.1186/s12014-016-9115-z

Chunchao Zhang, Samir Hanash + Show 4 more

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https://doi.org/10.1186/s12014-016-9115-z

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Abstract

BackgroundThe refractory nature of many cancers remains the main health challenge over the past century. The epigenetic drug, decitabine (DAC), represents one of the most promising therapeutic agents in cancers particularly in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). However, its ambiguous anti-tumor mechanism and the unpredictable drug-resistant nature in some population compromise its application in cancer therapy. In crosstalk with DNA methylation, histone post-translational modifications (PTMs) are the key players in modulating the downstream epigenetic status of tumor suppressor genes. This study targets the role of decitabine in epigenetic regulation in leukemia therapy and searches responsive predictors and therapeutic targets for pretreatment evaluation and drug development.ResultsA simple, fast, and robust proteomic strategy identified 15 novel PTMs and 60 PTM combinations in two leukemia cell lines (MDS-L and TF-1). Histone modification profiles have been generated and compared between DAC sensitive and resistant groups (n = 3) in response to DAC treatment. Among these histone PTMs, five of which were found differentially upon DAC treatment in drug sensitive and resistant cells: H3.3K36me3, H4K8acK12acK16ac in MDS-L cells; and H3.1K27me1, H3.1K36me1, H3.1K27me1K36me1 in TF-1 cells. They may serve as biomarkers in predicting leukemia and drug responsiveness. In addition, we also explored PTM differences in two cell lines which were developed from early and advanced stages of AML. Three PTMs (H3.1K27me3, H3.1K27me2K36me2 and H3.3K27me2K36me2) are highly abundant in TF-1 cells (advanced AML cell line), suggesting their relevance to leukemogenesis. Our method allowed deep analysis of histone proteins and elucidation of a large number of histone PTMs with high precision and sensitivity.ConclusionDAC-induced DNA hypomethylation has wide impact on chromatin modifications. This study represents first effort to investigate the undefined epigenetic mechanism of decitabine in leukemia therapy. The identification of 15 novel PTMs and the discovery of several marks have relevance to epigenetic directed therapies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12014-016-9115-z) contains supplementary material, which is available to authorized users.

Highlights

The refractory nature of many cancers remains the main health challenge over the past century
Research strategy and method development Owing to the challenges and difficulties in analyzing histone post-translational modifications (PTMs), we have developed a simple, fast, and robust quantitative LC– MS/MS proteomic method
(2) In comparison to label-free quantification, the use of internal standard derived from three SILAC-labeled cell lines reduces sample sizes and gives a better PTM coverage owing to PTM pattern varies from cell line to cell line

Summary

Introduction

The refractory nature of many cancers remains the main health challenge over the past century. The epigenetic drug, decitabine (DAC), represents one of the most promising therapeutic agents in cancers in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). Its ambiguous anti-tumor mecha‐ nism and the unpredictable drug-resistant nature in some population compromise its application in cancer therapy. In crosstalk with DNA methylation, histone post-translational modifications (PTMs) are the key players in modulating the downstream epigenetic status of tumor suppressor genes. This study targets the role of decitabine in epigenetic regulation in leukemia therapy and searches responsive predictors and therapeutic targets for pretreatment evalua‐ tion and drug development. As a crucial epigenetic mark on the genome, DNA methylation modulates many. DNA methylation is generally considered a repressive mark and is often associated with gene silencing [1, 8]. Global DNA hypomethylation as well as DNA hypermethylation in the promoter regions of tumor suppressor genes are common hallmarks of cancer cells [10,11,12]

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