High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation

Chromatin immunoprecipitation (ChIP) is an assay for interrogating protein-DNA interactions that is increasingly being used for drug target discovery and screening applications. Currently the complexity of the protocol and the amount of hands-on time required for this assay limits its use to low throughput applications; furthermore, variability in antibody quality poses an additional obstacle in scaling up ChIP for large scale screening purposes. To address these challenges, we report HTChIP, an automated microfluidic-based platform for performing high-throughput ChIP screening measurements of 16 different targets simultaneously, with potential for further scale-up. From chromatin to analyzable PCR results only takes one day using HTChIP, as compared to several days up to one week for conventional protocols. HTChIP can also be used to test multiple antibodies and select the best performer for downstream ChIP applications, saving time and reagent costs of unsuccessful ChIP assays as a result of poor antibody quality. We performed a series of characterization assays to demonstrate that HTChIP can rapidly and accurately evaluate the epigenetic states of a cell, and that it is sensitive enough to detect the changes in the epigenetic state induced by a cytokine stimulant over a fine temporal resolution. With these results, we believe that HTChIP can introduce large improvements in routine ChIP, antibody screening, and drug screening efficiency, and further facilitate the use of ChIP as a valuable tool for research and discovery.     

An iridium(iii)-based irreversible protein–protein interaction inhibitor of BRD4 as a potent anticancer agent

Bromodomain-containing protein 4 (BRD4) has recently emerged as an attractive epigenetic target for anticancer therapy. In this study, an iridium(iii) complex is reported as the first metal-based, irreversible inhibitor of BRD4. Complex 1a is able to antagonize the BRD4-acetylated histone protein–protein interaction (PPI) in vitro, and to bind BRD4 and down-regulate c-myc oncogenic expression in cellulo. Chromatin immunoprecipitation (ChIP) analysis revealed that 1a could modulate the interaction between BRD4 and chromatin in melanoma cells, particular at the MYC promoter. Finally, the complex showed potent activity against melanoma xenografts in an in vivo mouse model. To our knowledge, this is the first report of a Group 9 metal complex inhibiting the PPI of a member of the bromodomain and extraterminal domain (BET) family. We envision that complex 1a may serve as a useful scaffold for the development of more potent epigenetic agents against cancers such as melanoma.     

组蛋白翻译后修饰无标定量方法可靠性的比较

组蛋白翻译后修饰是一种表观遗传学修饰,参与调控细胞的新陈代谢等重要生理过程。蛋白质组学发展迅速,使监控组蛋白翻译后修饰的动态变化成为可能。目前主要有3种无标定量方法（谱图计数法、峰面积积分法和信号强度法）,但何种定量方法更可靠尚未见系统性的详细报道。在稳定同位素标记细胞培养技术（SILAC）基础上,对去乙酰化酶抑制剂（SAHA）调控细胞乙酰化修饰水平的定量数据进行对比,比较3种无标定量方法对组蛋白翻译后修饰进行的定量分析,利用定量结果的标准差（SD）评估定量的可靠性,最终发现基于峰面积积分法定量的结果可靠性最高。该研究对难以进行同位素标记实验的样本分析,尤其对临床样本、大样本的组蛋白修饰谱分析具有重要参考意义。     

质谱技术鉴定细胞中组蛋白翻译后修饰的研究进展*

组蛋白是真核细胞中构成染色质内核小体的主要元件,其翻译后修饰蕴藏着组蛋白密码,是表观遗传学的重要内容,影响染色质的结构和功能,进而调控基因表达。组蛋白翻译后修饰形式的鉴定是揭示组蛋白密码的关键,目前质谱技术已经成为分析组蛋白及其翻译后修饰的重要工具。本文综述了组蛋白翻译后修饰鉴定方法的新进展,介绍了基于质谱技术“bottom up”和“top down”的组蛋白分析策略,及CID、ECD和ETD等鉴定组蛋白修饰位点的质谱碎片裂解技术,并结合当前研究进展,评述了质谱技术在组蛋白翻译后修饰谱的鉴定、组蛋白各种变体的测定、以及在生理过程中组蛋白修饰丰度动态变化的定量分析等方面应用的新进展。     

Targeted Histone Peptides: Insights into the Spatial Regulation of the Methyltransferase PRC2 by using a Surrogate of Heterotypic Chromatin

Eukaryotic genomes are dynamically regulated through a host of epigenetic stimuli. The substrate for these epigenetic transactions, chromatin, is a polymer of nucleosome building blocks. In native chromatin, each nucleosome can differ from its neighbors as a result of covalent modifications to both the DNA and the histone packaging proteins. The heterotypic nature of chromatin presents a formidable obstacle to biochemical studies seeking to understand the role of context on epigenetic regulation. A chemical approach to the production of heterotypic chromatin that can be used in such studies is introduced. This method involves the attachment of a user‐defined modified histone peptide to a designated nucleosome within the polymer by using a peptide nucleic acid (PNA) targeting compound. This strategy was applied to dissect the effect of chromatin context on the activity of the histone methyltransferase PRC2. The results show that PRC2 can be stimulated to produce histone H3 methylation from a defined nucleation site.     

Molecular Mechanisms of Anticancer Activity of N-Glycosides of Indolocarbazoles LCS-1208 and LCS-1269

Novel indolocarbazole derivatives named LCS were synthesized by our research group. Two of them were selected as the most active anticancer agents in vivo. We studied the mechanisms of anticancer activity in accordance with the previously described effects of indolocarbazoles. Cytotoxicity was estimated by MTT assay. We analyzed LCS-DNA interactions by circular dichroism in cholesteric liquid crystals and fluorescent indicator displacement assay. The effect on the activity of topoisomerases I and II was studied by DNA relaxation assay. Expression of interferon signaling target genes was estimated by RT-PCR. Chromatin remodeling was analyzed–the effect on histone H1 localization and reactivation of epigenetically silenced genes. LCS-induced change in the expression of a wide gene set was counted by means of PCR array. Our study revealed the cytotoxic activity of the compounds against 11 cancer cell lines and it was higher than in immortalized cells. Both compounds bind DNA; binding constants were estimated—LCS-1208 demonstrated higher affinity than LCS-1269; it was shown that LCS-1208 intercalates into DNA that is typical for rebeccamycin derivatives. LCS-1208 also inhibits topoisomerases I and IIα. Being a strong intercalator and topoisomerase inhibitor, LCS-1208 upregulates the expression of interferon-induced genes. In view of LCSs binding to DNA we analyzed their influence on chromatin stability and revealed that LCS-1269 displaces histone H1. Our analysis of chromatin remodeling also included a wide set of epigenetic experiments in which LCS-1269 demonstrated complex epigenetic activity. Finally, we revealed that the antitumor effect of the compounds is based not only on binding to DNA and chromatin remodeling but also on alternative mechanisms. Both compounds induce expression changes in genes involved in neoplastic transformation and target genes of the signaling pathways in cancer cells. Despite of being structurally similar, each compound has unique biological activities. The effects of LCS-1208 are associated with intercalation. The mechanisms of LCS-1269 include influence on higher levels such as chromatin remodeling and epigenetic effects.     

In-gel NHS-propionate derivatization for histone post-translational modifications analysis in Arabidopsis thaliana

Post-translational modifications (PTMs) on histone are highly correlated with genetic and epigenetic regulation of gene expression from chromatin. Mass spectrometry (MS) has developed to be an optimal tool for the identification and quantification of histone PTMs. Derivatization of histones with chemicals such as propionic anhydride, N-hydroxysuccinimide ester (NHS-propionate) has been widely used in histone PTMs analysis in bottom-up MS strategy, which requires high purity for histone samples. However, biological samples are not always prepared with high purity, containing detergents or other interferences in most cases. As an alternative approach, an adaptation of in gel derivatization method, termed In-gel NHS, is utilized for a broader application in histone PTMs analysis and it is shown to be a more time-saving preparation method.     

Live cell imaging analysis of the epigenetic regulation of the human endothelial cell migration at single-cell resolution

Epigenetic regulation plays an important role in cell migration. Although many methods have been developed to measure the motility of mammalian cells, accurate quantitative assessments of the migration speed of individual cells remain a major challenge. It is difficult for conventional scratch assays to differentiate proliferation from migration during the so-called wound-healing processes because of the long experimental time required. In addition, it is also challenging to create identical conditions for evaluating cell migration by conventional methods. We developed a microfluidic device with precisely created blanks allowing for robust and reproducible cell migration inside accurately-controlled microenvironments to study the regulatory effect of the epigenetic regulator histone deacetylase 7 (HDAC7) on cell migration. Through analyzing time-lapse imaging of the cells migrating into individual blank regions, we can measure the migration speed parameter for human primary cells within a few hours, eliminating the confounding effect of cell proliferation. We also developed an automatic image analysis and a numeric model-based data fitting to set up an integrated cell migration analysis system at single-cell resolution. Using this system, we measured the motility of primary human umbilical vein endothelial cells (HUVECs) and the migration speed reduction due to the silencing of HDAC7 and various other genes. We showed that the migration behaviour of these human primary cells are clearly regulated by epigenetic mechanisms, demonstrating the great potential of this accurate and robust assay in the fields of quantitatively migration studies and high-throughput screening.     

石蜡包埋组织中组蛋白的提取分离和翻译后修饰的定量分析

组蛋白翻译后修饰(HPTMs)参与基因转录调控,其异常与肿瘤等重大疾病的发生发展密切相关。石蜡包埋组织是当前疾病研究的重要样本资源,对肿瘤机制和标志物研究具有重要意义。目前基于质谱的蛋白质组学技术已成为HPTMs分析的有力工具,而针对福尔马林固定石蜡包埋(FFPE)组织样品的HPTMs分析还十分有限。该研究发展了一种基于高效液相色谱-串联质谱的FFPE组织样本HPTMs分离分析新方法。通过研究并优化组蛋白的提取策略,建立了FFPE组织样本脱蜡水化处理、蛋白质提取与聚丙烯酰胺凝胶电泳分离相结合的组蛋白提取和分离方法。通过研究FFPE切片数量、组蛋白化学衍生化方法等对组蛋白鉴定的影响,确定了组蛋白处理的具体步骤。通过HPLC分离结合非依赖性采集模式的质谱分析,鉴定了组蛋白修饰的类型、位点和丰度。最后,将优化的实验方法应用于FFPE临床样本的HPTMs分析,鉴定了2例人乳腺浸润性癌和癌旁正常组织的HPTMs图谱,均获得了100种以上的不同组蛋白修饰形式的多肽。定量分析了他们的差异性水平,通过主成分降维分析,发现浸润性癌和癌旁正常组织之间组蛋白修饰丰度存在明显的差异,且差异性具有一定的规律,特别是涉及转录调控的组蛋白修饰与乳腺癌的预后和治疗靶点具有相关性,进而探讨了乳腺癌中异常HPTMs的生物学意义。该研究对临床石蜡样本中组蛋白修饰的分离分析以及肿瘤表观遗传标志物的检测进行了有益的探索。     

Epigenetic alterations in ultraviolet radiation-induced skin carcinogenesis: interaction of bioactive dietary components on epigenetic targets

The importance of epigenetic alterations in the development of various diseases including the cancers has been realized. As epigenetic changes are reversible heritable changes, these can be utilized as an effective strategy for the prevention of cancers. DNA methylation is the most characterized epigenetic mechanism that can be inherited without changing the DNA sequence. Although limited available data suggest that silencing of tumor suppressor genes in ultraviolet (UV) radiation-exposed epidermis leads to photocarcinogenesis and is associated with a network of epigenetic modifications including alterations in DNA methylation, DNA methyltransferases and histone acetylations. Various bioactive dietary components have been shown to protect skin from UV radiation-induced skin tumors in animal models. The role of bioactive dietary components, such as, (-)-epicatechins from green tea and proanthocyanidins from grape seeds has been assessed in chemoprevention of UV-induced skin carcinogenesis and underlying epigenetic mechanism in vitro and in vivo animal models. These bioactive components have the ability to block UV-induced DNA hypermethylation and histone modifications in the skin required for the silencing of tumor suppressor genes (e.g. Cip1/p21, p16(INK4a) ). This information is of importance for understanding the role of epigenetic modulation in UV-induced skin tumor and the chemopreventive mechanism of bioactive dietary components.     

Recoding the Cancer Epigenome by Intervening in Metabolism and Iron Homeostasis with Mitochondria-Targeted Rhenium(I) Complexes

The development and malignancy of cancer cells are closely related to the changes of the epigenome. In this work, a mitochondria-targeted rhenium(I) complex ( DFX-Re3 ), integrating the clinical iron chelating agent deferasirox ( DFX ), has been designed. By relocating iron to the mitochondria and changing the key metabolic species related to epigenetic modifications, DFX-Re3 can elevate the methylation levels of histone, DNA, and RNA. As a consequence, DFX-Re3 affects the events related to apoptosis, RNA polymerases, and T-cell receptor signaling pathways. Finally, it is shown that DFX-Re3 induces immunogenic apoptotic cell death and exhibits potent antitumor activity in vivo. This study provides a new approach for the design of novel epigenetic drugs that can recode the cancer epigenome by intervening in mitochondrial metabolism and iron homeostasis.     

Phytoestrogens Inhibiting Androgen Receptor Signal and Prostate Cancer Cell Proliferation

The androgen receptor(AR) signaling activated by dihydrotestosterone(DHT) plays critical roles in prostate cancer development and progression. Phytoestrogens, which are diphenolic compounds with estrogen and anti-estrogen effects, can bind to estrogen receptors. However, their function on AR signaling has not been fully elucidated. In this study, dual-luciferase reporter assay, immunobloting, docking system test, MTT assay, immunofluorescence and chromatin immunoprecipitation(ChIP) assays were employed to examine the potential effects of three phytoestrogens(genistein, daidzein, flavone) on DHT-activated prostate specific antigen(PSA) activation, cell proliferation and AR transactivation in lymph node carcinoma of prostate(LNCaP) cells. Phytoestrogens were detected to down-regulate DHT-activated AR-mediated PSA promoter transactivation by dual-luciferase reporter system. Furthermore, three phytoestrogens, especially genistein, were demonstrated to significantly decrease AR-activated PSA protein expression by Western blotting analysis. MTT experiment proves that phytoestrogens, especially genistein, remarkably inhibits the DHT-induced cell proliferation in LNCaP cells. To provide reasonable explanations for experimental phenomena mentioned above, we did docking system test and detected phytoestrogens to share the same AR-binding site with DHT. To further prove the competition between phytoestrogen and DHT on AR binding, we examined the effects of phytoestrogens on DHT-activated AR nuclear translocation and immunofluorescence analysis which confirms that phytoestrogens, especially genistein, inhibit DHT-activated androgen receptor nuclear translocation. Results from ChIP show that phytoestrogens down-regulate DHT-induces AR binding to the androgen response elements(AREs, including AREI, AREII, and AREIII) in PSA promoter. Genistein remarkably down-regulates AR, binding to the AREI located in -250― -39 bp and AREIII in -4170― -3978 bp in the presence of DHT. In general, three phytoestrogens were identified to inhibit DHT-AR binding by competitively binding to AR and inhibit AR-mediated transactivation. And genistein shows the strongest effects among three phytoestrogens. Our findings confirm that phytoestrogens are AR antagonist in the regulation of AR-related PSA activation and cell proliferation, which provides valuable insights into the treatment of prostate cancer.     

Antibody-free reading of the histone code using a simple chemical sensor array

The histone code refers to the complex network of histone post-translational modifications that control gene expression and are of high interest as drivers of a large number of human diseases. We report here on a mix-and-match toolkit of readily available dyes and calixarene host molecules that can be combined to form dye-displacement sensors that respond to a wide variety of cationic peptides. Using the data from only two or three such simple supramolecular sensors as a chemical sensor array produces fingerprints of data that discriminate robustly among many kinds of histone code elements. "Reads" that are accomplished include the discrimination of unmethylated, mono-, di-, and trimethylated lysines on a single histone tail sequence, identification of different modifications and combinations of modifications on a single histone tail sequence, identification of a single modification type in several different sequence contexts, and identification of isomeric dimethylarginine modifications. Reads that are sometimes troublesome for antibodies are achieved. We also report on the ability of the sensor array to report simultaneously on the concentrations and identities of histone modifications. This sensor array discriminates between post-translationally modified analytes without being limited to partners that contain a single, programmed binding interaction.     

Detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA via host–guest interactions inside α-hemolysin nanopores

Cytosine methylation and hydroxymethylation are both important epigenetic modifications of DNA in mammalian cells. Therefore, profiling DNA (hydroxy)methylation across the genome is vital for understanding their roles in gene regulation. Here, we report a nanopore-based approach for quick and reliable detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA at the single-molecule level. The single-stranded DNA containing 5-methylcytosine or 5-hydroxymethylcytosine was first selectively modified on the epigenetic base to attach a host–guest complex. Threading of the modified DNA molecules through α-hemolysin nanopores causes unbinding of the host–guest complex and generates highly characteristic current signatures. Statistical analysis of the signature events affords quantitative information about 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Our results suggest that other DNA modifications could also be detected with the developed method. Furthermore, we anticipate our nanopore sensing strategy to be generally useful in biochemical analysis and to find applications in the early diagnosis of diseases.