Integrated epigenome profiling of repressive histone modifications, DNA methylation and gene expression in normal and malignant urothelial cells

Epigenetic regulation of gene expression is commonly altered in human cancer. We have observed alterations of DNA methylation and microRNA expression that reflect the biology of bladder cancer. This common disease arises by distinct pathways with low and high-grade differentiation. We hypothesized that epigenetic gene regulation reflects an interaction between histone and DNA modifications, and differences between normal and malignant urothelial cells represent carcinogenic events within bladder cancer. To test this we profiled two repressive histone modifications (H3K9m3 and H3K27m3) using ChIP-Seq, cytosine methylation using MeDIP and mRNA expression in normal and malignant urothelial cell lines. In genes with low expression we identified H3K27m3 and DNA methylation each in 20-30% of genes and both marks in 5% of genes. H3K9m3 was detected in 5-10% of genes but was not associated with overall expression. DNA methylation was more closely related to gene expression in malignant than normal cells. H3K27m3 was the epigenetic mark most specifically correlated to gene silencing. Our data suggest that urothelial carcinogenesis is accompanied by a loss of control of both DNA methylation and H3k27 methylation. From our observations we identified a panel of genes with cancer specific-epigenetic mediated aberrant expression including those with reported carcinogenic functions and members potentially mediating a positive epigenetic feedback loop. Pathway enrichment analysis revealed genes marked by H3K9m3 were involved with cell homeostasis, those marked by H3K27m3 mediated pro-carcinogenic processes and those marked with cytosine methylation were mixed in function. In 150 normal and malignant urothelial samples, our gene panel correctly estimated expression in 65% of its members. Hierarchical clustering revealed that this gene panel stratified samples according to the presence and phenotype of bladder cancer.     

Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma

Background

Uterine leiomyomas, or fibroids, represent the most common benign tumor of the female reproductive tract. Fibroids become symptomatic in 30% of all women and up to 70% of African American women of reproductive age. Epigenetic dysregulation of individual genes has been demonstrated in leiomyoma cells; however, the in vivo genome-wide distribution of such epigenetic abnormalities remains unknown.

Principal Findings

We characterized and compared genome-wide DNA methylation and mRNA expression profiles in uterine leiomyoma and matched adjacent normal myometrial tissues from 18 African American women. We found 55 genes with differential promoter methylation and concominant differences in mRNA expression in uterine leiomyoma versus normal myometrium. Eighty percent of the identified genes showed an inverse relationship between DNA methylation status and mRNA expression in uterine leiomyoma tissues, and the majority of genes (62%) displayed hypermethylation associated with gene silencing. We selected three genes, the known tumor suppressors KLF11, DLEC1, and KRT19 and verified promoter hypermethylation, mRNA repression and protein expression using bisulfite sequencing, real-time PCR and western blot. Incubation of primary leiomyoma smooth muscle cells with a DNA methyltransferase inhibitor restored KLF11, DLEC1 and KRT19 mRNA levels.

Conclusions

These results suggest a possible functional role of promoter DNA methylation-mediated gene silencing in the pathogenesis of uterine leiomyoma in African American women.     

The therapeutic effect of memantine through the stimulation of synapse formation and dendritic spine maturation in autism and fragile X syndrome

Although the pathogenic mechanisms that underlie autism are not well understood, there is evidence showing that metabotropic and ionotropic glutamate receptors are hyper-stimulated and the GABAergic system is hypo-stimulated in autism. Memantine is an uncompetitive antagonist of NMDA receptors and is widely prescribed for treatment of Alzheimer's disease treatment. Recently, it has been shown to improve language function, social behavior, and self-stimulatory behaviors of some autistic subjects. However the mechanism by which memantine exerts its effect remains to be elucidated. In this study, we used cultured cerebellar granule cells (CGCs) from Fmr1 knockout (KO) mice, a mouse model for fragile X syndrome (FXS) and syndromic autism, to examine the effects of memantine on dendritic spine development and synapse formation. Our results show that the maturation of dendritic spines is delayed in Fmr1-KO CGCs. We also detected reduced excitatory synapse formation in Fmr1-KO CGCs. Memantine treatment of Fmr1-KO CGCs promoted cell adhesion properties. Memantine also stimulated the development of mushroom-shaped mature dendritic spines and restored dendritic spine to normal levels in Fmr1-KO CGCs. Furthermore, we demonstrated that memantine treatment promoted synapse formation and restored the excitatory synapses to a normal range in Fmr1-KO CGCs. These findings suggest that memantine may exert its therapeutic capacity through a stimulatory effect on dendritic spine maturation and excitatory synapse formation, as well as promoting adhesion of CGCs.     

Identification of new autoantigens for primary biliary cirrhosis using human proteome microarrays

Primary biliary cirrhosis (PBC) is a chronic cholestatic liver disease of unknown etiology and is considered to be an autoimmune disease. Autoantibodies are important tools for accurate diagnosis of PBC. Here, we employed serum profiling analysis using a human proteome microarray composed of about 17,000 full-length unique proteins and identified 23 proteins that correlated with PBC. To validate these results, we fabricated a PBC-focused microarray with 21 of these newly identified candidates and nine additional known PBC antigens. By screening the PBC microarrays with additional cohorts of 191 PBC patients and 321 controls (43 autoimmune hepatitis, 55 hepatitis B virus, 31 hepatitis C virus, 48 rheumatoid arthritis, 45 systematic lupus erythematosus, 49 systemic sclerosis, and 50 healthy), six proteins were confirmed as novel PBC autoantigens with high sensitivities and specificities, including hexokinase-1 (isoforms I and II), Kelch-like protein 7, Kelch-like protein 12, zinc finger and BTB domain-containing protein 2, and eukaryotic translation initiation factor 2C, subunit 1. To facilitate clinical diagnosis, we developed ELISA for Kelch-like protein 12 and zinc finger and BTB domain-containing protein 2 and tested large cohorts (297 PBC and 637 control sera) to confirm the sensitivities and specificities observed in the microarray-based assays. In conclusion, our research showed that a strategy using high content protein microarray combined with a smaller but more focused protein microarray can effectively identify and validate novel PBC-specific autoantigens and has the capacity to be translated to clinical diagnosis by means of an ELISA-based method.     

陕北风沙区不同植被覆盖下的土壤养分特征

选取了陕北定边县板凳滩风沙区四种典型植被覆盖下的风沙土壤,对其基本养分含量进行了测定。分析不同类型植被覆盖下的土壤养分含量特征、土壤养分含量层次特征以及土壤各层次养分含量之间的相关性,为风沙区土壤生态恢复重建及侵蚀土壤质量的恢复保育提供了科学依据。结果表明:(1)不同植被覆盖下的土壤对有机质、全氮、速效氮、速效磷的保持能力均为:小蒿草>羊草>沙蒿>苦豆子>无植被;对全磷的保持能力,各植被覆盖条件下差异不显著,但小蒿草覆盖下含量最高,羊草最低,且低于无植被;从土壤对全钾的保持能力来看,羊草覆盖下的全钾含量最高,小蒿草最低。(2)不同植被覆盖下的土壤养分含量层次变化除全磷和全钾变化微弱外,土壤有机质、全氮、速效氮、速效磷、速效钾含量均随着土层深度的增加而逐渐下降,且降低速度基本呈现出小蒿草>羊草>沙蒿>苦豆子>无植被。(3)不同植被覆盖下的土壤各层次养分含量之间的相关性以羊草最为密切,大体呈显著中度及以上正相关;沙蒿和苦豆子覆盖下的相关性稍弱,基本呈中度正相关;而小蒿草覆盖下的相关系数正负均有,相关性较为复杂。     

Monitoring pesticide resistance of Tetranychus cinnabarinus in Kunming' s flower regions

采用玻片浸渍法测定了昆明地区花卉朱砂叶螨Tetranychus cinnabarinus (Boisduval)对阿维菌素、甲氨基阿维菌素苯甲酸盐、溴虫腈、丁醚脲、炔螨特和哒螨灵的抗性.结果表明,昆明北郊和呈贡地区玫瑰上的朱砂叶螨雌成螨对阿维菌素与甲氨基阿维菌素苯甲酸盐产生了极高的抗药性,阿维菌素对2个地区的朱砂叶螨的LC50分别为40.25 mg·L -1和19.67 mg·L-1,相对毒力指数分别为敏感品系的2 441.08倍和1 192.86倍;甲氨基阿维菌素苯甲酸盐对其LC50分别为118.18 mg·L-1和9.24 mg·L-1,相对毒力指数是敏感品系的2 805.73倍和219.35倍.昆明北郊的朱砂叶螨对溴虫腈的相对毒力指数是敏感品系的2 371.40倍,呈贡和晋宁分别为162.01倍和173.38倍.丁醚脲对北郊、呈贡和晋宁朱砂叶螨的LC50分别为244.58 mg·L-1、385.41 mg·L-1和54.93 mg·L-1,相对毒力指数在3.01倍～21.10倍之间.北郊、呈贡和晋宁的朱砂叶螨种群对炔螨特和哒螨灵的LC50分别为155.39 mg·L-1、424.49 mg·L-1和62.70 mg·L-1,其相对毒力指数是敏感品系的6.45倍、17.63倍和2.60倍.朱砂叶螨对药剂抗药性水平趋势从高到低为:阿维菌素、甲氨基阿维菌素苯甲酸盐＞溴虫腈、丁醚脲＞炔螨特、哒螨灵,抗性最高的地区为昆明北郊,晋宁相对较低.     

Functions and Characteristics of Whey Protein in Sports Nutrition

乳清蛋白是牛乳中一类营养价值较高的优质蛋白,必需氨基酸种类齐全,组成模式与人体相似,并含有丰富的支链氨基酸和多种生物活性物质,能够提高机体的抗氧化能力,增强机体免疫力,促进骨骼肌蛋白质的合成,抑制肌肉蛋白分解,加速训练后体能的恢复,对于运动人群而言,是补充优质蛋白的良好来源.本文就合理的补充乳清蛋白对缓解运动性疲劳、提高运动能力的研究进展进行了综述.