Highly Selective Electrochemical Detection of 5-Formyluracil Relying on (2-Benzimidazolyl) Acetonitrile Labeling

The identification of formylpyrimidines in DNA is crucial for a better understanding of epigenetics. Although many techniques have been explored to detect their content, more accurate methods of formylpyrimidine determination are still required due to the relatively lower sensitivity or lack of selectivity in current methods. Herein, an electrochemical method based on the covalent bonding of the azido derivative of (2-benzimidazolyl) acetonitrile (azi-BIAN) and the aldehyde group of 5-formyluracil (5fU) was proposed for the selective detection of 5fU in the presence of 5-formylcytosine (5fC) and apyrimidinic (AP) sites. Target DNA containing 5fU was first treated with azi-BIAN and then incubated with DBCO-PEG4-Biotin to introduce a biotin group by copper-free click chemistry. Next, the sulfhydryl group was attached to the 5' end of above DNA through T4 polynucleotide kinase-catalyzed reaction. Subsequently, the labeled DNA was assembled onto the AuNPs-modified glassy carbon electrode (AuNPs/GCE) through Au-S bonds, and the streptavidin-horseradish peroxidase conjugate (SA-HRP) was further immobilized onto the surface of the above electrode by specific recognition between biotin and streptavidin. Finally, HRP catalyzed hydroquinone oxidation to benzoquinone to enhance the current signal, which was related to the amount of 5fU in nucleic acids. This method demonstrated a good linear relationship with 5fU concentrations ranging from 0.1 to 10 nM. Moreover, the level of 5fU in γ-irradiated nucleic acids was also successfully detected, indicating that the combination of molecule-depended chemical recognition and electrochemical sensing is a promising method for the selective and sensitive detection of 5fU.

Analysis of Multiple Human Tumor Cases Reveals the Carcinogenic Effects of PKP3

Plakophilins (PKPs) act as a key regulator of different signaling programs and control a variety of cellular processes ranging from transcription, protein synthesis, growth, proliferation, and tumor development. The function and possible mechanism of PKP3 in ovarian cancer (OC) remain unknown. It is extremely important to investigate the expression and prognostic values of PKP3, as well as their possible mechanisms, and immune infiltration in OC. Therefore, in this paper we explored the potential oncogenic role of PKP3 in 33 tumors based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. The result outcomes showed that PKP3 is highly expressed in most cancers, and the expression level and prognosis of PKP3 showed little significance in cancer patients. Moreover, oncologists have found that members of the plakophilin family have different degrees of abnormality in ovarian cancer. PKP3 played a key part in carcinogenesis and aggressiveness of OC as well as malignant biological activity and can be used as a biomarker for early diagnosis and prognosis evaluation in OC.

Evaluation of clinical formalin-fixed paraffin-embedded tissue quality for targeted-bisulfite sequencing

Formalin-fixed paraffin-embedded (FFPE) tissues are promising biological resources for genetic research. Recent improvements in DNA extraction from FFPE samples allowed the use of these tissues for multiple sequencing methods. However, fundamental research addressing the application of FFPE-derived DNA for targeted-bisulfite sequencing (TB-seq) is lacking. Here, we evaluated the suitability of FFPE-derived DNA for TB-seq. We conducted TB-seq using FFPE-derived DNA and corresponding fresh frozen (FF) tissues of patients with kidney cancer and compared the quality of DNA, libraries, and TB-seq statistics between the two preservation methods. The approximately 600-bp average fragment size of the FFPE-derived DNA was significantly shorter than that of the FF-derived DNA. The sequencing libraries constructed using FFPE-derived DNA and the mapping ratio were approximately 10 times and 10% lower, respectively, than those constructed using FF-derived DNA. In the mapped data of FFPE-derived DNA, duplicated reads accounted for > 60% of the obtained sequence reads, with lower mean on-target coverage. Therefore, the standard TB-seq protocol is inadequate for obtaining high-quality data for epigenetic analysis from FFPE-derived DNA, and technical improvements are necessary for enabling the use of archived FFPE resources.

Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches

Genomic imprinting results in monoallelic expression of genes in mammals and flowering plants. Understanding the function of imprinted genes improves our knowledge of the regulatory processes in the genome. In this study, we have employed classification and clustering algorithms with attribute weighting to specify the unique attributes of both imprinted (monoallelic) and biallelic expressed genes. We have obtained characteristics of 22 known monoallelically expressed (imprinted) and 8 biallelic expressed genes that have been experimentally validated alongside 208 randomly selected genes in bovine (Bos taurus). Attribute weighting methods and various supervised and unsupervised algorithms in machine learning were applied. Unique characteristics were discovered and used to distinguish mono and biallelic expressed genes from each other in bovine. To obtain the accuracy of classification, 10-fold cross-validation with concerning each combination of attribute weighting (feature selection) and machine learning algorithms, was used. Our approach was able to accurately predict mono and biallelic genes using the genomics and proteomics attributes.

Identifying Cancer Specific Driver Modules Using a Network-Based Method

Detecting driver modules is a key challenge for understanding the mechanisms of carcinogenesis at the pathway level. Identifying cancer specific driver modules is helpful for interpreting the different principles of different cancer types. However, most methods are proposed to identify driver modules in one cancer, but few methods are introduced to detect cancer specific driver modules. We propose a network-based method to detect cancer specific driver modules (CSDM) in a certain cancer type to other cancer types. We construct the specific network of a cancer by combining specific coverage and mutual exclusivity in all cancer types, to catch the specificity of the cancer at the pathway level. To illustrate the performance of the method, we apply CSDM on 12 TCGA cancer types. When we compare CSDM with SpeMDP and HotNet2 with regard to specific coverage and the enrichment of GO terms and KEGG pathways, CSDM is more accurate. We find that the specific driver modules of two different cancers have little overlap, which indicates that the driver modules detected by CSDM are specific. Finally, we also analyze three specific driver modules of BRCA, BLCA, and LAML intersecting with well-known pathways. The source code of CSDM is freely accessible at https://github.com/fengli28/CSDM.git.

DNA methylation of TOMM40-APOE-APOC2 in Alzheimer's disease

The apolipoprotein E (APOE) ε4 allele is the major genetic risk factor for Alzheimer's disease (AD). Multiple regulatory elements, spanning the extended TOMM40-APOE-APOC2 region, regulate gene expression at this locus. Regulatory element DNA methylation changes occur under different environmental conditions, such as disease. Our group and others have described an APOE CpG island as hypomethylated in AD, compared to cognitively normal controls. However, little is known about methylation of the larger TOMM40-APOE-APOC2 region. The hypothesis of this investigation was that regulatory element methylation levels of the larger TOMM40-APOE-APOC2 region are associated with AD. The aim was to determine whether DNA methylation of the TOMM40-APOE-APOC2 region differs in AD compared to cognitively normal controls in post-mortem brain and peripheral blood. DNA was extracted from human brain (n = 12) and peripheral blood (n = 67). A methylation array was used for this analysis. Percent methylation within the TOMM40-APOE-APOC2 region was evaluated for differences according to tissue type, disease state, AD-related biomarkers, and gene expression. Results from this exploratory analysis suggest that regulatory element methylation levels within the larger TOMM40-APOE-APOC2 gene region correlate with AD-related biomarkers and TOMM40 or APOE gene expression in AD.

Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns

Abnormal DNA methylation is an important epigenetic regulator involving tumorigenesis. Deciphering cancer common and specific DNA methylation patterns is essential for us to understand the mechanisms of tumor development. The Cancer Genome Atlas (TCGA) project provides a large number of samples of different cancers that enable a pan-cancer study of DNA methylation possible. Here we investigate cancer common and specific DNA methylation patterns among 5480 DNA methylation profiles of 15 cancer types from TCGA. We first define differentially methylated CpG sites (DMCs) in each cancer and then identify 5450 hyper- and 4433 hypomethylated pan-cancer DMCs (PDMCs). Intriguingly, three adjacent hypermethylated PDMC constitute an enhancer region, which potentially regulates two tumor suppressor genes BVES and PRDM1 negatively. Moreover, we identify six distinct motif clusters, which are enriched in hyper- or hypomethylated PDMCs and are associated with several well-known cancer hallmarks. We also observe that PDMCs relate to distinct transcriptional groups. Additionally, 55 hypermethylated and 7 hypomethylated PDMCs are significantly associated with patient survival. Lastly, we find that cancer-specific DMCs are enriched in known cancer genes and cell-type-specific super-enhancers. In summary, this study provides a comprehensive investigation and reveals meaningful cancer common and specific DNA methylation patterns.

Placental lipoprotein lipase DNA methylation alterations are associated with gestational diabetes and body composition at 5 years of age

Gestational diabetes mellitus (GDM) is associated with obesity in childhood. This suggests that consequences of in utero exposure to maternal hyperglycemia extend beyond the fetal development, possibly through epigenetic programming. The aims of this study were to assess whether placental DNA methylation (DNAm) marks were associated with maternal GDM status and to offspring body composition at 5 years old in a prospective birth cohort. DNAm levels were measured in the fetal side of the placenta in 66 samples (24 from GDM mothers) using bisDNA-pyrosequencing. Anthropometric and body composition (bioimpedance) were measured in children at 5 years of age. Mann-Whitney and Spearman tests were used to assess associations between GDM, placental DNAm levels at the lipoprotein lipase (LPL) locus and children's weight, height, body mass index (BMI), body fat, and lean masses at 5 years of age. Weight, height, and BMI z-scores were computed according to the World Health Organization growth chart. Analyses were adjusted for gestational age at birth, child sex, maternal age, and pre-pregnancy BMI. LPL DNAm levels were positively correlated with birth weight z-scores (r = 0.252, P = 0.04), and with mid-childhood weight z-scores (r = 0.314, P = 0.01) and fat mass (r = 0.275, P = 0.04), and negatively correlated with lean mass (r = -0.306, P = 0.02). We found a negative correlation between LPL DNAm and mRNA levels in placenta (r = -0.459; P < 0.001), which highlights the regulation of transcriptional activity by these epivariations. We demonstrated that alterations in fetal placental DNAm levels at the LPL gene locus are associated with the anthropometric profile in children at 5 years of age. These findings support the concept of fetal metabolic programming through epigenetic changes.

Rapid and specific hypomethylation of enhancers in endothelial cells during adaptation to cell culturing

Epigenetics, including DNA methylation, is one way for a cell to respond to the surrounding environment. Traditionally, DNA methylation has been perceived as a quite stable modification; however, lately, there have been reports of a more dynamic CpG methylation that can be affected by, for example, long-term culturing. We recently reported that methylation in the enhancer of the gene encoding the key fibrinolytic enzyme tissue-type plasminogen activator (t-PA) was rapidly erased during cell culturing. In the present study we used sub-culturing of human umbilical vein endothelial cells (HUVECs) as a model of environmental challenge to examine how fast genome-wide methylation changes can arise. To assess genome-wide DNA methylation, the Infinium HumanMethylation450 BeadChip was used on primary, passage 0, and passage 4 HUVECs. Almost 2% of the analyzed sites changed methylation status to passage 4, predominantly displaying hypomethylation. Sites annotated as enhancers were overrepresented among the differentially methylated sites (DMSs). We further showed that half of the corresponding genes concomitantly altered their expression, most of them increasing in expression. Interestingly, the stroke-related gene HDAC9 increased its expression several hundredfold. This study reveals a rapid hypomethylation of CpG sites in enhancer elements during the early stages of cell culturing. As many methods for methylation analysis are biased toward CpG rich promoter regions, we suggest that such methods may not always be appropriate for the study of methylation dynamics. In addition, we found that significant changes in expression arose in genes with enhancer DMSs. HDAC9 displayed the most prominent increase in expression, indicating, for the first time, that dynamic enhancer methylation may be central in regulating this important stroke-associated gene.