Optimized ChIP-seq method facilitates transcription factor profiling in human tumors
Optimized ChIP-seq method facilitates transcription factor profiling in human tumors
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DOI：
10.26508/lsa.201800115
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发表时间：
2019-02-01
影响因子：
4.4
通讯作者：
Zwart, Wilbert
中科院分区：
文献类型：
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作者：
Singh, Abhishek A.;Schuurman, Karianne;Zwart, Wilbert
由于技术限制和起始材料数量少，临床标本中转录因子的染色质免疫沉淀(ChIP)-seq分析具有挑战性，通常导致低富集和低信噪比。在这里，我们提出了一种优化的方案，用于人类组织中转录因子ChIP-seq分析，对所有分析的转录因子产生类似于100%的成功率。作为概念的证明和说明该方法的一般适用性，我们分析了来自乳腺癌、前列腺癌和子宫内膜癌的人体组织。除标准甲醛固定外，还加入了戊二酸二辛酰，大大提高了数据质量。为了说明优化方案的敏感性，我们从单个芯针前列腺癌活检标本中提供了三个独立因素（AR， FOXA1和H3K27ac）的高质量ChIP-seq数据。综上所述，双交联极大地提高了人类肿瘤样本转录因子ChIP-seq的质量，进一步促进和加强了对有限数量组织的转化研究。
Chromatin immunoprecipitation (ChIP)-seq analyses of transcription factors in clinical specimens are challenging due to the technical limitations and low quantities of starting material, often resulting in low enrichments and poor signal-to-noise ratio. Here, we present an optimized protocol for transcription factor ChIP-seq analyses in human tissue, yielding an similar to 100% success rate for all transcription factors analyzed. As proof of concept and to illustrate general applicability of the approach, human tissue from the breast, prostate, and endometrial cancers were analyzed. In addition to standard formaldehyde fixation, disuccinimidyl glutarate was included in the procedure, greatly increasing data quality. To illustrate the sensitivity of the optimized protocol, we provide high-quality ChIP-seq data for three independent factors (AR, FOXA1, and H3K27ac) from a single core needle prostate cancer biopsy specimen. In summary, double-cross-linking strongly improved transcription factor ChIP-seq quality on human tumor samples, further facilitating and enhancing translational research on limited amounts of tissue.