Paternal Exercise Improves the Metabolic Health of Offspring via Epigenetic Modulation of the Germline

Background/Aims: Epigenetic regulation is considered the main molecular mechanism underlying the developmental origin of health and disease’s (DOHAD) hypothesis. Previous studies that have investigated the role of paternal exercise on the metabolic health of the offspring did not control for the amount and intensity of the training or possible effects of adaptation to exercise and produced conflicting results regarding the benefits of parental exercise to the next generation. We employed a precisely regulated exercise regimen to study the transgenerational inheritance of improved metabolic health. Methods: We subjected male mice to a well-controlled exercise -training program to investigate the effects of paternal exercise on glucose tolerance and insulin sensitivity in their adult progeny. To investigate the molecular mechanisms of epigenetic inheritance, we determined chromatin markers in the skeletal muscle of the offspring and the paternal sperm. Results: Offspring of trained male mice exhibited improved glucose homeostasis and insulin sensitivity. Paternal exercise modulated the DNA methylation profile of PI3Kca and the imprinted H19/Igf2 locus at specific differentially methylated regions (DMRs) in the skeletal muscle of the offspring, which affected their gene expression. Remarkably, a similar DNA methylation profile at the PI3Kca, H19, and Igf2 genes was present in the progenitor sperm indicating that exercise-induced epigenetic changes that occurred during germ cell development contributed to transgenerational transmission. Conclusion: Paternal exercise might be considered as a strategy that could promote metabolic health in the offspring as the benefits can be inherited transgenerationally.

Aqueous Extract of Alstonia boonei Bark Reduces Chronic Hyperglycemia and Prevents its Complications through Increase of Hepatic Global Dna Methylation in Diabetic Wistar Rats

Aim: DNA methylation profile is involved in several physiological processes. Its alterations in the liver of diabetic patients characterized by global hypomethylation are associated with the pathophysiology of type 2 diabetes and its complications. The present study has evaluated the effect of the aqueous extract of Alstonia boonei barks on the global methylation of hepatic DNA in association with hyperglycemia and diabetes complications induced by high-fat diet (HFD) feeding and administering of streptozotocin (STZ) which mimics the metabolic abnormalities very similar to those seen in human Type 2 diabetes. Methods: A. boonei barks were harvested, processed, dried, ground and an aqueous extraction was prepared (ratio 1/10 w/v). An in vivo study was conducted in an animal model of high-fat-streptozotocin (HF-STZ) induced diabetes. Rats were divided into five groups of five rats each: a normoglycemic group, an untreated hyperglycemic group, three hyperglycemic groups including two test groups receiving aqueous extract of A. boonei barks (AEAB) by esophageal gavage at the doses of 200 and 400 mg/kg body weight once daily and a reference group receiving metformin at 10 mg/kg body weight. After 28 days of experimentation during which fasting blood glucose levels were taken every 14 days under fasting conditions, the animals were sacrificed. Plasma and liver homogenate samples from the sacrificed rats were used for biochemical assays (markers of oxidative stress such as malondialdehyde level, superoxide dismutase (SOD) and catalase activity, and markers of lipid profile such as total cholesterol, and triglycerides, HDL-c, LDL-c and VLDL-c). The analysis of the global DNA methylation profile was performed by the immunoprecipitation. Pearson's correlation was used to evaluate the relationship between the values. Results: The aqueous extract increased the hepatic DNA methylation by 0.41% and 0.63% at 200 and 400 mg/kg body weight, respectively, compared to metformin (0.47%±0, 05). This effect was significantly associated with the hypoglycemic effect obtained at 400 mg/kg body weight with a decrease in initial blood glucose level of -29.87%. Conclusion: AEAB reduces chronic hyperglycemia and prevents its complications by increasing global hepatic DNA methylation.

Transcriptomic Remodelling of Fetal Endothelial Cells During Establishment of Inflammatory Memory

Inflammatory memory involves the molecular and cellular ‘reprogramming’ of innate immune cells following exogenous stimuli, leading to non-specific protection against subsequent pathogen exposure. This phenomenon has now also been described in non-hematopoietic cells, such as human fetal and adult endothelial cells. In this study we mapped the cell-specific DNA methylation profile and the transcriptomic remodelling during the establishment of inflammatory memory in two distinct fetal endothelial cell types – a progenitor cell (ECFC) and a differentiated cell (HUVEC) population. We show that both cell types have a core transcriptional response to an initial exposure to a viral-like ligand, Poly(I:C), characterised by interferon responsive genes. There was also an ECFC specific response, marked by the transcription factor ELF1, suggesting a non-canonical viral response pathway in progenitor endothelial cells. Next, we show that both ECFCs and HUVECs establish memory in response to an initial viral exposure, resulting in an altered subsequent response to lipopolysaccharide. While the capacity to train or tolerize the induction of specific sets of genes was similar between the two cell types, the progenitor ECFCs show a higher capacity to establish memory. Among tolerized cellular pathways are those involved in endothelial barrier establishment and leukocyte migration, both important for regulating systemic immune-endothelial cell interactions. These findings suggest that the capacity for inflammatory memory may be a common trait across different endothelial cell types but also indicate that the specific downstream targets may vary by developmental stage.

Methylome and transcriptome analyses of soybean response to bean pyralid larvae

Background Bean pyralid is one of the major leaf-feeding insects that affect soybean crops. DNA methylation can control the networks of gene expressions, and it plays an important role in responses to biotic stress. However, at present the genome-wide DNA methylation profile of the soybean resistance to bean pyralid has not been reported so far. Results Using whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analyzed the highly resistant material (Gantai-2-2, HRK) and highly susceptible material (Wan82–178, HSK), under bean pyralid larvae feeding 0 h and 48 h, to clarify the molecular mechanism of the soybean resistance and explore its insect-resistant genes. We identified 2194, 6872, 39,704 and 40,018 differentially methylated regions (DMRs), as well as 497, 1594, 9596 and 9554 differentially methylated genes (DMGs) in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48 comparisons, respectively. Through the analysis of global methylation and transcription, 265 differentially expressed genes (DEGs) were negatively correlated with DMGs, there were 34, 49, 141 and 116 negatively correlated genes in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48, respectively. The MapMan cluster analysis showed that 114 negatively correlated genes were clustered in 24 pathways, such as protein biosynthesis and modification; primary metabolism; secondary metabolism; cell cycle, cell structure and component; RNA biosynthesis and processing, and so on. Moreover, CRK40; CRK62; STK; MAPK9; L-type lectin-domain containing receptor kinase VIII.2; CesA; CSI1; fimbrin-1; KIN-14B; KIN-14 N; KIN-4A; cytochrome P450 81E8; BEE1; ERF; bHLH25; bHLH79; GATA26, were likely regulatory genes involved in the soybean responses to bean pyralid larvae. Finally, 5 DMRs were further validated that the genome-wide DNA data were reliable through PS-PCR and 5 DEGs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. The results showed an excellent agreement with deep sequencing. Conclusions Genome-wide DNA methylation profile of soybean response to bean pyralid was obtained for the first time. Several specific DMGs which participated in protein kinase, cell and organelle, flavonoid biosynthesis and transcription factor were further identified to be likely associated with soybean response to bean pyralid. Our data will provide better understanding of DNA methylation alteration and their potential role in soybean insect resistance.

Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile

Background: More than 150 types of brain tumors have been documented. Accurate diagnosis is important for making appropriate therapeutic decisions in treating the diseases. The goal of this study is to develop a DNA methylation profile-based classifier to accurately identify various kinds of brain tumors.Methods: Thirteen datasets of DNA methylation profiles were downloaded from the Gene Expression Omnibus (GEO) database, of which GSE90496 and GSE109379 were used as the training set and the validation set, respectively, and the remaining 11 sets were used as the independent test set. The random forest algorithm was used to select the CpG sites based on the importance of the features and a multilayer perceptron (MLP) model was trained to classify the samples. Deconvolution with the debCAM package was used to explore the cellular composition difference among tumors.Results: From training datasets with 2,801 samples, 396,568 CpG sites were retained after preprocessing, of which 767 were selected as the modeling features. A three-layer MLP model was developed, which consists of 1,320 nodes in the hidden layer, to predict the histological types of brain tumors. The prediction accuracy is 99.2, 87.0, and 96.58%, respectively, on the training, validation and test sets. The results of deconvolution analysis showed that the cell proportions of different tumor subtypes were different, and it is approximately enough to distinguish different tumor entities.Conclusion: We developed a classifier that is robust for the classification of central nervous system tumors, and tried to analyze the reasons for the classification performance.

Restriction-modification systems and DNA methylation profile of Pectobacterium carotovorum 2A

The methylation profile of Pectobacterium carotovorum 2A genome was studied using the Oxford Nanopore sequencing technology. The specificity of the methylase subunits of the three restriction-modification systems of this strain was determined. Analysis of homologous systems showed the uniqueness of the type I restriction-modification system and the type IV restriction system specific to methylated DNA of this strain. The work confirms the applicability of Oxford Nanopore technology to the analysis of bacterial DNA modifications and is also the first example of such an analysis for Pectobacterium spp.

Methylation Drivers and Prognostic Implications in Sinonasal Poorly Differentiated Carcinomas

Background: Poorly differentiated sinonasal carcinomas (PDSNCs) are rare and aggressive malignancies, which include squamous cell carcinoma (SCC), sinonasal undifferentiated carcinoma (SNUC), and neuroendocrine carcinomas (NEC). Several epigenetic markers have been suggested to support the histopathological classification, predict prognosis, and guide therapeutic decision. Indeed, molecularly distinct subtypes of sinonasal carcinomas, including SMARCB1-INI1 or SMARCA4 deficient sinonasal carcinoma, isocitrate dehydrogenase (IDH)-mutant SNUC, ARID1A mutant PDSNCs, and NUT carcinomas, have recently been proposed as separate entities. Identification of aberrant DNA methylation levels associated with these specific epigenetic driver genes could be useful for prognostic and therapeutic purpose. Methods: Histopathological review and immunohistochemical study was performed on 53 PDSNCs. Molecular analysis included mutational profile by NGS, Sanger sequencing, and MLPA analyses, and global DNA methylation profile using LINE-1 bisulfite-PCR and pyrosequencing analysis. Results: Nine SWI/SNF complex defective cases and five IDH2 p.Arg172x cases were identified. A significant correlation between INI-1 or IDH2 defects and LINE-1 hypermethylation was observed (p = 0.002 and p = 0.032, respectively), which were associated with a worse prognosis (p = 0.007). Conclusions: Genetic and epigenetic characterization of PDSNCs should be performed to identify distinct prognostic entities, which deserved a tailored clinical treatment.