Isolation and characterisation of DNA cytosine 5-methyltransferase from human placenta

DNA cytosine 5-methyltransferase has been extensively purified (about 2600-fold) from the soft tissue of human placenta by chromatography on DEAE-cellulose and hydroxyapatite, and by an affinity step on agarose-immobilized S-adenosylhomocysteine. The isolated enzyme has a molecular weight of 135000 and methylates DNA from various sources in native and heat-denatured forms. The synthetic copolymer poly(dG-dC)·poly(dG-dC) is methylated in B- and Z-conformation to about the same extent. DNA containing hemimethylated sites was isolated from P815 cells grown in the presence of 5-azacytidine. This P815 DNA was used to measure the ‘maintenance’ DNA methylase activity, whereas 5-methylcytosine-free procaryotic DNA served as a substrate for the ‘de novo’ DNA methylase activity in our enzyme preparation. The crude extract as well as the highly purified DNA methylase are capable of transferring methyl groups to these two types of substrate. The fact that both types of activity co-chromatograph during the isolation procedure suggests that one enzyme molecule may exercise both the ‘maintenance’ and ‘de novo’ activity.     

Improved reporting of DNA methylation data derived from studies of the human placenta

Epigenetic variation is increasingly hypothesized as a mechanism underlying the effect of the in utero environment on long-term postnatal health; however, there is currently little clear data to support this in humans. A number of biological and technical factors provide challenges for the design of clinical epigenetic studies: from the type of cells or tissues that are available to the large range of predicted confounders that may impact findings. The human placenta, in addition to other neonatal tissues and whole blood, is commonly sampled for the study of epigenetic modifications. However there is little conformity for the most appropriate methods for study design, data analysis, and importantly, data interpretation. Here we present general recommendations for the reporting of DNA methylation in biological samples, with specific focus on the placenta. We outline key guidelines for: (1) placental sampling, (2) data analysis and presentation, and (3) interpretation of DNA methylation data. We emphasize the need to consider methodological noise, increase statistical power and to ensure appropriate adjustment for biological covariates. Finally, we highlight that epigenetic changes may be non-pathological and not necessarily translate into disease-associated changes. Improved reporting of DNA methylation data will be critical to identify epigenetic-based effects and to better understand the full phenotypic impact of these widely-reported epigenomic changes.     

Complex roles of CpG in liposomal delivery of DNA and oligonucleotides

Unmethylated CpG in bacterial DNA has recently been recognized as a danger signal to the mammalian immune system. This CpG signal can be greatly amplified when DNA is delivered via a lipidic vector. The CpG effects are affected by the administration route, and can be either beneficial or harmful. In this review, we will summarize our current understanding about the mechanism of action of the immunostimulatory motifs. Emphasis will be placed on the discussion of the complicated roles of CpG when CpG DNA or oligonucleotides are administered in vivo using liposomes as a delivery vehicle.     

增加CpG基元的汉坦病毒核蛋白基因疫苗的免疫作用

以往的研究表明非甲基化胞嘧啶鸟嘌呤二核苷酸为基元构成的特定结构是一种很有希望的候选疫苗佐剂。为了研究增加CpG基元的汉坦病毒核蛋白基因疫苗的免疫作用,在本实验中,将重组真核表达质粒 pcDNA3.1 S(ISS)直接肌注免疫BALB/c 小鼠,分别用ELISA法检测血清特异性抗体的变化,MTT法检测 T细胞增殖反应,以及用ELISA kit检测免疫鼠脾细胞上清液中细胞因子IL 4和IFN γ的动态变化,从而了解免疫鼠的体液免疫反应和细胞免疫反应。结果显示 pcDNA3.1 S(ISS)接种组的小鼠血清抗体水平、T细胞增殖反应以及细胞因子IFN γ的产生水平较对照组 pcDNA3.1 S和空载体 pcDNA3.1 接种组的要高。而细胞因子 IL 4 较对照组却无明显变化。由此可见,增加CpG基元的质粒能够增强其所诱导的免疫反应,可用于那些需要借助强有力细胞免疫来清除病原体的疫苗研制中。     

Differentiation of trophoblast lineage is associated with DNA methylation and demethylation.

Our previous study has shown that the placenta and kidney had different genomic methylation patterns regarding CpG island loci detected by restriction landmark genomic scanning (RLGS). To investigate whether differentiation involves changes in DNA methylation, we analyzed the rat Rcho-1 cell line, which retains trophoblast cell features and differentiates from stem cells into trophoblast giant cells in vitro. By RLGS, a total of 1,232 spots were identified in the Rcho-1 stem and differentiated giant cells. Four spots (0.3%) were detected only in giant cells, implying that the loci were originally methylated, but became demethylated during differentiation. Another four spots (0.3%) were detected only in stem cells, implying that these loci, originally unmethylated, became methylated during differentiation. DNAs from three loci that became methylated during differentiation were cloned and sequenced. All showed high homologies with expressed sequence tags (ESTs) or with genomic DNA of other species, suggesting that these loci are biologically important. Thus, the eight differentially methylated loci should be good tools to study epigenetic modification specific to differentiation of trophoblast giant cells.     

Molecular approaches for the detection and identification of bifidobacteria and lactobacilli in the human gastrointestinal tract

In this review an overview of various molecular techniques and their application for the detection and identification of bifidobacteria and lactobacilli in the gastrointestinal (GI) tract is presented. The techniques include molecular typing techniques such as amplified ribosomal DNA restriction analysis (ARDRA), randomly amplified polymorphic DNA (RAPD), pulsed field gel electrophoresis (PFGE), ribotyping and community profiling techniques such as PCR coupled to temperature and denaturing gradient gel electrophoresis (PCR-TGGE and PCR-DGGE, respectively). Special attention is given to oligonucleotide probes and primers that target the ribosomal RNA (rRNA) sequences and their use in PCR and different hybridisation techniques such as DNA microarrays and fluorescent in situ hybridisation (FISH). In addition, recent findings based on the molecular studies of bifidobacteria and lactobacilli in the GI-tract are reviewed.     

DNA adducts in human placenta exposed to ambient environment and passive cigarette smoke during pregnancy

BACKGROUND: The risk of human diseases and abnormal development under the relatively reduced toxic environmental exposure conditions of passive cigarette smoke and urban pollution is emerging as significant. To assess the genotoxic potential of such exposure, we analyzed the DNA adducts of polynuclear aromatic hydrocarbons (PAH), a proven marker of genotoxicity, in human placental DNA samples of pregnancies monitored for passive cigarette smoke exposure. METHODS: Maternal exposure to active and passive cigarette smoke was evaluated by verbal disclosure and urinary nicotine and cotinine measurements. PAH-DNA adducts were assayed by ELISA using a polyclonal antibody against benzo[alpha]pyrene-diol-epoxide-DNA in placental DNA. Birth weights of infants were recorded in these monitored pregnancies. RESULTS: Urinary nicotine and cotinine values were reduced in the passive smoke-exposed group compared to smokers and similar to those in the nonsmoker ambient exposure group. PAH-DNA and nicotine/cotinine values were not correlated with birth weight of the infant. PAH-DNA adducts were present in approximately 25% of samples exposed to passive cigarette smoke and ambient environment. CONCLUSIONS: The study has revealed that a subpopulation of humans is predisposed to accumulating PAH adducts independent of high levels of PAH sources (e.g., maternal cigarette smoke exposure). Because DNA adducts promote genomic changes, it is likely that this subpopulation is susceptible to diverse changes in the genome that may influence human development.     

免疫佐剂CpG DNA的研究进展

CpG DNA存在广泛的免疫效应,其免疫效应有赖于DNA中的模体,同时具有种属特异性和细胞特异性。CpG DNA的作用机制目前还不很清楚,但此方面的研究导致了许多新的发现,目前CpG DNA已有了多方面的应用。     

三种细菌DNA及CpG寡核苷酸抗肿瘤免疫的比较实验研究

用大肠埃希菌、铜绿假单胞菌和双歧杆菌的DNA与CpG寡聚核苷酸 (CpGoligodeoxynucleotides ,CpGODN)对荷瘤鼠进行治疗 ,比较 3种细菌DNA及CpGODN的抗肿瘤免疫作用 ,以筛选最好的细菌DNA及CpG序列用于肿瘤治疗。分别提取 3种细菌DNA并合成 2条CpGODN序列 ,在肝癌HcaFA3细胞株荷瘤小鼠模型上进行免疫治疗 ,以存活期、抑瘤率、NK/Mφ细胞活性及细胞因子 (IFN γ、TNF α、IL 2、IL 12等 )分泌活性等为指标 ,比较 3种细菌DNA之间及CpGODN的抗肿瘤免疫效果。 3种细菌DNA均能使荷瘤鼠的存活期延长 1倍以上 ,但三者之间无显著性差异 (P >0 .0 5 )。抑瘤率为 6 4 .0 3%～ 79.5 0 % (P <0 .0 1) ,而CpGODN的抑瘤率为 4 5 %～ 5 1%之间 (P <0 .0 5 ) ,3种细菌DNA以及CpGODN均能显著增强NK细胞和Mφ细胞的杀伤活性 (P <0 .0 5 ) ,但细菌DNA在诱导细胞因子 (IL 2、IFN、TNF等 )以及下调肿瘤细胞端粒酶活性方面 ,CpGODN作用强于细菌DNA。     

Utilisation of enterobacterial repetitive intergenic consensus (ERIC) sequence-based PCR to fingerprint the genomes of Bifidobacterium isolates and other probiotic bacteria

Enterobacterial repetitive intergenic consensus based on PCR (ERIC-PCR) was used to generate DNA fingerprints for bifidobacteria and other probiotic bacteria. Two primers (ERIC 1R and ERIC 2) used in ERIC-PCR revealed that all of the probiotic bacteria tested possess enterobacterial repetitive intergenic consensus sequences with the PCR products ranging from 250 bp to 5000 bp. The bacterial strains can be differentiated by comparing fingerprint patterns. The dendrogram of the fingerprints revealed that most of the bifidobacterial wild type strains fell into one cluster at similarity level of approximately 79%.     

AMP-deaminase from human term placenta

AMP-deaminase from human term placenta was chromatographed on a phosphocellulose column and physico-chemical and immunological properties of the purified enzyme were investigated. At physiological pH7.0, in the absence of regulatory ligands (control conditions) studied AMP-deaminase manifested sigmoid-shaped substrate saturation kinetics, with half-saturation parameter (S_0.5) value of about 7 mM. Addition of important allosteric effectors (ATP, ADP or orthophosphate) modified kinetic properties of studied AMP-deaminase, influencing mainly the value of S_0.5 parameter. Micromolar concentrations of stearylo-CoA inhibited potently the enzyme making it no longer sensitive towards 1 mM ATP-induced activation. SDS-PAGE electrophoresis of the purified enzyme revealed presence of 68 kDa protein fragment, reacting with anti-(human) liver AMP-deaminase antibodies. Experimental results presented indicate that liver type of AMP-deaminase is an enzyme form present in human term placenta.     

Characterization of the Cell-Bound Polysaccharides of Bifidobacterium adolescentis 94 BIM

The cell-bound polysaccharides (PSs) of Bifidobacterium adolescentis 94 BIM were stripped from the cell surface with 2% sodium dodecyl sulfate (SDS), 1.5% Cetavlon, and 1% Triton X-100 and purified by precipitation with 5 volumes of ethanol. According to the extraction conditions used, the polysaccharide preparations were designated as PS-SDS-6°C, PS-SDS-100°C, PS-Cet, and PS-Trit. The gel-permeation chromatography of the first two preparations with the use of a Bio-Gel P-10 column and 1% acetic acid as the eluant yielded two peaks, F1 and F2, which contained carbohydrates and no phosphorus. All polysaccharides were primarily composed of glucose and galactose. The polysaccharides PS-Cet and PS-Trit were found to be branched and contain glucose residues at the terminal position, position 4, and position 6, and galactose residue at position 3. PS-SDS-6°C has a glucose residue at position 4.     

Identification method based on PCR combined with automated ribotyping for tracking probiotic Lactobacillus strains colonizing the human gut and vagina

AIMS: A molecular methodology based on PCR-associated automated ribotyping was developed to specifically detect the Lactobacillus strains of two probiotic products (an orally administered lyophilized preparation and vaginal tablets) in human faeces and vaginal swabs. METHODS AND RESULTS: The 16S-23S rDNA sequences and the ribotype profiles of the probiotic lactobacilli were characterized and new species-specific primer sets were designed. The identification of faecal and vaginal lactobacilli isolated from subjects administered with the probiotic products was performed by using PCR with species-specific primers followed by strain-specific automated ribotyping. CONCLUSIONS: The PCR-ribotyping identification allowed to study the colonization patterns of the probiotic lactobacilli in the human gut and vagina evidencing the strains with the best survival capability. SIGNIFICANCE AND IMPACT OF THE STUDY: The proposed molecular method represents a powerful tool of strain-specific identification, useful for differentiating exogenous from indigenous strains in any microbial ecosystem and for rationally choosing probiotic bacteria with the best chance of survival in the host.     

The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors

The placenta relies on phenotypes that are characteristic of cancer to successfully implant the embryo in the uterus during early pregnancy. Notably, it has to invade its host tissues, promote angiogenesis—while surviving hypoxia—, and escape the immune system. Similarities in DNA methylation patterns between the placenta and cancers suggest that common epigenetic mechanisms may be involved in regulating these behaviors. We show here that megabase-scale patterns of hypomethylation distinguish first from third trimester chorionic villi in the placenta, and that these patterns mirror those that distinguish many tumors from corresponding normal tissues. We confirmed these findings in villous cytotrophoblasts isolated from the placenta and identified a time window at the end of the first trimester, when these cells come into contact with maternal blood, as the likely time period for the methylome alterations. Furthermore, the large genomic regions affected by these patterns of hypomethylation encompass genes involved in pathways related to epithelial-mesenchymal transition, immune response, and inflammation. Analyses of expression profiles corresponding to genes in these hypomethylated regions in colon adenocarcinoma tumors point to networks of differentially expressed genes previously implicated in carcinogenesis and placentogenesis, where nuclear factor kappa B is a key hub. Taken together, our results suggest the existence of epigenetic switches involving large-scale changes of methylation in the placenta during pregnancy and in tumors during neoplastic transformation. The characterization of such epigenetic switches might lead to the identification of biomarkers and drug targets in oncology as well as in obstetrics and gynecology.     

Characterization of the folate receptor in human molar placenta

We have characterized a high-affinity folate receptor in human molar placenta tissue. Radioligand binding exhibited characteristics typical of other high-affinity folate binding proteins. Those included, positive cooperativity, a tendency to increased binding affinity with decreasing receptor concentration, a slow ligand dissociation at pH 7.4 becoming rapid at pH 3.5, and inhibition by folate analogues. The folate receptor cross-reacted with antibodies against human milk folate binding protein, e.g. the syncytothrophoblastic layer of molar placenta tissue sections showed strongly positive immunostaining. The gel filtration profile contained two radioligand-bound peaks (25 and 100 kDa), however, with considerable overlap. Only a single band of 70 kDa was seen on SDS-PAGE immunoblotting. The folate receptor in placental tissue may play a crucial role in the transfer of folate from maternal circulation to the fetus.     

Regions of variable DNA methylation in human placenta associated with newborn neurobehavior

The placenta regulates the in utero environment and functionally impacts fetal development. Candidate gene studies identified variation in placental DNA methylation is associated with newborn neurologic and behavioral outcomes including movement quality, lethargic behavior, attention, and arousal. We sought to identify novel regions of variable DNA methylation associated with newborn attention, lethargy, quality of movement, and arousal by performing an epigenome-wide association study in 335 infants from a US birth cohort. Methylation status was quantified using the Illumina HumanMethylation450 BeadChip array and associations to newborn outcomes assessed by the NICU Network Neurobehavioral Scales (NNNS) were identified while incorporating established bioinformatics algorithms to control for confounding by cell type composition. Methylation of CpGs within FHIT (cg15970800) and ANKRD11 (cg16710656) demonstrated genome-wide significance (P < 1.8 × 10^?7) in specific associations with infant attention. CpGs whose differential methylation was associated with all 4 neurobehavioral outcomes were common to 50 genes involved in biological processes relating to cellular adhesion and nervous system development. Comprehensive methylation profiling identified relationships between methylation of FHIT and ANKRD11, which have been previously linked to neurodevelopment and behavioral outcomes in genetic association studies. Subtle changes in DNA methylation of these genes within the placenta may impact normal variation of a newborn's ability to alter and track visual and auditory stimuli. Gene ontology analysis suggested that those genes with variable methylation related to these outcomes are over-represented in biological pathways involved in brain development and placental physiology, supportive of our hypothesis for a key role of the placenta in neurobehavioral outcomes.     

Monitoring and survival of Lactobacillus gasseri SBT2055 in the human intestinal tract

The monitoring and survival of Lactobacillus gasseri SBT2055 in the human intestinal tract was investigated with seven healthy subjects having a low number of fecal lactobacilli. An increase of fecal lactobacilli (10(3.2-5.2) CFU/g feces) was recognized after ingestion of yogurt with SBT2055 by the subjects. A high positive rate of L. gasseri in fecal lactobacilli detected from the subjects (over 70% at 2nd weeks of feeding) was also observed during the ingestion period using the species-specific PCR system. These findings indicate that the SBT2055 strain in yogurt survived in the human intestinal tract and was recovered from human feces.     

Birthweight is associated with DNA promoter methylation of the glucocorticoid receptor in human placenta

Birthweight has been associated with a number of health outcomes throughout life. Crucial to proper infant growth and development is the placenta, and alterations to placental gene function may reflect differences in the intrauterine environment which functionally contribute to infant growth and may ultimately affect the child’s health. To examine if epigenetic alteration to the glucocorticoid receptor (GR) gene was linked to infant growth, we analyzed 480 human placentas for differential methylation of the GR gene exon 1F and examined how this variation in methylation extent was associated with fetal growth. Multivariable linear regression revealed a significant association (p &lt; 0.0001) between differential methylation of the GR gene and large for gestational age (LGA) status. Our work is one of the first to link infant growth as a measure of the intrauterine environment and epigenetic alterations to the GR and suggests that DNA methylation may be a critical determinant of placental function.