Structure of the Catalytic Domain of EZH2 Reveals Conformational Plasticity in Cofactor and Substrate Binding Sites and Explains Oncogenic Mutations

Polycomb repressive complex 2 (PRC2) is an important regulator of cellular differentiation and cell type identity. Overexpression or activating mutations of EZH2, the catalytic component of the PRC2 complex, are linked to hyper-trimethylation of lysine 27 of histone H3 (H3K27me3) in many cancers. Potent EZH2 inhibitors that reduce levels of H3K27me3 kill mutant lymphoma cells and are efficacious in a mouse xenograft model of malignant rhabdoid tumors. Unlike most SET domain methyltransferases, EZH2 requires PRC2 components, SUZ12 and EED, for activity, but the mechanism by which catalysis is promoted in the PRC2 complex is unknown. We solved the 2.0 Å crystal structure of the EZH2 methyltransferase domain revealing that most of the canonical structural features of SET domain methyltransferase structures are conserved. The site of methyl transfer is in a catalytically competent state, and the structure clarifies the structural mechanism underlying oncogenic hyper-trimethylation of H3K27 in tumors harboring mutations at Y641 or A677. On the other hand, the I-SET and post-SET domains occupy atypical positions relative to the core SET domain resulting in incomplete formation of the cofactor binding site and occlusion of the substrate binding groove. A novel CXC domain N-terminal to the SET domain may contribute to the apparent inactive conformation. We propose that protein interactions within the PRC2 complex modulate the trajectory of the post-SET and I-SET domains of EZH2 in favor of a catalytically competent conformation.     

The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

Background

Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes.

Methodology/Principal Findings

We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes.

Conclusion

The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.     

Ginsenoside Rg-1 Protects Retinal Pigment Epithelium (RPE) Cells from Cobalt Chloride (CoCl2) and Hypoxia Assaults

Severe retinal ischemia causes persistent visual impairments in eye diseases. Retinal pigment epithelium (RPE) cells are located near the choroidal capillaries, and are easily affected by ischemic or hypoxia. Ginsenoside Rg-1 has shown significant neuroprotective effects. This study was performed to test the cytoprotective effect of ginsenoside Rg-1 in RPE cells against hypoxia and cobalt chloride (CoCl₂) assaults, and to understand the underlying mechanisms. We found that Rg-1 pre-administration significantly inhibited CoCl₂- and hypoxia-induced RPE cell death and apoptosis. Reactive oxygen specisis (ROS)-dependent p38 and c-Jun NH(2)-terminal kinases (JNK) MAPK activation was required for CoCl₂-induced RPE cell death, and Rg-1 pre-treatment significantly inhibited ROS production and following p38/JNK activation. Further, CoCl₂ suppressed pro-survival mTOR complex 1 (mTORC1) activation in RPE cells through activating of AMP-activated protein kinase (AMPK), while Rg-1 restored mTORC1 activity through inhibiting AMPK activation. CoCl₂-induced AMPK activation was also dependent on ROS production, and anti-oxidant N-acetylcysteine (NAC) prevented AMPK activation and RPE cell death by CoCl₂. Our results indicated that Rg-1 could be further investigated as a novel cell-protective agent for retinal ischemia.     

A Functional Variant rs1820453 in YAP1 and Breast Cancer Risk in Chinese Population

Background

To investigate the association between rs1820453 which located in the promoter region of yes-associated protein 1 (YAP1) gene and breast cancer (BC) risk.

Method and Findings

We conducted a hospital-based case-control study including a total of 480 BC cases and 545 cancer-free controls in Chinese population. Then the expression quantitative trait locus (e-QTL) analysis was performed to explore the possible function of rs1820453 to the YAP1 gene expression. The association between rs1820453 and BC risk was significantly identified with the odds ratio (OR) was 1.27 (95 % confidence interval (CI) =1.03-1.57) under allelic model when adjusted by age and menopausal status. In addition, the correlation analysis of rs1820453 and YAP1 expression level found that this variant was significantly associated with the gene expression in Chinese population. When compared with level of mRNA expression of the AA genotype (6.011±0.046), the mRNA expression level in CC genotype (5.903±0.026) was statistically lower (P=0.024).

Conclusion

The results from this study suggested that rs1820453 A>C change may affect the gene expression and contribute to the risk of developing BC in Chinese population though larger sample-size studies along with functional experiments were anticipated to warrant the results.     

Prevalence and Trends of the Abdominal Aortic Aneurysms Epidemic in General Population - A Meta-Analysis

Objective

To conduct a meta-analysis assessing the prevalence and trends of the abdominal aortic aneurysms (AAA) epidemic in general population.

Method

Studies that reported prevalence rates of AAA from the general population were identified through MEDLINE, EMBASE, Web of Science, and reference lists for the period between 1988 and 2013. Studies were included if they reported prevalence rates of AAA in general population from the community. In stratified analyses possible sources of bias, including areas difference, age, gender and diameter of aneurysms were examined. Publication bias was assessed with Egger''s test method.

Results

56 studies were identified. The overall pooled prevalence of AAA was 4.8% (4.3%, 5.3%). Stratified analyses showed the following results, areas difference: America 2.2% (2.2%, 2.2%), Europe 2.5% (2.4%, 2.5%), Australia 6.7% (6.5%, 7.0%), Asia 0.5% (0.3%, 0.7%); gender difference: male 6.0% (5.3%, 6.7%), female 1.6% (1.2%, 1.9%); age difference: 55–64years 1.3% (1.2%, 1.5%), 65–74 years 2.8% (2.7%, 2.9%), 75–84 years1.2%(1.1%, 1.3%), ≥85years0.6% (0.4%, 0.7%); aortic diameters difference: 30–39 mm, 3.3% (2.8%, 3.9%), 40–49 mm,0.7% (0.4%,1.0%), ≥50 mm, 0.4% (0.3%, 0.5%). The prevalence of AAA has decreased in Europe from 1988 to 2013. Hypertension, smoking, coronary artery disease, dyslipidemia, respiratory disease, cerebrovascular disease, claudication and renal insufficiency were risk factors for AAA in Europe.

Conclusion

AAA is common in general population. The prevalence of AAA is higher in Australia than America and Europe. The pooled prevalence in western countries is higher than the Asia. Future research requires a larger database on the epidemiology of AAA in general population.     

Acute Toxicity of Intravenously Administered Titanium Dioxide Nanoparticles in Mice

Background

With a wide range of applications, titanium dioxide (TiO₂) nanoparticles (NPs) are manufactured worldwide in large quantities. Recently, in the field of nanomedicine, intravenous injection of TiO₂ nanoparticulate carriers directly into the bloodstream has raised public concerns on their toxicity to humans.

Methods

In this study, mice were injected intravenously with a single dose of TiO₂ NPs at varying dose levels (0, 140, 300, 645, or 1387 mg/kg). Animal mortality, blood biochemistry, hematology, genotoxicity and histopathology were investigated 14 days after treatment.

Results

Death of mice in the highest dose (1387 mg/kg) group was observed at day two after TiO₂ NPs injection. At day 7, acute toxicity symptoms, such as decreased physical activity and decreased intake of food and water, were observed in the highest dose group. Hematological analysis and the micronucleus test showed no significant acute hematological or genetic toxicity except an increase in the white blood cell (WBC) count among mice 645 mg/kg dose group. However, the spleen of the mice showed significantly higher tissue weight/body weight (BW) coefficients, and lower liver and kidney coefficients in the TiO₂ NPs treated mice compared to control. The biochemical parameters and histological tissue sections indicated that TiO₂ NPs treatment could induce different degrees of damage in the brain, lung, spleen, liver and kidneys. However, no pathological effects were observed in the heart in TiO₂ NPs treated mice.

Conclusions

Intravenous injection of TiO₂ NPs at high doses in mice could cause acute toxicity effects in the brain, lung, spleen, liver, and kidney. No significant hematological or genetic toxicity was observed.     

Investigation of the binding network of IGF-I on the cavity surface of IGFBP4

Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employed to study the interaction mechanism of IGFBP4 and IGF-I by molecular dynamics (MD) simulation. In IGF-I, residues Gly7 to Asp12 were found to be the hot spots and they mainly anchored on the N-domain of IGFBP4. The contact area, the shape and size of protein, the surroundings of the binding site, the hydrophobic and electrostatic interaction between the two proteins worked as a complex network to regulate the protein-protein interaction. It was also found that the unfolding of the helix was not inevitable in the mutant, and it could be regulated by careful selection of the substituted amino acid.

Epigenetic alterations in folate transport genes in placental tissue from fetuses with neural tube defects and in leukocytes from subjects with hyperhomocysteinemia

The objectives of this study were to identify tissue-specific differentially methylated regions (T-DMR’s) in the folate transport genes in placental tissue compared with leukocytes, and from placental tissues obtained from normal infants or with neural tube defects (NTDs). Using pyrosequencing, we developed methylation assays for the CpG islands (CGIs) and the CGI shore regions of the folate receptor α (FOLR1), proton-coupled folate transporter (PCFT) and reduced folate carrier 1 (RFC1) genes. The T-DMRs differed in location for each gene and the difference in methylation ranged between 2 and 54%. A higher T-DMR methylated fraction was associated with a lower mRNA level of the FOLR1 and RFC1 genes. Methylation fractions differed according to RFC1 80G > A genotype in the NTD cases and in leukocytes from subjects with high total plasma homocysteine (tHcy). There were no differences in methylated fraction of folate transporter genes between NTD cases and controls. We suggest that T-DMRs participate in the regulation of expression of the FOLR1 and RFC1 genes, that the RFC1 80G > A polymorphism exerts a gene-nutrition interaction on DNA methylation in the RFC1 gene, and that this interaction appears to be most prominent in NTD-affected births and in subjects with high tHcy concentrations.