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.

The role of secondary cytoreductive surgery for recurrent mucinous epithelial ovarian cancer (mEOC)

BACKGROUND

Mucinous epithelial ovarian cancer (mEOC) may exhibit a distinct biological behavior in epithelial ovarian cancer (EOC). The role of secondary cytoreductive surgery was evaluated in patients with recurrent mEOC, and the prognosis was assessed.

METHODS

Twenty-one patients with stages IIc to IV mEOC who experienced disease recurrence and received secondary cytoreductive surgery at Fudan University Cancer Hospital between Jan. 1997 and Dec. 2005 were retrospectively reviewed. Survival curves were generated using the Kaplan-Meier method and the significant comparison of survival rate was estimated by the log-rank test.

RESULTS

The median progression-free interval (PFI) was 14 months (range, 5-46 months) after the first cytoreduction. Seven patients (33%) who received secondary cytoreductive surgery were optimally cytoreduced with residual disease less than or equal 1cm, and the other 14 patients (67%) underwent suboptimal surgical cytoreduction. The overall median survival time was 27 months (range, 8-64 months). The median survival time after recurrence was 10 months (range, 3-32 months). There was no significant statistical difference in median survival between patients with optimal and suboptimal secondary surgical cytoreduction, with an estimated survival of 10 months and 9.8 months, respectively (P>0.05).

CONCLUSION

Optimal primary cytoreductive surgery for advanced mEOC was very important. Once it recurs, the prognosis is very poor. Patients with recurrent mEOC should be carefully assessed before performing secondary cytoreductive surgery, as this may have limited impact on the overall survival rates.

Downregulation of Wnt2 and beta-catenin by siRNA suppresses malignant glioma cell growth

Increasing evidence suggests that aberrant activation of Wnt signaling is involved in tumor development and progression. Our earlier study on gene expression profile in human gliomas by microarray found that some members of Wnt family were overexpressed. To further investigate the involvement of Wnt signaling in gliomas, the expression of core components of Wnt signaling cascade in 45 astrocytic glioma specimens with different tumor grades was examined by reverse transcription-PCR and immunohistochemistry. Wnt2, Wnt5a, frizzled2 and beta-catenin were overexpressed in gliomas. Knockdown of Wnt2 and its key mediator beta-catenin in the canonical Wnt pathway by siRNA in human U251 glioma cells inhibited cell proliferation and invasive ability, and induced apoptotic cell death. Furthermore, treating the nude mice carrying established subcutaneous U251 gliomas with siRNA targeting Wnt2 and beta-catenin intratumorally also delayed the tumor growth. In both in vitro and in vivo studies, downregulation of Wnt2 and beta-catenin was associated with the decrease of PI3K/p-AKT expression, indicating the interplay between Wnt/beta-catenin and PI3K/AKT signaling cascades. In conclusion, the canonical Wnt pathway is of critical importance in the gliomagenesis and intervention of this pathway may provide a new therapeutic approach for malignant gliomas.

Tailored regimen of interferon alpha for HBeAg-positive chronic hepatitis B: a prospective controlled study

The response to interferon-alpha treatment of patients with chronic hepatitis B under the current protocol is not satisfactory. The aim of this study was to try an alternative approach to improve treatment outcome. Of 374 HBeAg-positive patients, 127 of them received 5 million units of interferon-alpha thrice weekly for 6 months and constituted the control group, while 247 in the study group received the same dosage but the duration of treatment was tailored. The study protocol provided for continuation of treatment if HBV DNA levels were continuously decreasing. The treatment ended when viral, antigenic and biochemical endpoints were reached or when HBV DNA levels were no longer decreasing. The median length of tailored treatment was 10 (range 6-24) months. The end-of-treatment response rates were 39.3% and 23.6% (P = 0.002), and after 12-month, follow-up, the sustained response rates were 40.5% and 28.3% (P = 0.013) in the study and control groups, respectively. Excluding the patients who dropped out, 228 and 115 completed a median of 40- and 44-month-long follow-up; the long-term response was thus 45.3% and 33.1% (P = 0.014) in the respective groups. Interferon-alpha treatment tailored in length demonstrated significantly increased efficacy in patients with chronic hepatitis B.