DEEPAligner: Deep encoding of pathways to align epigenetic signatures

Background and objectiveRecently, differential DNA Methylation is known to affect the regulatory mechanism of biological pathways. A pathway encompasses a set of interacting genes or gene products that altogether perform a given biological function. Pathways often encode strong methylation signatures that are capable of distinguishing biologically distinct subtypes. Even though Next Generation Sequencing techniques such as MeDIP-seq and MBD-isolated genome sequencing (MiGS) allow for genome-wide identification of clinical and biological subtypes, there is a pressing need for computational methods to compare epigenetic signatures across pathways.MethodsA novel alignment method, called DEEPAligner (Deep Encoded Epigenetic Pathway Aligner), is proposed in this paper that finds functionally consistent and topologically sound alignments of epigenetic signatures from pathway networks. A deep embedding framework is used to obtain epigenetic signatures from pathways which are then aligned for functional consistency and local topological similarity.ResultsExperiments on four benchmark cancer datasets reveal epigenetic signatures that are conserved in cancer-specific and across-cancer subtypes.ConclusionThe proposed deep embedding framework obtains highly coherent signatures that are aligned for biological as well as structural orthology. Comparison with state-of-the-art network alignment methods clearly suggest that the proposed method obtains topologically and functionally more consistent alignments.Availabilityhttp://bdbl.nitc.ac.in/DEEPAligner     

Mechanistic study on DNA mutation of the cytosine methylation reaction at C5 position

DNA methylation is a crucial epigenetic mark connected to conventionally changing the DNA bases, typically by adding methyl groups into DNA bases. Methylation of cytosine at the C5 position (5-methylcytosine) occurs mostly in the context of cytosine-phosphate-guanine dinucleotides, the methylation of which has important impacts on gene regulation and expression. However, the mechanistic details of this reaction are still debatable concerning the concertedness of the key reaction steps and the roles played by the base that abstracts the proton in the β-elimination and water molecules at the active site. To gain a deeper insight into the formation of 5-mehtylcytosine, an extensive density functional theory (DFT) study was performed with the B3LYP functional in conjunction with different basis sets. Our study has clearly established the mechanistic details of this methylation approach, based on which the roles of conserved active site residues, such as glutamic acid and waters, are well understood. Our results show that the reaction of 5-methylcytosine follows a concerted mechanism in which water molecules are critically involved. Moreover, arginine and alanine give more significant catalytic effects than glutamic acid on the 5-methylcytosine process. Considering the effect of Alanine, Arginine, and one water bridging molecule, the activation energy is 31 kJ mol^?1 calculated at B3LYP/6-31G(d) level of theory.     

Histone deacetylase inhibitor induced the production of three novel prenylated tryptophan analogs in the entomopathogenic fungus, Torrubiella luteorostrata

Suberoyl bis-hydroxamic acid (SBHA), a histone deacetylase (HDAC) inhibitor, led to significant changes in the secondary metabolism of an entomopathogenic fungus, Torrubiella luteorostrata, and induced the production of three new prenylated tryptophan analogs, luteorides A-C (1-3). The structures are characterized by the presence of an (E)-oxime group, which is an unusual functional group in natural products, and a 3-methylbuta-1,3-dienyl unit as a common substituent. The method of culturing entomopathogenic fungi in the presence of HDAC inhibitors, such as SBHA, is convenient and attractive for obtaining novel secondary metabolites.     

In silico study of cancer stage-specific DNA methylation pattern in White breast cancer patients based on TCGA dataset

BackgroundBreast cancer is one of the most common types of cancer among women. As current breast cancer treatments are still ineffective, we assess the methylation pattern of White breast cancer patients across cancer stage based on The Cancer Genome Atlas (TCGA) dataset. Significant hypermethylation and hypomethylation can regulate the gene expression, thus becoming potential biomarkers in breast cancer tumorigenesis.MethodsDNA methylation data was downloaded using TCGA Assembler 2 based on race-specific metadata of TCGA - Breast Invasive Carcinoma (TCGA-BRCA) project from Genomic Data Commons (GDC) Data Portal. After the data was divided into each cancer stage, duplicated data of each patient was removed using OMICSBind, while differentially-expressed probes were identified using edgeR. The resulting probes were validated based on correlation and regression analysis with the gene expression, ANOVA between cancer stages, ROC curve per stage, as well as databases.ResultsBased on the White dataset, we found 66 significant hypermethylated genes with logFC > 1.8 between Stage I-III. From this number, three epigenetic-regulated, stage-specific genes are proposed to be the detection biomarkers of breast cancer due to significant aberrant gene expression and/or low mutation ratio among breast cancer patients: ABCC9 (Stage III), SHISA3 (Stage II), and POU4F1 (Stage I-II).ConclusionsOur study shows that ABCC9, SHISA3, and POU4F1 are potential stage-specific detection biomarkers of breast cancer for White individuals, whereas their roles in other races need to be studied further.     

Procaine Inhibiting Human Bladder Cancer Cell Proliferation by Inducing Apoptosis and Demethylating APAF1 CpG Island Hypermethylated

Studies have shown that aberrant DNA methylation of apoptotic protease activating factor-1(APAF1) is an important epigenetic mechanism of gene regulation in the progression of bladder cancer. In this article, we have proved that procaine, an inhibitor of DNA methyltransferases, could inhibit the proliferation of T24 and 5637 human bladder cancer cells by inducing their apoptosis. The mechanism studies reveal that procaine could induce demethylation of APAF1 gene in T24 or 5637 cells, subsequently activating caspase-3/9. It was also shown that the serum soluble fas ligand(sFasL) was activated, and the expression of matrix metallopeptidase 9(MMP-9) was down-regulated. Procaine seems to induce cell death by different pathways, and it might be used as a potential agent for bladder cancer treatment.     

金属锰暴露致神经毒性的多组学研究进展

锰是环境重金属污染物之一,长期暴露于金属锰或其无机化合物主要引发锰中毒或亚临床神经功能缺陷。锰暴露诱导的神经毒性对遗传易感性、基因表达调控、代谢稳态的影响机制复杂,涉及多靶点,然而常规机制研究往往只能局限于单一通路。鉴于工作场所和环境中重金属锰的分布日益广泛,需要更明确地界定锰的神经毒性作用网络,实现多靶点预防和治疗。多组学技术及其相关分析可在不同的功能水平上对疾病发生发展进程中的差异化进行描述。综述了基因组学、表观遗传学、转录组学、代谢组学在金属锰暴露致神经毒性中的研究结果,探讨潜在的代表性生物标志物,支持多组学方法的整合应用,构建锰的神经毒性作用网络,并对未来研究方向提出展望。     

BTG1蛋白及其上下游信号通路对X射线和碳离子辐射的应激响应

BTG1是重要的抗细胞增殖蛋白,在细胞对外界胁迫如电离辐射等的应激响应过程中发挥重要功能。到目前为止,电离辐射诱导BTG1蛋白表达水平的长期变化情况、其对细胞基因组稳定性的影响及上下游相关的信号通路仍未完全阐明。通过荧光定量PCR技术发现BTG1对X射线和碳离子的应激呈现出先迅速升高再缓慢下降的过程。此外,微核实验表明,通过转染基因的质粒过表达载体或siRNA的方法外源性增加或抑制786-O细胞内BTG1的表达水平均能够显著影响碳离子辐照诱导的基因组不稳定性。深入研究发现电离辐射诱导的NF-кB的表达和活化可能通过引起SKA2基因的表达而间接地调控BTG1的表达,而BTG1则可能激活PRMT1的活性而引起基因组表观遗传学的改变,进而影响细胞的基因组稳定性、细胞周期调控以及凋亡等进程。BTG1, an important anti-proliferative gene, plays critical roles in cellular response to stresses, including ionizing radiation (IR). However, the long term expression of BTG1 induced by IR and its upstream/downstream signal pathways have not been elucidated clearly until now. The qRT-PCR results showed that the expression level of BTG1 in 786-O cells was rapidly elevated by IR in a short time, and then decreased slowly. In addition, upregulation or downregulation by transfection of BTG1 overexpression vector or siRNA could significantly affect the carbon ion radiation-induced genomic instability. Further study indicated that IRinduced BTG1 expression may be regulated by NF-B-mediated activation of SKA2 indirectly; On the other hand, expression of BTG1 may cause epigenetic changes by activating PRMT1, and subsequently influence the genomic stability, cell cycle regulation and apoptosis.