Identification of surrogate prognostic biomarkers for allergic asthma in nasal epithelial brushing samples by WGCNA.

BACKGROUND: Allergic asthma is a lower respiratory tract disease of Th2 inflammation with multiple molecular mechanisms. The upper and lower airways can be unified by the concept of a united airway and, as such, gene expression studies of upper epithelial cells may provide effective surrogate biomarkers for the prognostic study of allergic asthma. OBJECTIVE: To identify surrogate biomarkers in upper airway epithelial cells for the prognostic study of allergic asthma. METHODS: Nasal epithelial cell gene expression in 40 asthmatic and 17 healthy control subjects were analyzed by weighted gene coexpression network analysis (WGCNA) to identify gene network modules and profiles in allergic asthma. Functional enrichment analysis was performed on the coexpression genes in certain highlighted modules. RESULTS: A total of 13 coexpression modules were constructed by WGCNA from 2804 genes in nasal epithelial brushing samples of the 40 asthmatic and 17 healthy subjects. The number of genes in these modules ranged from 1086 (Turquoise module) to 45 (Salmon). Eight coexpression modules were found to be significantly correlated (P < 0.05) with two clinic traits, namely disease status, and severity. Four modules were positively correlated ( P < 0.05) with the traits and these, therefore, contained genes that are mostly overexpressed in asthma. Contrastingly, the four other modules were found to be negatively correlated with the clinic traits. Functional enrichment analysis of the positively correlated modules showed that one (Magenta) was mainly enriched in mast cell activation and degranulation; another (Pink) was largely involved in immune cell response; the third (Yellow) was predominantly enriched in transmembrane signal pathways; and the last (Blue) was mainly enriched in substructure components of the cells. The hub genes in the modules were KIT, KITLG, GATA2, CD44, PTPRC, and CFTR, and these were confirmed as having significantly higher expression in the nasal epithelial cells. Combining the six hub genes enabled a relatively high capacity for discrimination between asthmatics and healthy subjects with an area under the receiver operating characteristic (ROC) curve of 0.924. CONCLUSIONS: Our findings provide a framework of coexpression gene modules from nasal epithelial brushing samples that could be used for the prognostic study of allergic asthma.

RNF135 is a positive regulator of IFN expression and involved in RIG-I signaling pathway by targeting RIG-I.

RIG-I-like receptors (RLRs) play a key role in antiviral and inflammatory responses. Increasing evidence indicates that ubiquitination is crucial for regulation of RIG-I signaling pathway. Several ubiquitin ligases were reported to be involved in RIG-I-mediated signal transduction. In the present study, we demonstrated zebrafish RING finger protein 135 (zbRNF135) was a critical player in the regulation of RIG-I signaling pathway. zbRNF135 mRNA was widely expressed in different tissues of zebrafish. The expression of zbRNF135 was up-regulated post poly(I:C) treatment in vivo and in vitro. Furthermore, the expression profiles of RIG-I signaling pathway related genes (LGP2, MDA5, RIG-I, MAVS, TRAF3, IRF3 and IRF7), together with its downstream molecules (IFN1, ISG15, Mx and PKR), were up-regulated by overexpression of zbRNF135 in ZF4 cells. Luciferase and ubiquitination assays revealed that overexpression of zbRNF135 facilitated zebrafish RIG-I (zbRIG-I)-mediated IFN1 promoter activation by mediating K63-linked ubiquitination of zbRIG-I. The co-immunoprecipitation assay showed that zbRNF135 specifically interacted with zbRIG-I. Our study indicated that zbRNF135 participated in innate immune response through modulating RIG-I signaling pathway.

A large lung gene expression study identifying IL1B as a novel player in airway inflammation in COPD airway epithelial cells.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a chronic and progressive lung disease characterized by a mixture of small airway disease and lung tissue parenchymal destruction. Abnormal inflammatory responses to cigarette smoking and other noxious particles are generally thought to be responsible for causing of COPD. Since airway inflammation is a key factor in COPD progress, it is crucial to unravel its underlying molecular mechanisms. Unbiased analysis of genome-wide gene expression profiles in lung small airway epithelial cells provides a powerful tool to investigate this. METHODS: Gene expression data of GSE611906, GSE20257, GSE8545 were downloaded from GEO database. All 288 lung small airway samples in these cohorts, including donors with (n = 61) and without (n = 227) COPD, were chosen for differential gene expression analysis. The gene ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses, gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network analysis were performed. Subsequently, the analyses of IL1B expression level, the Pearson correlation between IL1B and several COPD biomarkers were performed using other cohorts to validate our main findings. RESULTS: With a change ≥ twofold and P value < 0.05 cutoff, we found 38 genes were up-regulated and 114 genes were down-regulated in patients with COPD compared with health controls, while using cutoff fold change 1.5 and P value < 0.05, there were 318 genes up-regulated and 333 genes down-regulated. Among the most up-regulated genes were IL1B, CCL2, CCL23, and CXCL14, all implicated in inflammation triggering. GO, KEGG and WGCNA analysis all disclosed IL1B was highly correlated to COPD disease trait. The expression profile of IL1B was further validated using independent cohorts from COPD airway epithelium, lung tissue, sputum, and blood. We demonstrated higher IL1B gene expression in COPD small airway epithelial cells, but not in COPD lung tissue, sputum, and blood. Strong co-expression of IL1B with COPD biomarkers, such as DUOX2, MMP12, CCL2, and CXCL14, were validated in silico analysis. Finally, PPI network analysis using enriched data showed IL1B, CCL2, CCL7 and BMP7 were in the same hub node with high degrees. CONCLUSIONS: We identified IL1B was significantly up-regulated in COPD small airway epithelial cells and propose IL1B as a novel player in airway inflammation in COPD.

Differences in Albizia odoratissima genetic diversity between Hainan Island and mainland populations in China.

Background: This study aimed at exploring unique population genetic characteristics of Albizia odoratissima (Linn. f) Benth on Hainan Island to provide a scientific basis for its rational utilization and protection. Methods: It analyzed the genetic diversity and structure of 280 individuals from 10 subpopulations of A. odoratissima from Hainan Island and Baise City using 16 expression sequence markers - simple sequence repeat markers. Results: The genetic diversity of Hainan population (I = 0.7290, He = 0.4483) was lower than that of the Baise population (I = 0.8722, He = 0.5121). Compared with the Baise population (Nm = 2.0709, FST = 0.1077), the Hainan Island population (Nm = 1.7519, FST = 0.1249) exhibited lower gene flow and higher degree of genetic differentiation. Molecular variance and genetic differentiation analyses showed that the main variation originated from individuals within the subpopulation. There were significant differences in the genetic structure between Hainan and Baise populations. It grouped according to geographical distance, consistent with the Mantel test results (R2 = 0.77, p = 0.001). In conclusion, the genetic diversity of the island A. odoratissima population was lower than that distributed on land, the two populations exhibited obvious genetic structure differences. Both the degrees of inbreeding and genetic differentiation were higher in the island population than in the land population.

Effects of Processing Conditions on the Properties of Monoammonium Phosphate Microcapsules with Melamine-Formaldehyde Resin Shell.

To develop monoammonium phosphate (MAP) as a novel acid source for durable intumescent fire retardants (IFR), MAP microcapsules (MCMAPs) containing MAP as the internal core and melamine-formaldehyde (MF) as the external shell were prepared by in situ polymerization in this study. The influences of synthesis conditions (including reaction temperature, polymerization time, and reaction pH value) on the properties of obtained MCMAPs (MAP content, yield, morphologies, and thermal properties) were then investigated systematically. The morphologies, chemical structures, and thermal properties were characterized by optical microscopy, scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), Fourier transform infrared (FTIR) spectroscopy, and thermogravimetry analyzer (TGA). The results show that MAP was well encapsulated by MF resin. No microcapsules are obtained at <55 °C or with polymerization times <1 h. Optimal preparation conditions of reaction temperature, polymerization time, and reaction pH value are 75 °C, 3 h, and 5.5, respectively. Those results provide process reference and theoretical basis for preparing MCMAPs and could promote the application of MAP microcapsules in wood flame-retardant materials.

p62 promotes proliferation, apoptosis­resistance and invasion of prostate cancer cells through the Keap1/Nrf2/ARE axis.

Prostate cancer poses a public health threat to hundreds of people around the world. p62 has been identified as a tumor suppressor, however, the mechanism by which p62 promotes prostate cancer remains poorly understood. The present study aimed to investigate whether p62 promotes proliferation, apoptosis resistance and invasion of prostate cancer cells via the Kelch­like ECH­associated protein 1/nuclear factor erytheroid­derived 2­like 2/antioxidant response element (Keap1/Nrf2/ARE) axis. Immunohistochemical staining and immunoblotting were performed to determine the protein levels. Rates of proliferation, invasion and apoptosis of prostate cancer cells were assessed using an RTCA system and flow cytometric assays. Levels of reactive oxygen species (ROS) were assessed using Cell ROX Orange reagent and mRNA levels of Nrf2 target genes were detected by qRT­PCR. It was revealed that p62 increased the levels and activities of Nrf2 by suppressing Keap1­mediated proteasomal degradation in prostate cancer cells and tissues, and high levels of p62 promoted growth of prostate cancer through the Keap1/Nrf2/ARE system. Silencing of Nrf2 in DU145 cells overexpressing p62 led to decreases in the rate of cell proliferation and invasion and an increase in the rate of cell apoptosis. p62 activated the Nrf2 pathway, promoted the transcription of Nrf2­mediated target genes and suppressed ROS in prostate cancer. Therefore, p62 promoted the development of prostate cancer by activating the Keap1/Nrf2/ARE pathway and decreasing p62 may provide a new strategy to ameliorate tumor aggressiveness and suppress tumorigenesis to improve clinical outcomes.

Expression profiles of genes associated with inflammatory responses and oxidative stress in lung after heat stroke.

BACKGROUND: Heat stroke (HS) is a physically dysfunctional illness caused by hyperthermia. Lung, as the important place for gas-exchange and heat-dissipation organ, is often first to be injured. Lung injury caused by HS impairs the ventilation function of lung, which will subsequently cause damage to other tissues and organs. Nevertheless, the specific mechanism of lung injury in heat stroke is still unknown. METHODS: Rat lung tissues from controls or HS models were harvested. The gene expression profile was identified by high-throughput sequencing. DEGs were calculated using R and validated by qRT-PCR. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and cell-enrichment were performed using differential expression genes (DEGs). Finally, lung histopathology was accessed by H&E staining. RESULTS: About 471 genes were identified to be DEGs, of which 257 genes were up-regulated, and 214 genes were down-regulated. The most up-regulated and down-regulated DEGs were validated by qRT-PCR, which confirmed the tendency of expression. GO, KEGG, and protein-protein interaction (PPI)-network analyses disclosed DEGs were significantly enriched in leukocyte migration, response to lipopolysaccharide, NIK/NF-kappaB signaling, response to reactive oxygen species, response to heat, and the hub genes were Tnf, Il1b, Cxcl2, Ccl2, Mmp9, Timp1, Hmox1, Serpine1, Mmp8 and Csf1, most of which were closely related to inflammagenesis and oxidative stress. Finally, cell-enrichment analysis and histopathologic analysis showed Monocytes, Megakaryotyes, and Macrophages were enriched in response to heat stress. CONCLUSIONS: The present study identified key genes, signal pathways and infiltrated-cell types in lung after heat stress, which will deepen our understanding of transcriptional response to heat stress, and might provide new ideas for the treatment of HS.

Metformin attenuates hepatoma cell proliferation by decreasing glycolytic flux through the HIF-1α/PFKFB3/PFK1 pathway.

AIMS: Enhanced aerobic glycolysis is an essential hallmark of malignant cancer. Blocking the glycolytic pathway has been suggested as a therapeutic strategy to impair the proliferation of tumor cells. Metformin, a widely used anti-diabetes drug, exhibits anti-tumor properties. However, the underlying molecular mechanism of its action linking glucose metabolism with the suppression of proliferation has not been fully clarified. MAIN METHODS: Stable isotope tracing technology and gas chromatography-mass spectrometry method were utilized to analyze the effect of metformin on glycolytic flux in HCC cells. Western blot and immunohistochemistry were utilized to analyze the expression of phosphofructokinase-1 (PFK1) and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) in HCC cells or xenograft tumor tissues. Lactate measurement and glucose uptake assay were used to analyze the level of lactate and glucose in the presence of frucose-2,6-diphosphate (F2,6BP) in HCC cells treated with metformin. KEY FINDINGS: We found that metformin significantly impaired hepatoma cell proliferation by inhibiting the glycolytic flux via PFK1 blockade. Interestingly, activation of PFK1 by F2,6BP reverses the inhibitory effect of metformin on hepatoma cell proliferation and glycolysis. Mechanistically, PFKFB3，a potent allosteric activator of PFK1, was markedly suppressed through inhibiting hypoxia-induced factor 1 (HIF-1α) accumulation mediated by metformin. SIGNIFICANCE: Taken together these data indicate that HIF-1α/PFKFB3/PFK1 regulatory axis is a vital determinant of glucose metabolic reprogramming in hepatocellular carcinoma, which gives new insights into the action of metformin in combatting liver cancer.

An anoxic-aerobic system for simultaneous biodegradation of phenol and ammonia in a sequencing batch reactor.

A laboratory-scale sequencing batch reactor (SBR) was investigated to treat artificial pretreated coal gasification wastewater that was mainly contained of ammonia and phenol. The efficiency of SBR fed with increasing phenol concentrations (from 150 to 300 mg l-1) and the relationship among phenol, nitrogen removal, and the microbial community structure were evaluated. When the phenol feeding concentration was increased to about 300 mg l-1, the removal efficiency was above 99.0%, demonstrating the robustness of phenol removal capacity. The study showed that most phenol was degraded in anoxic stage. The average removal efficiencies of ammonia and total nitrogen were 98.4 and 81.9%, respectively, with average NH4+-N concentration of 107.5 mg l-1 and COD/N 7.5. Low temperature caused sludge loss that led to the decreased performance. Increasing the temperature could not recover the performance effectively. The data from bacterial analysis revealed that Delftia, Hydrogenophaga, and unclassified Xanthomonadaceae played a significant role in phenol degradation before the temperature increase, while uncultured Syntrophococcus sp. and unclassified Rhodocyclaceae were responsible for phenol degradation after the temperature increase. These results imply that the SBR holds potential for the simultaneous removal of phenolic compounds and nitrogen through aerobic ammonia oxidation and anoxic denitrification with phenol as the co-organic carbon source.

Negative regulation of Sirtuin 1 by AMP-activated protein kinase promotes metformin-induced senescence in hepatocellular carcinoma xenografts.

Increasing evidence suggests that therapy-induced senescence (TIS), a novel therapeutic approach in which low doses of therapeutic drugs or radiation are used to induce senescence, suppresses tumor development. Our previous in vitro studies have demonstrated that a low dose of metformin promoted hepatoma cell senescence instead of apoptosis via activation of AMP-activated protein kinase (AMPK) and inactivation of Sirtuin 1 (SIRT1) deacetylase activity. However, the intricate relationship between AMPK and SIRT1, and how they cooperate to induce senescence remains elusive. We showed here that persistent exposure to a low concentration of metformin led to AMPK activation in a mouse xenograft model of human hepatocellular carcinoma (HCC), resulting in senescence. Intriguingly, AMPK counter-regulated SIRT1 via direct phosphorylation in metformin-mediated senescence in hepatoma cells. Taken together, these findings suggest that a low dose of metformin could potentially be used as a TIS-inducing therapeutic drug for HCC, and that this occurs by inducing senescence of HCC cells via the AMPK-SIRT1 pathway.