CoT: a transformer-based method for inferring tumor clonal copy number substructure from scDNA-seq data.

Single-cell DNA sequencing (scDNA-seq) has been an effective means to unscramble intra-tumor heterogeneity, while joint inference of tumor clones and their respective copy number profiles remains a challenging task due to the noisy nature of scDNA-seq data. We introduce a new bioinformatics method called CoT for deciphering clonal copy number substructure. The backbone of CoT is a Copy number Transformer autoencoder that leverages multi-head attention mechanism to explore correlations between different genomic regions, and thus capture global features to create latent embeddings for the cells. CoT makes it convenient to first infer cell subpopulations based on the learned embeddings, and then estimate single-cell copy numbers through joint analysis of read counts data for the cells belonging to the same cluster. This exploitation of clonal substructure information in copy number analysis helps to alleviate the effect of read counts non-uniformity, and yield robust estimations of the tumor copy numbers. Performance evaluation on synthetic and real datasets showcases that CoT outperforms the state of the arts, and is highly useful for deciphering clonal copy number substructure.

Symptomatic HIV infection and in-hospital outcomes for patients with acute myocardial infarction undergoing percutaneous coronary intervention from national inpatient sample.

Human immunodeficiency virus (HIV) infection increases the risk of acute myocardial infarction (AMI). However, little is known about its association with in-hospital outcomes and temporal trends in patients with AMI undergoing percutaneous coronary intervention (PCI). We queried patients with AMI who underwent PCI from the National Inpatient Sample Database (2003-2015) and stratified them into three groups: symptomatic, asymptomatic, and HIV-negative. After 1:2 case-control matching (CCM), logistic regression analysis was conducted to determine how HIV infection affected in-hospital outcomes. We also evaluated their recent trends from 2003 to 2015. The total weighted national estimate of 2,191,129 AMI cases included 2,178,995 HIV/AIDS-negative, 4994 asymptomatic, and 7140 symptomatic HIV cases. Symptomatic but not asymptomatic patients with HIV suffered more than triple the in-hospital mortality (adjusted odds ratio (aOR) 3.6, 95% confidence interval (CI) 2.5-5.2), over one-fold incidence of acute kidney injury (aOR 2.6 95% CI 1.9-3.4) and cardiogenic shock risk (aOR 1.9, 95% CI 1.3-2.7), a longer length of hospital stay (beta 1.2, 95% CI 1.0-1.5), and had more procedures (beta 1.3, 95% CI 1.2-1.5). These disparities relating to symptomatic HIV infection persisted from 2003 to 2015. In patients with AMI who underwent PCI, symptomatic HIV infection was associated with higher in-hospital mortality and more severe outcomes.

Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening.

Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.

Comprehensive Pan-Cancer Analysis of MTF2 Effects on Human Tumors.

Understanding oncogenic processes and underlying mechanisms to advance research into human tumors is critical for effective treatment. Studies have shown that Metal regulatory transcription factor 2（MTF2) drives malignant progression in liver cancer and glioma. However, no systematic pan-cancer analysis of MTF2 has been performed. Here, we use University of California Santa Cruz, Cancer Genome Atlas , Genotype-Tissue Expression data, Tumor Immune Estimation Resource, and Clinical Proteomic Tumor Analysis Consortium bioinformatics tools to explore differential expression of MTF2 across different tumor types. MTF2 was found to be highly expressed in the cancer lines that were available through the respective databases included in the study, and overexpression of MTF2 may lead to a poor prognosis in tumor patients such as glioblastoma multiforme, brain lower grade glioma, KIPAN, LIHC, adrenocortical carcinoma, etc. We also validated MTF2 mutations in cancer, compared MTF2 methylation levels in normal and primary tumor tissues, analyzed the association of MTF2 with the immune microenvironment, and validated the functional role of MTF2 in glioma U87 and U251 and breast cancer MDA-MB-231 cell lines by cytometry. This also indicates that MTF2 has a promising application prospect in cancer treatment.

Chilling-induced peach flavor loss is associated with expression and DNA methylation of functional genes.

INTRODUCTION: Flavor is a major contributor to consumer preference. Despite being effective at extending the fruit's commercial life, cold storage also results in a significant loss of flavor volatiles. To date, there has been few studies on the metabolic dynamics and the mechanism underlying the regulatory networks that modulate flavor loss during cold storage for fruit. METHODS: The volatile contents were detected by Gas Chromatography-Mass Spectrometer (GC-MS). Weighted gene co-expression network analysis (WGCNA) was used to identify structure genes and transcription factors (TFs). DNA methylation was analyzed by whole-genome methylation sequencing during cold storage. RESULTS: We generated a temporal map, over hourly to weekly timescales, for the effects of chilling on flavor volatiles by combining metabolome, transcriptome, and DNA methylome in peach fruit. Based on the big data analysis, we developed a regulatory network for volatile formation and found that a decrease in volatiles during cold storage was significantly correlated with a decrease in the expression of synthesis genes. Moreover, TFs associated with these structure genes were identified. Expression of genes involved in ethylene biosynthesis was reduced while cold tolerance pathway was activated in response to low temperature. Functions of those genes were confirmed through transgenic experiments and across peach cultivars, suggesting our dataset is a useful tool for elucidating regulatory factors that have not yet been clarified in relation to flavor and cold tolerance. Genome wide DNA methylation was induced by chilling and peaked at 7 d followed by a decline during 28 d cold storage. Reduction of gene expression was accompanied by major changes in the methylation status of their promoters, including PpACS1, PpAAT1, PpTPS3 and PpMADS2. CONCLUSION: Our study revealed the mechanism for chilling-induced flavor loss of peach fruit through time-course transcriptome and DNA methylome analysis.

Genome-Wide Analysis of Calmodulin Binding Transcription Activator (CAMTA) Gene Family in Peach (Prunus persica L. Batsch) and Ectopic Expression of PpCAMTA1 in Arabidopsis camta2,3 Mutant Restore Plant Development.

Calmodulin-binding transcription activator (CAMTA) is a transcription factor family containing calmodulin (CaM) binding sites and is involved in plant development. Although CAMTAs in Arabidopsis have been extensively investigated, the functions of CAMTAs remain largely unclear in peaches. In this study, we identified five peach CAMTAs which contained conserved CG-1 box, ANK repeats, CaM binding domain (CaMBD) and IQ motifs. Overexpression in tobacco showed that PpCAMTA1/2/3 were located in the nucleus, while PpCAMTA4 and PpCAMTA5 were located in the plasma membrane. Increased expression levels were observed for PpCAMTA1 and PpCAMTA3 during peach fruit ripening. Expression of PpCAMTA1 was induced by cold treatment and was inhibited by ultraviolet B irradiation (UV-B). Driven by AtCAMTA3 promoter, PpCAMTA1/2/3 were overexpressed in Arabidopsis mutant. Here, we characterized peach PpCAMTA1, representing an ortholog of AtCAMTA3. PpCAMTA1 expression in Arabidopsis complements the developmental deficiencies of the camta2,3 mutant, and restored the plant size to the wild type level. Moreover, overexpressing PpCAMTA1 in camta2,3 mutant inhibited salicylic acid (SA) biosynthesis and expression of SA-related genes, resulting in a susceptibility phenotype to Pst DC3000. Taken together, our results provide new insights for CAMTAs in peach fruit and indicate that PpCAMTA1 is associated with response to stresses during development.

Downregulation of TRIM33 Promotes Survival and Epithelial-Mesenchymal Transition in Gastric Cancer.

Among all malignancies worldwide, gastric cancer is the fifth most common cancer with the third highest mortality rate. One of the main reasons for the low survival rate is the recurrence and metastasis that occurs in many patients after surgery. Numerous studies have shown that abnormal TRIM33 expression is associated with the progression of malignant tumors. TRIM33 can function either as a tumor suppressor or tumor promoter in different cancers. Our data showed that TRIM33 was highly expressed in stomach cancer, and in human gastric cancer tissues, low expression of TRIM33 was associated with poor prognosis in patients with gastric cancer. To clarify the function of TRIM33 in survival and epithelial-mesenchymal transition in gastric cancer cells, we investigated the effect of TRIM33 knockdown in several gastric cancer cell lines. Downregulation of TRIM33 in BGC-823 and SGC-7901 cells enhanced the proliferation, colony formation, and migratory ability of these gastric cancer cells. It also promoted epithelial-mesenchymal transition; transfection of cells with siRNA targeting TRIM33 led to the upregulation of vimentin and N-Cadherin expression, and downregulation of E-Cadherin expression. Meanwhile, the transforming growth factor beta pathway was activated: levels of transforming growth factor beta were elevated and the expressions of p-Smad2, Smad2, Smad3, and Smad4 were activated. To confirm the role of TRIM33 in vivo, a xenograft model was established in nude mice. Immunohistochemical analysis identified that the protein levels of TRIM33, p-Smad2, Smad2, Smad3, Smad4, vimentin, and N-Cadherin were increased, and E-Cadherin levels were decreased, in xenograft tumors from the si-TRIM33 group. Taken together, these results suggest that TRIM33 may be a potential marker for the diagnosis and prognosis of gastric cancer. Furthermore, it may also serve as a novel target for gastric cancer treatment.

Metabolism of Carotenoids and ß-Ionone Are Mediated by Carotenogenic Genes and PpCCD4 Under Ultraviolet B Irradiation and During Fruit Ripening.

Carotenoids are essential pigments widely distributed in tissues and organs of higher plants, contributing to color, photosynthesis, photoprotection, nutrition, and flavor in plants. White- or yellow-fleshed colors in peach were determined by expression of carotenoids cleavage dioxygenase (PpCCD) genes, catalyzing the degradation of carotenoids. The cracked volatile apocarotenoids are the main contributors to peach aroma and flavor with low sensory threshold concentration. However, the detailed regulatory roles of carotenoids metabolism genes remained unclear under UV-B irradiation. In our study, metabolic balance between carotenoids and apocarotenoids was regulated by the expression of phytoene synthase (PSY), ß-cyclase (LCY-B), ε-cyclase (LCY-E), and PpCCD4 under UV-B irradiation. The transcript levels of PpPSY, PpLCY-B, PpLCY-E, and PpCHY-B were elevated 2- to 10-fold compared with control, corresponding to a nearly 30% increase of carotenoids content after 6 h UV-B irradiation. Interestingly, the total carotenoids content decreased by nearly 60% after 48 h of storage, while UV-B delayed the decline of lutein and ß-carotene. The transcript level of PpLCY-E increased 17.83-fold compared to control, partially slowing the decline rate of lutein under UV-B irradiation. In addition, the transcript level of PpCCD4 decreased to 30% of control after 48 h UV-B irradiation, in accordance with the dramatic reduction of apocarotenoid volatiles and the delayed decrease of ß-carotene. Besides, ß-ionone content was elevated by ethylene treatment, and accumulation dramatically accelerated at full ripeness. Taken together, UV-B radiation mediated the metabolic balance of carotenoid biosynthesis and catabolism by controlling the transcript levels of PpPSY, PpLCY-B, PpLCY-E, and PpCCD4 in peach, and the transcript level of PpCCD4 showed a positive relationship with the accumulation of ß-ionone during the ripening process. However, the detailed catalytic activity of PpCCD4 with various carotenoid substrates needs to be studied further, and the key transcript factors involved in the regulation of metabolism between carotenoids and apocarotenoids need to be clarified.

Peach fruit PpNAC1 activates PpFAD3-1 transcription to provide ω-3 fatty acids for the synthesis of short-chain flavor volatiles.

Volatile organic compounds (VOCs) derived from fatty acids are major contributors to fruit flavor and affect human preferences. The ω-3 fatty acid linolenic acid 3 (18:3) serves as an important precursor for synthesis of (E)-2-hexenal and (Z)-3-hexenol. These short-chain C6 VOCs provide unique fresh notes in multiple fruit species. Metabolic engineering to improve fruit aroma requires knowledge of the regulation of fatty acid-derived VOCs. Here, we determined that ripe fruit-specific expression of PpFAD3-1 contributes to 18:3 synthesis in peach fruit. However, no significant increases in (E)-2-hexenal and (Z)-3-hexenol were detected after overexpressing PpFAD3-1. Interestingly, overexpressing the PpNAC1 transcription factor increased the content of 18:3 and enhanced the production of its derived volatiles. Moreover, induced expression of genes responsible for downstream VOC synthesis was observed for transgenic tomato fruit overexpressing PpNAC1, but not for transgenic fruit overexpressing PpFAD3-1. Electrophoretic mobility shift and ChIP-Seq assays showed that PpNAC1 activated PpFAD3-1 expression via binding to its promoter. Therefore, PpNAC1 plays an important role in modulating fatty acid flux to produce fruit flavor-related VOCs. In addition to PpNAC1, PpFAD3-1 expression was also associated with epigenetic modifications during peach fruit ripening. Taken together, our results provide new insights into the molecular mechanisms regulating biosynthesis of fatty acid and short-chain VOCs in fruit.

Ferulic acid attenuates high glucose-induced apoptosis in retinal pigment epithelium cells and protects retina in db/db mice.

Background: Herein, we aimed to present evidence that Ferulic acid (FA), a phenolic acid, can alleviate high glucose (HG)-induced retinal pigment epithelium (RPE) cell apoptosis and protect retina in db/db mice. Methods: ARPE-19 cells (a human RPE cell line) were divided into four groups: control group; HG group (30 mmol/L glucose); HG+FA group (30 mmol/L glucose and 10 mmol/L FA). Cell viability and apoptosis were detected using CCK-8 and Annexin-5 staining, respectively. Apoptosis-related markers including P53, BAX and Bcl2 were examined by RT-qPCR, western blot and immunohistochemistry. Totally, 30 male db/db mice were randomly divided into db/db group (5 ml/kg saline) and FA group (0.05 g/kg FA). After treatment for 2 months, retinal samples were subjected to hematoxylin and eosin (H&E) and Masson staining. Moreover, immunofluorescence was used to detect apoptosis-related markers. Blood samples were collected for measuring cholesterol, triglyceride (TG), low-density lipoprotein (LDL) and high-density lipoprotein (HDL) levels. Results: FA treatment markedly increased cell viability and suppressed cell apoptosis of ARPE-19 cells compared to the HG-exposed group. Furthermore, FA ameliorated the abnormal expression levels of P53, BAX and Bcl2 in HG-induced ARPE-19 cells. In animal models, FA attenuated pathological changes in the retina tissues of diabetic mice. Consistent with in vitro models, FA significantly ameliorated the expression of apoptosis-related markers in retina tissues. Biochemical test results showed that FA reduced hyperlipidemia in diabetic mice. Conclusion: Our findings suggest that FA alleviates HG-induced apoptosis in RPE cells and protects retina in db/db mice, which can be associated with P53 and BAX inactivation and Bcl2 activation.

Grafting Hollow Covalent Organic Framework Nanoparticles with Thermal-Responsive Polymers for the Controlled Release of Preservatives.

Covalent organic frameworks (COFs) hold great potential in various applications because of their well-defined pore structures and morphologies. However, most COF materials demonstrate poor dispersibility in solvents that significantly limits their processing and applications. Herein, we report the synthesis of COF-based hollow nanoparticles (h-NPs) with good water dispersibility, high capacity, and thermal responsiveness to load essential oil molecules for longer-term preservation of fruits. Imine-based COF h-NPs possessing a pore width of 1.3 nm, inner/outer diameters of ∼150/239 nm, and high crystallinity were synthesized and grafted with water-soluble polymers such as polyethylene glycol or poly(N-isopropylacrylamide) (PNIPAM) with molecular weights of 1-3 kDa. The h-NP products with grafting densities of 0.6-2.1 nm-2 can be well dispersed in water at room temperature. PNIPAM-grafted ones are temperature-responsive in that they can precipitate out from the dispersion at 40 °C and redisperse at 25 °C for at least 15 cycles. The h-NPs are used as nanocarriers to load essential oils such as hexanal and trans-2-hexenal with a high capacity of 1.1 g/g for fruit fresh-keeping, and the encapsulated preservatives can be released controllably at 25-40 °C as regulated by the grafted polymers. As a result, the storage time of cherry tomatoes can be prolonged by 4 days compared to the control run. Moreover, these h-NPs can be recycled and reused. Our work highlights the potential of COF nanomaterials grafting with stimuli-responsive polymers for controlled release application in various food preservation.

Linalool synthesis related PpTPS1 and PpTPS3 are activated by transcription factor PpERF61 whose expression is associated with DNA methylation during peach fruit ripening.

The monoterpene linalool is a major contributor to flavor of multiple fruit species. Although great progress has been made in identifying genes related to linalool formation, transcriptional regulation for the pathway remains largely unknown. As a super transcription factor family, roles of AP2/ERF in regulating linalool production have not been elucidated. Peach linalool is catalyzed by terpene synthases PpTPS1 and PpTPS3. Here, we observed that expression of PpERF61 correlated with these two PpTPSs during fruit ripening by transcriptome co-expression analysis. Dual-luciferase assay and EMSA results indicated that PpERF61 activated the PpTPS1 and PpTPS3 transcription by binding to the DRE/CRT motif in their promoters. Transient overexpressing PpERF61 in peach fruit significantly increased PpTPS1 and PpTPS3 expression and linalool content. Further study revealed significant correlation between PpERF61 transcripts and linalool contents across 30 peach cultivars. Besides transcriptional regulation, accumulated linalool was associated with DNA demethylation of PpERF61 during peach fruit ripening. In addition, interactions between PpERF61 and PpbHLH1 were evaluated, indicating these two transcription factors were associated with linalool production during peach fruit ripening. Overall, our results revealed a new insight into the regulation of linalool synthesis in fruit.

[Overexpression of CD47 inhibits apoptosis of SW480 human colon cancer cells by blocking Fas/FasL pathway].

Objectives To study the effect of overexpression of CD47 on apoptosis of human colon cancer SW480 cells and its underlying mechanism. Methods The expression of CD47 in thirty-four tumors was analyzed, along with its correlation to immune cell infiltration, apoptosis, adhesion and angiogenesis in colon cancer by referring to the TCGA database. Meanwhile we packaged an lentivirus vector expressing CD47 and successfully transfected SW480 cells with this vector to stably express CD47. These cells were divided into blank control group, empty body virus infection group and CD47 overexpression group, and then used for the following assays. The infection efficiency was detected by fluorescence microscope and Western blot analysis; the apoptosis rate was detected by flow cytometry; the expression of FasL, caspase-8 and caspase-3 was detected by Western blot analysis. Results The TCGA database analysis showed that CD47 was overexpressed in a variety of tumors, including colon cancer. The mRNA level of CD47 was related to the infiltration of CD4+ T cells, CD8+ T cells, B cells, macrophages and neutrophils in the colon cancer microenvironment. The expression of CD47 involved in biological processes such as apoptosis, adhesion and angiogenesis. Furthermore, the protein-protein interaction network suggested that CD47 interacted with proteins related to death receptor pathway. The apoptosis rate of SW480 cells and the expression of FasL, Caspase-8 and caspase-3 protein in overexpressing CD47 group was significantly higher than the blank control group and empty vector virus infection group. Conclusion The CD47 is highly expressed and is associated with immune cell infiltration in colon cancer. Overexpression of CD47 may inhibit apoptosis by blocking Fas/FasL pathway in human colon cancer SW480 cells.

Synthesis of flavour-related linalool is regulated by PpbHLH1 and associated with changes in DNA methylation during peach fruit ripening.

Linalool is one of the common flavour-related volatiles across the plant kingdom and plays an essential role in determining consumer liking of plant foods. Although great process has been made in identifying terpene synthase (TPS) genes associated with linalool synthesis, much less is known about regulation of this pathway. We initiated study by identifying PpTPS3 encoding protein catalysing enantiomer (S)-(+)-linalool synthesis, which is a major linalool component (˜70%) observed in ripe peach fruit. Overexpression of PpTPS3 led to linalool accumulation, while virus-induced gene silencing of PpTPS3 led to a 66.5% reduction in linalool content in peach fruit. We next identified transcription factor (TF) PpbHLH1 directly binds to E-box (CACATG) in the PpTPS3 promoter and activates its expression based on yeast one-hybrid assay and EMSA analysis. Significantly positive correlation was also observed between PpbHLH1 expression and linalool production across peach cultivars. Peach fruit accumulated more linalool after overexpressing PpbHLH1 in peach fruit and reduced approximately 54.4% linalool production after silencing this TF. DNA methylation analysis showed increased PpTPS3 expression was associated with decreased 5 mC level in its promoter during peach fruit ripening, but no reverse pattern was observed for PpbHLH1. Arabidopsis and tomato fruits transgenic for peach PpbHLH1 synthesize and accumulate higher levels of linalool compared with wild-type controls. Taken together, these results would greatly facilitate efforts to enhance linalool production and thus improve flavour of fruits.

PFKFB4 as a promising biomarker to predict a poor prognosis in patients with gastric cancer.

Gastric cancer (GC) is one of the most common types of cancer worldwide. Previous studies have reported that phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (PFKFB4) functions as an oncoprotein in various types of cancer. However, the association between PFKFB4 and GC remains unclear. The present study analyzed the expression levels of PFKFB4 in 148 GC tissue samples, including 46 tumor tissues with matched adjacent normal tissues, using immunohistochemistry, compared the expression levels of PFKFB4 between GC and adjacent normal tissues, and determined the association between PFKFB4 expression levels and patient clinicopathological characteristics. In addition, survival curves were generated using the Kaplan-Meier (KM) plotter database to evaluate the association between PFKFB4 expression and GC prognosis. The results revealed that PFKFB4 expression was upregulated in GC tissues compared with in adjacent normal tissues. PFKFB4 expression was associated with patient age, tumor size, pathological tumor (pT) stage and tumor-node-metastasis (pTNM) stage, and upregulated expression levels of PFKFB4 were observed in tumor tissues from patients <65 years old (compared with that in patients ≥65 years old), as well as patients with a larger tumor size and an advanced stage (pT and pTNM stage) disease. In addition, KM survival analysis demonstrated that patients with low PFKFB4 expression had a significantly improved overall survival (OS), first progression survival and post-progression survival times compared with those with high PFKFB4 expression. Furthermore, PFKFB4 expression was negatively associated with OS time in patients with late pT and pTNM stage disease. In conclusion, the results of the present study indicated that the upregulated PFKFB4 expression in GC tissues may serve as a biomarker for a more advanced disease and a poor prognosis in patients with GC.

IDH1 gene mutation activates Smad signaling molecules to regulate the expression levels of cell cycle and biological rhythm genes in human glioma U87­MG cells.

Isocitrate dehydrogenase1 (IDH1) mutation is the most important genetic change in glioma. The most common IDH1 mutation results in the amino acid substitution of arginine 132 (Arg/R132), which is located at the active site of the enzyme. IDH1 Arg132His (R132H) mutation can reduce the proliferative rate of glioma cells. Numerous diseases follow circadian rhythms, and there is growing evidence that circadian disruption may be a risk factor for cancer in humans. Dysregulation of the circadian clock serves an important role in the development of malignant tumors, including glioma. Brain­Muscle Arnt­Like protein 1 (BMAL1) and Circadian Locomotor Output Cycles Kaput (CLOCK) are the main biological rhythm genes. The present study aimed to further study whether there is an association between IDH1 R132H mutation and biological rhythm in glioma, and whether this affects the occurrence of glioma. The Cancer Genome Atlas (TCGA) database was used to detect the expression levels of the biological rhythm genes BMAL1 and CLOCK in various types of tumor. Additionally, U87­MG cells were infected with wild­type and mutant IDH1 lentiviruses. Colony formation experiments were used to detect cell proliferation in each group, cell cycle distribution was detected by flow cytometry and western blotting was used to detect the expression levels of wild­type and mutant IDH1, cyclins, biological rhythm genes and Smad signaling pathway­associated genes in U87­MG cells. TCGA database results suggested that BMAL1 and CLOCK were abnormally expressed in glioma. Cells were successfully infected with wild­type and mutant IDH1 lentiviruses. Colony formation assay revealed decreased cell proliferation in the IDH1 R132H mutant group. The cell cycle distribution detected by flow cytometry indicated that IDH1 gene mutation increased the G1 phase ratio and decreased the S phase ratio in U87­MG cells. The western blotting results demonstrated that IDH1 R132H mutation decreased the expression levels of the S phase­associated proteins Cyclin A and CDK2, and increased the expression levels of the G1 phase­associated proteins Cyclin D3 and CDK4, but did not significantly change the expression levels of the G2/M phase­associated protein Cyclin B1. The expression levels of the positive and negative rhythm regulation genes BMAL1, CLOCK, period (PER s (PER1, 2 and 3) and cryptochrom (CRY)s (CRY1 and 2) were significantly decreased, those of the Smad signaling pathway­associated genes Smad2, Smad3 and Smad2­3 were decreased, and those of phosphorylated (p)­Smad2, p­Smad3 and Smad4 were increased. Therefore, the present results suggested that the IDH1 R132H mutation may alter the cell cycle and biological rhythm genes in U87­MG cells through the TGF­ß/Smad signaling pathway.

Transcriptional and epigenetic analysis reveals that NAC transcription factors regulate fruit flavor ester biosynthesis.

Flavor-associated volatile chemicals make major contributions to consumers' perception of fruits. Although great progress has been made in establishing the metabolic pathways associated with volatile synthesis, much less is known about the regulation of those pathways. Knowledge of how those pathways are regulated would greatly facilitate efforts to improve flavor. Volatile esters are major contributors to fruity flavor notes in many species, providing a good model to investigate the regulation of volatile synthesis pathways. Here we initiated a study of peach (Prunus persica L. Batsch) fruits, and identified that the alcohol acyltransferase PpAAT1 contributes to ester formation. We next identified the transcription factor (TF) PpNAC1 as an activator of PpAAT1 expression and ester production. These conclusions were based on in vivo and in vitro experiments and validated by correlation in a panel of 30 different peach cultivars. Based on homology between PpNAC1 and the tomato (Solanum lycopersicum) TF NONRIPENING (NOR), we identified a parallel regulatory pathway in tomato. Overexpression of PpNAC1 enhances ripening in a nor mutant and restores synthesis of volatile esters in tomato fruits. Furthermore, in the NOR-deficient mutant tomatoes generated by CRISPR/Cas9, lower transcript levels of SlAAT1 were detected. The apple (Malus domestica) homolog MdNAC5 also stimulates MdAAT1 expression via binding to this gene's promoter. In addition to transcriptional control, epigenetic analysis showed that increased expression of NACs and AATs is associated with removal of the repressive mark H3K27me3 during fruit ripening. Our results support a conserved molecular mechanism in which NAC TFs activate ripening-related AAT expression, which in turn catalyzes volatile ester formation in multiple fruit species.

Inhibition of Nrf2/HO-1 signaling pathway by Dextran Sulfate suppresses angiogenesis of Gastric Cancer.

Purpose: To investigate the role of Nrf2/HO-1 signaling pathway in angiogenesis and whether dextran sulfate (DS) could suppress angiogenesis by inhibiting Nrf2/HO-1 signaling pathway in gastric cancer. Methods: In vitro; Western blot analyzed the expression of Nrf2 in gastric cell lines. Tube formation assay observed the effect of gradient concentration DS on the angiogenic potential of HGC-27 cells. Immunofluorescence,western blot and qPCR analyzed the effects of DS on the expression of Nrf2, HO-1 and VEGF under gradient hypoxia time. Immunofluorescence,western blot,qPCR and tube formation assay analyzed the effects of up-regulating or down-regulating Nrf2/HO-1 signaling pathway on VEGF expression and angiogenic potential in HGC-27 cells. In vivo: Construct nude mouse intraperitoneal implantation metastasis model. Immunohistochemistry and western blot analyzed the effects of DS on the expression of Nrf2, HO-1, VEGF and MVD in nude mice. Immunohistochemistry detected the expression of Nrf2, HO-1, VEGF and MVD in human paracancerous tissue and gastric cancer tissues with different degrees of differentiation. Results: The expression of Nrf2 increased most significantly in HGC-27 cell line. DS reduced the angiogenic potential and the expression of Nrf2, HO-1 and VEGF in HGC-27 cells. Down-regulation of Nrf2/HO-1 signaling pathway decreased VEGF expression and angiogenic potential in HGC-27 cells. Up-regulation of Nrf2/HO-1 signaling pathway increased VEGF expression and angiogenic potential in HGC-27 cells. DS reduced the expression of Nrf2, HO-1, VEGF and MVD in nude mice. Nrf2, HO-1, VEGF and MVD showed low expression in paracancerous tissue but high expression in gastric cancer tissues. They were weak, moderate and strong in well, moderately and poorly differentiated gastric cancer tissues, respectively. Conclusion: Nrf2/HO-1 signaling pathway may positively regulate gastric cancer angiogenesis and DS may suppress the angiogenesis by inhibiting Nrf2/HO-1 signaling pathway in gastric cancer.

Polycomb-like 2 regulates PRC2 components to affect proliferation in glioma cells.

INTRODUCTION: The Polycomb group (PcG) is an important family of transcriptional regulators that controls growth and tumorigenesis. The PcG mainly consists of two complexes, PRC1 and Polycomb Repressive Complex 2 (PRC2). Polycomb-like 2 (PCL2) is known to interact with the PRC2 protein. The role of PCL2 in the development and progression of glioma is unclear. METHODS: We use The Cancer Genome Atlas (TCGA) database to detect the expression of PCL2 in various tumors. 117 cases of clinical glioma (WHOI-IV) were collected, and PCL2 expression and localization were detected by immunohistochemical staining. Glioma cells U87/U251 were infected with overexpressed and interfered PCL2. CCK8 assay, colony formation assay, EdU method, cell cycle and apoptosis were used to detect cell proliferation and apoptosis. Western blot was used to detect the expression of PRC2-related core proteins. After DZNeP intervention, PRC2 protein expression was again measured to discuss the mechanism of PCL2 action. RESULTS: TCGA database results and immunohistochemical staining results suggest that PCL2 is highly expressed in gliomas. We found that the PCL2 gene promoted tumor cell proliferation, enhanced the colony formation ability, and increased S phase in the cell cycle. The overexpression of PCL2 upregulated the expression levels of EZH2 and EED (two core members of PRC2), decreased the expression of SUZ12, increased the level of H3K27 trimethylation (H3K27me3), H3K4 dimethylation (H3K4me2), and decreased H3K9 dimethylation (H3K9me2). The result after interfering with PCL2 was the opposite. CONCLUSIONS: As an important accessory protein of PRC2, PCL2 can not only change the expression of PRC2 components, but also affect the expression level of Histone methylation. Therefore, PCL2 may be an important hub for regulating the synergy among PRC2 members. This study revealed PCL2 as a new target for tumor research and open up a new avenue for future research in glioma.

Genome-Wide Identification and Functional Analysis of Carboxylesterase and Methylesterase Gene Families in Peach (Prunus persica L. Batsch).

Carboxylesterases (CXE) and methylesterases (MES) are hydrolytic enzymes that act on carboxylic esters and are involved in plant metabolic processes and defense responses. A few functions of plant CXE and MES genes have been identified but very little information is available about the role of most members. We made a comprehensive study of this gene family in a commercially important species, peach (Prunus persica L. Batsch). A total of 33 peach CXE genes and 18 MES genes were identified and shown to be distributed unevenly between the chromosomes. Based on phylogenetic analysis, CXEs and MESs clustered into two different branches. Comparison of the positions of intron and differences in motifs revealed the evolutionary relationships between CXE and MES genes. RNA-seq revealed differential expression patterns of CXE/MESs in peach flower, leaf, and ripening fruit and in response to methyl jasmonate (MeJA) and ultraviolet B treatment. Transcript levels of candidate genes were verified by real-time quantitative PCR. Heterologous expression in Escherichia coli identified three CXEs that were involved in the hydrolysis of volatile esters in vitro. Furthermore, two recombinant MES proteins were identified that could hydrolyze MeJA and methyl salicylate. Our results provide an important resource for the identification of functional CXE and MES genes involved in the catabolism of volatile esters, responses to biotic and abiotic stresses and activation of signaling molecules such as MeJA and methyl salicylate.