Evaluating DNA methylation and gene expression variability in the human term placenta

Obtaining representative samples from a term placenta for gene-expression studies is confounded by both within placental heterogeneity and sampling effects such as sample location and processing time. Epigenetic processes involved in the regulation of gene expression, such as DNA methylation, may show similar variability, but are less well studied. Therefore, we investigated the nature of within and between- placenta variation in gene expression and DNA methylation of genes that were chosen for being differentially expressed or methylated by cell type within the placenta.

METHODS

In total, two or more samples from each of 38 normal term placentae were utilized. The expression levels of CDH1, CDH11, ID2, PLAC1 and KISS1 were evaluated by real-time PCR. DNA methylation levels of LINE1 elements and CpGs within the promoter regions of KISS1, PTPN6, CASP8, and APC were similarly quantified by pyrosequencing.

RESULTS

Despite considerable sample-to-sample variability within each placenta, the within-placenta correlation for both gene expression and methylation was significant for each studied gene. Most of this variability was not due to sample location. However, between placental differences in gene expression were inflated by the dramatic effect of processing time (0-24 h) on mRNA levels, particularly for PLAC1 and KISS1 (both expressed in the apical syncytiotrophoblast). In contrast, DNA methylation levels remained relatively constant over this same time period.

CONCLUSION

Due to extensive site-to-site variability, multiple sampled sites are needed to accurately represent a placenta for molecular studies. Furthermore, mRNA quantitation of some genes may be hampered by its rapid degradation post-delivery (and possibly perinatally) and thus processing time should be considered in such analyses. Within-placenta correlations in expression and methylation from unrelated genes raise the possibility that methylation and expression variation may potentially reflect cell composition differences between samples rather than true differences occurring at the cellular level.

Prioritisation of associations between protein domains and complex diseases using domain-domain interaction networks

It is of vital importance to find genetic variants that underlie human complex diseases and locate genes that are responsible for these diseases. Since proteins are typically composed of several structural domains, it is reasonable to assume that harmful genetic variants may alter structures of protein domains, affect functions of proteins and eventually cause disorders. With this understanding, the authors explore the possibility of recovering associations between protein domains and complex diseases. The authors define associations between protein domains and disease families on the basis of associations between non-synonymous single nucleotide polymorphisms (nsSNPs) and complex diseases, similarities between diseases, and relations between proteins and domains. Based on a domain-domain interaction network, the authors propose a 'guilt-by-proximity' principle to rank candidate domains according to their average distance to a set of seed domains in the domain-domain interaction network. The authors validate the method through large-scale cross-validation experiments on simulated linkage intervals, random controls and the whole genome. Results show that areas under receiver operating characteristic curves (AUC scores) can be as high as 77.90%, and the mean rank ratios can be as low as 21.82%. The authors further offer a freely accessible web interface for a genome-wide landscape of associations between domains and disease families.

Preparation, characterization, adsorption kinetics and thermodynamics of novel magnetic chitosan enwrapping nanosized gamma-Fe2O3 and multi-walled carbon nanotubes with enhanced adsorption properties for methyl orange

A novel magnetic composite bioadsorbent composed of chitosan wrapping magnetic nanosized gamma-Fe(2)O(3) and multi-walled carbon nanotubes (m-CS/gamma-Fe(2)O(3)/MWCNTs) was prepared under relative mild conditions and was characterized. Adsorption of methyl orange (MO) onto m-CS/gamma-Fe(2)O(3)/MWCNTs was investigated with respect to pH, initial MO concentration, coexisting anions and temperature. Results of characterizations indicated that magnetic nanosized gamma-Fe(2)O(3) and MWCNTs have been wrapped by crosslinked chitosan. Introduction of MWCNTs could obviously increase the adsorption capacity (q(e)) of MO onto bioadsorbent by 2.2 times. Kinetics data and adsorption isotherm were better fitted by pseudo-second-order kinetic model and by Langmuir isotherm, respectively. Values of activation parameters such as free energy ( big up tri, openG degrees ), enthalpy ( big up tri, openH degrees ) and entropy (DeltaS degrees ) were determined as 3.15-3.78 kJ mol(-1), -9.94 kJ mol(-1) and -20.65 J mol(-1)k(-1), respectively, indicating that the adsorption was feasible, spontaneous and exothermic process in nature. After adsorption, m-CS/gamma-Fe(2)O(3)/MWCNTs could be effectively and fleetly separated by applying a magnetic field.

Genetic variation in glutathione metabolism and DNA repair genes predicts survival of small-cell lung cancer patients

BACKGROUND

Small-cell lung cancer (SCLC) carries the worst prognosis among lung cancer diagnoses. Combined radiation and chemotherapy is the standard of care; however, treatment outcomes vary. Variability in the rate at which chemotherapy agents are metabolized and in the capacity of repairing DNA damage has been hypothesized to be partly responsible for the treatment response variation. Genes in the glutathione metabolism and DNA repair pathways were tested through tag single-nucleotide polymorphisms (SNPs) to assess their association with survival in SCLC.

PATIENTS AND METHODS

Blood DNA from 248 patients with primary SCLC was genotyped for 419 tag SNPs from 49 genes in the glutathione and DNA repair pathways. Association analyses with patient survival were carried out at single-SNP, whole-gene, and haplotype levels after adjusting for age, gender, tumor stage, treatment modalities, and smoking history.

RESULTS

Among the 375 SNPs successfully genotyped, 21 SNPs, located on 11 genes, showed significant association with survival. Whole-gene analyses confirmed 3 of the 11 genes: GSS, ABCC2, and XRCC1. Haplotype analyses of these three genes identified haplotype combinations and genomic locations underlying the observed SNP associations.

CONCLUSION

Genetic variations in genes involved in the glutathione and DNA repair pathways are associated with SCLC survival.

Induction of tumoricidal activity in mouse peritoneal macrophages by ginseng polysaccharide

This study examined the effects of ginseng polysaccharide (GPS) on mouse peritoneal macrophage (PM)-mediated cytotoxicity towards K562, HL-60, or KG1alpha cells. GPS had no direct effect on killing of tumor cells. However, when mouse PMs were treated with GPS, cytotoxic activity against K562, HL-60, or KG1alpha cells was significantly induced. In addition, phagocytic activity was enhanced in GPS-treated mouse PMs compared to the control. The expressions of CD(68), ACP and alpha-ANE in mouse PMs were increased by the treatment with GPS. Moreover, the levels of cytokines, including tumor necrosis factor-alpha (TNF-alpha), interleukin-1 (IL-1), IL-6 were increased and the production of nitric oxide (NO) was enhanced. Taken together, these results suggest that GPS possess a potent antitumor activity by stimulating macrophage and a potentiality as an immunomodulator against diseases such as cancer.

Total saponins of Panax ginseng (TSPG) promote erythroid differentiation of human CD34+ cells via EpoR-mediated JAK2/STAT5 signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Total saponins of Panax ginseng (TSPG), main constituents extracted from Panax ginseng, a highly valued traditional Chinese medicine, have been shown to be an effective agent on hematopoiesis.

OBJECTIVE

To investigate the effect and mechanism underlying in which TSPG promote human CD34(+) hematopoietic stem and progenitor cells to differentiate into erythroid-lineage cells.

MATERIALS AND METHODS

The effect of TSPG on erythroid differentiation of purified CD34(+) cells derived from umbilical cord blood (UCB) was determined by methylcellulose assay system and colorimetry for hemoglobin content. The changes of EpoR expression in umbilical cord blood mononuclear cells (UCB-MNCs) and purified CD34(+) cells were detected with Western blotting and flow cytometry, respectively, and observed under laser scanning confocal microscope (LSCM). RT-PCR was performed to examine EpoR mRNA expression in CD34(+) cells. The effects of TSPG-pretreatment on Epo-induced JAK(2) and STAT(5) tyrosine phosphorylation were analyzed by immunoprecipitation.

RESULTS

The addition of TSPG (20-70 mg/L) increased the colony formation rate of BFU-E. TSPG (50 mg/L) alone used significantly increased the hemoglobin content, the addition of AG490 evidently reduced TSPG-induced elevation of hemoglobin content. TSPG increased the expression of EpoR on the surface membrane of CD34(+) cells but did not change the expression of EpoR in total UCB-MNCs. TSPG also increased the expression of EpoR mRNA in CD34(+) cells. TSPG markedly enhanced Epo-induced tyrosine phosphorylation of JAK(2) and STAT(5) in UCB-MNCs.

CONCLUSION

These findings suggest that TSPG may enhance the erythroid differentiation of hematopoietic stem and progenitor cells via Epo/EpoR-mediated JAK(2)/STAT(5) signaling pathway.