Breast Cancer DNA Methylation Profiles Are Associated with Tumor Size and Alcohol and Folate Intake

Although tumor size and lymph node involvement are the current cornerstones of breast cancer prognosis, they have not been extensively explored in relation to tumor methylation attributes in conjunction with other tumor and patient dietary and hormonal characteristics. Using primary breast tumors from 162 (AJCC stage I–IV) women from the Kaiser Division of Research Pathways Study and the Illumina GoldenGate methylation bead-array platform, we measured 1,413 autosomal CpG loci associated with 773 cancer-related genes and validated select CpG loci with Sequenom EpiTYPER. Tumor grade, size, estrogen and progesterone receptor status, and triple negative status were significantly (Q-values <0.05) associated with altered methylation of 209, 74, 183, 69, and 130 loci, respectively. Unsupervised clustering, using a recursively partitioned mixture model (RPMM), of all autosomal CpG loci revealed eight distinct methylation classes. Methylation class membership was significantly associated with patient race (P<0.02) and tumor size (P<0.001) in univariate tests. Using multinomial logistic regression to adjust for potential confounders, patient age and tumor size, as well as known disease risk factors of alcohol intake and total dietary folate, were all significantly (P<0.0001) associated with methylation class membership. Breast cancer prognostic characteristics and risk-related exposures appear to be associated with gene-specific tumor methylation, as well as overall methylation patterns.     

Towards quantitative assays with peptide chips: a surface engineering approach

The development of peptide and protein microarrays has created enormous opportunities in biomedical research. Current chip-based assays are well suited for identifying candidate protein or enzyme activities but still require conventional solution phase experiments to validate hits. Here, three surface-engineering strategies for microarray design are described and are illustrated in the development of a peptide chip for the quantitative analysis of kinase activity on solid support. These strategies promise to widen the application of microarrays by permitting the evaluation of hits in a chip-based format.     

Decorticate, decerebrate and opisthotonic posturing and seizures in Kenyan children with cerebral malaria

Background

Intermittent preventive treatment of malaria during pregnancy (IPTp) is a key intervention in the national strategy for malaria control in Tanzania. SP, the current drug of choice, is recommended to be administered in the second and third trimesters of pregnancy during antenatal care (ANC) visits. To allow for a proper design of planned scaling up of IPT services in Tanzania it is useful to understand the IPTp strategy's acceptability to health managers, ANC service providers and pregnant women. This study assesses the knowledge, attitudes and practices of these groups in relation to malaria control with emphasis on IPTp services.

Methods

The study was conducted in February 2004, in Korogwe District, Tanzania. It involved in-depth interviews with the district medical officer (DMO), district hospital medical officer in charge and relevant health service staff at two peripheral dispensaries, and separate focus group discussions (FGDs) with district Council Health Management Team members at district level and pregnant women at dispensary and community levels.

Results

Knowledge of malaria risks during pregnancy was high among pregnant women although some women did not associate coma and convulsions with malaria. Contacting traditional healers and self-medication with local herbs for malaria management was reported to be common. Pregnant women and ANC staff were generally aware of SP as the drug recommended for IPTp, albeit some nurses and the majority of pregnant women expressed concern about the use of SP during pregnancy. Some pregnant women testified that sometimes ANC staff allow the women to swallow SP tablets at home which gives a room for some women to throw away SP tablets after leaving the clinic. The DMO was sceptical about health workers' compliance with the direct observed therapy in administering SP for IPTp due to a shortage of clean water and cups at ANC clinics. Intensified sensitization of pregnant women about the benefits of IPTp was suggested by the study participants as an important approach for improving IPTp compliance.

Conclusion

The successful implementation of the IPTp strategy in Tanzania depends on the proper planning of, and support to, the training of health staff and sustained sensitization of pregnant women at health facility and community levels about the benefits of IPTp for the women and their unborn babies.     

Breast reconstruction with abdominal flaps after abdominoplasties.

After the reported safe transverse rectus abdominis myocutaneous (TRAM) flap after liposuction of the abdomen, two cases of bipedicled reconstruction with this flap after abdominoplasty were successfully performed. This operation has not previously been considered possible because of the transection of the perforator arteries during the undermining of the abdomen. To examine the possible reperfusion of the perforator arteries, the authors studied the perforator arteries of 10 patients before they underwent abdominoplasty and at 1 week, 3 months, and 6 months after the operation. The arteries were studied with color-duplex scanning and power Doppler, using 10-MHz superficial probes, and their position was marked on a map. A cadaver study of a woman who had had an abdominoplasty 10 years before her death is also presented. In every patient, reperfusion of all perforator arteries was documented, starting from the control at 1 month. In no case was the caliber of the reperfused vessels more than 40 percent of the original diameter (maximum: 0.53 mm). This was also confirmed by the cadaver study. In conclusion, after an abdominoplasty operation, constant reperfusion of the perforator arteries of the rectus muscles occurs. However, the diameter of the arteries may not be enough to provide the necessary blood supply for a TRAM flap, which is therefore strongly discouraged by the authors after abdominoplasty in favor of a vertical rectus abdominis muscle (VRAM) flap. A liposuction, which does not necessarily disrupt the perforators, is not an absolute contraindication for a TRAM flap, provided that an accurate color-duplex scanning study is done.     

A novel approach to the discovery of survival biomarkers in glioblastoma using a joint analysis of DNA methylation and gene expression

Glioblastoma multiforme (GBM) is the most aggressive of all brain tumors, with a median survival of less than 1.5 years. Recently, epigenetic alterations were found to play key roles in both glioma genesis and clinical outcome, demonstrating the need to integrate genetic and epigenetic data in predictive models. To enhance current models through discovery of novel predictive biomarkers, we employed a genome-wide, agnostic strategy to specifically capture both methylation-directed changes in gene expression and alternative associations of DNA methylation with disease survival in glioma. Human GBM-associated DNA methylation, gene expression, IDH1 mutation status, and survival data were obtained from The Cancer Genome Atlas. DNA methylation loci and expression probes were paired by gene, and their subsequent association with survival was determined by applying an accelerated failure time model to previously published alternative and expression-based association equations. Significant associations were seen in 27 unique methylation/expression pairs with expression-based, alternative, and combinatorial associations observed (10, 13, and 4 pairs, respectively). The majority of the predictive DNA methylation loci were located within CpG islands, and all but three of the locus pairs were negatively correlated with survival. This finding suggests that for most loci, methylation/expression pairs are inversely related, consistent with methylation-associated gene regulatory action. Our results indicate that changes in DNA methylation are associated with altered survival outcome through both coordinated changes in gene expression and alternative mechanisms. Furthermore, our approach offers an alternative method of biomarker discovery using a priori gene pairing and precise targeting to identify novel sites for locus-specific therapeutic intervention.     

Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures

We investigated DNA methylomes of pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large inter-compartmental backbones. The deviations were exaggerated in lamina-associated domains, with differences corresponding to methylation clusters and/or cytogenetic groups. Our data also suggested a pivotal role of polycomb and CTBP2 in de novo methylation, which may be traced back to bivalency status of embryonic stem cells. Driven by these potent epigenetic modulations, suppression of polycomb target genes was observed along with disruption of developmental fate and cell cycle and mismatch repair pathways and altered activities of key upstream regulators.     

Impact of rainfall manipulations and biotic controls on soil respiration in Mediterranean and desert ecosystems along an aridity gradient

Spatially heterogeneous ecosystems form a majority of land types in the vast drylands of the globe. To evaluate climate‐change effects on CO₂ fluxes in such ecosystems, it is critical to understand the relative responses of each ecosystem component (microsite). We investigated soil respiration (R_s) at four sites along an aridity gradient (90–780 mm mean annual precipitation, MAP) during almost 2 years. In addition, R_s was measured in rainfall manipulations plots at the two central sites where ～30% droughting and ～30% water supplementation treatments were used over 5 years. Annual R_s was higher by 23% under shrub canopies compared with herbaceous gaps between shrubs, but R_s at both microsites responded similarly to rainfall reduction. Decreasing precipitation and soil water content along the aridity gradient and across rainfall manipulations resulted in a progressive decline in R_s at both microsites, i.e. the drier the conditions, the larger was the effect of reduction in water availability on R_s. Annual R_s on the ecosystem scale decreased at a slope of 256/MAP g C m^?2 yr^?1 mm^?1 (r²=0.97). The reduction in R_s amounted to 77% along the aridity gradient and to 16% across rainfall manipulations. Soil organic carbon (SOC) decreased with declining precipitation, and variation in SOC stocks explained 77% of the variation in annual R_s across sites, rainfall manipulations and microsites. This study shows that rainfall manipulations over several years are a useful tool for experimentally predicting climate‐change effects on CO₂ fluxes for time scales (such as approximated by aridity gradients) that are beyond common research periods. Rainfall reduction decreases rates of R_s not only by lowering biological activity, but also by drastically reducing shrub cover. We postulate that future climate change in heterogeneous ecosystems, such as Mediterranean and deserts shrublands will have a major impact on R_s by feedbacks through changes in vegetation structure.