Genome-Wide Transcriptomic and Metabolomic Analyses Unveiling the Defence Mechanisms of Populus tremula against Sucking and Chewing Insect Herbivores.

Plants and insects coevolved as an evolutionarily successful and enduring association. The molecular arms race led to evolutionary novelties regarding unique mechanisms of defence and detoxification in plants and insects. While insects adopt mechanisms to conquer host defence, trees develop well-orchestrated and species-specific defence strategies against insect herbivory. However, current knowledge on the molecular underpinnings of fine-tuned tree defence responses against different herbivore insects is still restricted. In the current study, using a multi-omics approach, we unveiled the defence response of Populus tremula against aphids (Chaitophorus populialbae) and spongy moths (Lymantria dispar) herbivory. Comparative differential gene expression (DGE) analyses revealed that around 272 and 1203 transcripts were differentially regulated in P. tremula after moth and aphid herbivory compared to uninfested controls. Interestingly, 5716 transcripts were differentially regulated in P. tremula between aphids and moth infestation. Further investigation showed that defence-related stress hormones and their lipid precursors, transcription factors, and signalling molecules were over-expressed, whereas the growth-related counterparts were suppressed in P. tremula after aphid and moth herbivory. Metabolomics analysis documented that around 37% of all significantly abundant metabolites were associated with biochemical pathways related to tree growth and defence. However, the metabolic profiles of aphid and moth-fed trees were quite distinct, indicating species-specific response optimization. After identifying the suitable reference genes in P. tremula, the omics data were further validated using RT-qPCR. Nevertheless, our findings documented species-specific fine-tuning of the defence response of P. tremula, showing conservation on resource allocation for defence overgrowth under aphid and moth herbivory. Such findings can be exploited to enhance our current understanding of molecular orchestration of tree responses against herbivory and aid in developing insect pest resistance P. tremula varieties.

DNA hypermethylation of tumor suppressor genes TWIST1, GATA4, MUS81 and NTRK1 in endometrial hyperplasia.

OBJECTIVE: To investigate DNA methylation of specific tumor suppressor genes in endometrial hyperplasia compared to normal endometrial tissue. File and methodology: To search for epigenetic events, methylation-specific multiplex ligation-dependent probe amplification was employed to compare the methylation status of 40 tissue samples with atypical endometrial hyperplasia, 40 tissue samples with endometrial hyperplasia without atypia, and 40 control tissue samples with a normal endometrium. RESULTS AND CONCLUSION: Differences in DNA methylation among the groups were found in TWIST1, GATA4, MUS81, and NTRK1 genes (TWIST1: atypical hyperplasia 67.5%, benign hyperplasia 2.5%, normal endometrium 22.5%; P < 0.00001; GATA4: atypical hyperplasia 95%, benign hyperplasia 65%, normal endometrium 22.5%; P < 0.00001; MUS81: atypical hyperplasia 57.5%, benign hyperplasia 22.5%, normal endometrium 5%; P < 0.00001; NTRK1: atypical hyperplasia 65%, benign hyperplasia 27.5%, normal endometrium 10%; P < 0.00001). Higher methylation rates were observed for the tumor suppressor genes of TWIST1, GATA4, MUS81, and NTRK1 in samples with atypical endometrial hyperplasia compared to samples with normal endometrial tissue, and higher methylation rates were found in samples with atypical endometrial hyperplasia compared to samples of benign endometrial hyperplasia. DNA methylation of TWIST1, GATA4, MUS81, and NTRK1 is involved in the pathogenesis of atypical endometrial hyperplasia.

Next-Generation Sequencing Approach in Methylation Analysis of HNF1B and GATA4 Genes: Searching for Biomarkers in Ovarian Cancer.

DNA methylation is well-known to be associated with ovarian cancer (OC) and has great potential to serve as a biomarker in monitoring response to therapy and for disease screening. The purpose of this study was to investigate methylation of HNF1B and GATA4 and correlate detected methylation with clinicopathological characteristic of OC patients. The study group consisted of 64 patients with OC and 35 control patients. To determine the most important sites of HNF1B and GATA4, we used next-generation sequencing. For further confirmation of detected methylation of selected regions, we used high-resolution melting analysis and methylation-specific real-time polymerase chain reaction (PCR). Selected regions of HNF1B and GATA4 were completely methylation free in all control samples, whereas methylation-positive pattern was observed in 32.8% (HNF1B) and 45.3% (GATA4) of OC samples. Evaluating both genes together, we were able to detect methylation in 65.6% of OC patients. We observed a statistically significant difference in HNF1B methylation between samples with different stages of OC. We also detected subtype specific methylation in GATA4 and a decrease of methylation in late stages of OC. The combination of unmethylated HNF1B and methylated GATA4 was associated with longer overall survival. In our study, we employed innovative approach of methylation analysis of HNF1B and GATA4 to search for possible epigenetic biomarkers. We confirmed the significance of the HNF1B and GATA4 hypermethylation with emphasis on the need of selecting the most relevant sites for analysis. We suggest selected CpGs to be further examined as a potential positive prognostic factor.

DNA methylation of selected tumor suppressor genes in endometrial hyperplasia.

AIMS: To investigate DNA methylation of specific gene promoters in endometrial hyperplasia compared to normal endometrial tissue. MATERIALS AND METHODS: To search for epigenetic events, methylation-specific multiplex ligation-dependent probe amplification was employed to compare the methylation status of 64 tissue samples with atypical endometrial hyperplasia, 60 tissue samples with endometrial hyperplasia without atypia, and 40 control tissue samples with normal endometrium. RESULTS: Differences in DNA methylation among the groups were found in PTEN, CDH13, and MSH6 promoters (PTEN: atypical hyperplasia 32%, benign hyperplasia 6.8%, normal endometrium 10%; P=0.004; CDH13: atypical hyperplasia, 50%; benign hyperplasia, 43%; normal endometrium 8.1%; P=0.003; MSH6 atypical hyperplasia 84%, benign hyperplasia, 62%; normal endometrium, 52%; P=0.008.) Higher rates of CDH13 promoter methylation were identified in the groups with both forms of endometrial hyperplasia when compared to the control group (atypical hyperplasia, P=0.003, benign hyperplasia, P=0.0002). A higher rate of DNA methylation of the PTEN and MSH6 promoters was observed in samples with atypical endometrial hyperplasia than in samples with benign endometrial hyperplasia (PTEN: P=0.02; MSH6: P=0.01) and samples with normal endometrial tissue (PTEN, P=0.04; MSH6, P=0.006). CONCLUSION: DNA methylation of CDH13, PTEN, and MSH6 appear to be involved in the development of endometrial hyperplasia.

Biochemical Responses in Populus tremula: Defending against Sucking and Leaf-Chewing Insect Herbivores.

The main biochemical traits were estimated in poplar leaves under biotic attack (aphids and spongy moth infestation). Changes in the abundance of bioactive compounds in genetically uniform individuals of European aspen (Populus tremula), such as proline, polyphenolic compounds, chlorophylls a and b, and volatile compounds, were determined between leaves damaged by sucking insects (aphid-Chaitophorus nassonowi) and chewing insects (spongy moth-Lymantria dispar) compared to uninfected leaves. Among the nine analyzed phenolic compounds, only catechin and procyanidin showed significant differences between the control leaves and leaves affected by spongy moths or aphids. GC-TOF-MS volatile metabolome analysis showed the clear separation of the control versus aphids-infested and moth-infested leaves. In total, the compounds that proved to have the highest explanatory power for aphid-infested leaves were 3-hexenal and 5-methyl-2-furanone, and for moth-infested leaves, trans-α-farnesene and 4-cyanocyclohexane. The aphid-infested leaves contained around half the amount of chlorophylls and twice the amount of proline compared to uninfected leaves, and these results evidenced that aphids influence plant physiology more than chewing insects.

The Influence of the Initial Treatment of Oak Wood on Increasing the Durability of Exterior Transparent Coating Systems.

This study determined the impact of undertaking an initial treatment of oak wood by sealing its surface pores with epoxy resin, focusing on the durability of transparent coating systems when exposed outdoors. Throughout the exposure period, various parameters including color, gloss, surface wettability, and both macroscopic and microscopic surface evaluation were continuously monitored. The study involved two sets of samples: one set underwent the pretreatment, while the other did not. Subsequently, four coating systems were applied to the samples, comprising two solvent-based and two water-based coatings. The experiment was conducted over a period of two years, utilizing natural weathering methods within the premises of the Czech University of Life Sciences in Prague. The pretreatment with epoxy resin exhibited enhanced durability for all paint systems. The analysis showed a significant difference in gloss and color after 12 months of weathering exposure without any significant effect on surface wettability and sealing. However, after 24 months of the weathering exposure, no significant differences between the sealed and unsealed surface were observed. The most significant change in properties was noted for the water-based coatings used in coating systems number 3 and 4, and these coatings were rated as the best.

Durability of the Exterior Transparent Coatings on Nano-Photostabilized English Oak Wood and Possibility of Its Prediction before Artificial Accelerated Weathering.

Changes in surface material characteristics can significantly affect the adhesion and overall life of coatings on wood. In order to increase the durability of transparent exterior coatings, it is possible to use the surface modification of wood with UV-stabilizing substances. In this work, selected types of surface modifications using benzotriazoles, HALS, ZnO and TiO2 nanoparticles, and their combinations were applied to oak wood (Quercus robur, L.). On such modified surfaces, the surface free energy, roughness, and contact wetting angle with three selected types of exterior transparent coatings were subsequently determined. An oil-based coating, waterborne acrylic thick layer coating, and thin-layer synthetic coating were tested and interaction with the aforementioned surface modifications was investigated after 6 weeks of accelerated artificial weathering. The results of changes in the initially measured surface characteristics of the modified oak wood were compared to the real results of degradation of coatings after artificial accelerated weathering. The positive effect of surface modification, in particular the mixture of benzotriazoles, HALS, and ZnO nanoparticles on all kinds of coatings was proven, and the best results were observed in thick-film waterborne acrylic coating. The changes in the measured surface characteristics corresponded to the observed durability of the coatings only when measured by wetting using drops of the tested coatings.

Aberrant methylation of PCDH17 gene in high-grade serous ovarian carcinoma.

BACKGROUND: Aberrant DNA methylation of protocadherins (PCDHs) has been associated with development and progression of various types of cancer. It could represent possible direction in the search for critically needed tumor biomarkers for ovarian cancer. OBJECTIVE: To investigate methylation of δ2 group of non-clustered PCDHs in high-grade serous ovarian carcinoma (HGSOC) tissue in comparison with control tissue. METHODS: We used next-generation sequencing for detecting regions with the most altered methylation. For further confirmation of discovered alterations we used methylation-sensitive high-resolution melting analysis. RESULTS: PCDH17 methylation was detected in almost 70% of HGSOC patients without any methylation in the group of control samples and was found both in the late stage tumors as well as in the early stage ones. Other selected PCDHs did not show any relevant changes in methylation. Subsequent gene expression analysis of PCDH17 revealed decreased expression in all of the tumor samples in comparison to the control ones. Statistically significant negative correlation was found between methylation and levels of expression suggesting potentially methylation-based silencing. CONCLUSIONS: Methylation of PCDH17 could play an important role in development and progression of HGSOC and has potential to become a target in the search for new clinical biomarkers.