Hepatocellular Carcinoma Displays Distinct DNA Methylation Signatures with Potential as Clinical Predictors

Background

Hepatocellular carcinoma (HCC) is characterized by late detection and fast progression, and it is believed that epigenetic disruption may be the cause of its molecular and clinicopathological heterogeneity. A better understanding of the global deregulation of methylation states and how they correlate with disease progression will aid in the design of strategies for earlier detection and better therapeutic decisions.

Methods and Findings

We characterized the changes in promoter methylation in a series of 30 HCC tumors and their respective surrounding tissue and identified methylation signatures associated with major risk factors and clinical correlates. A wide panel of cancer-related gene promoters was analyzed using Illumina bead array technology, and CpG sites were then selected according to their ability to classify clinicopathological parameters. An independent series of HCC tumors and matched surrounding tissue was used for validation of the signatures. We were able to develop and validate a signature of methylation in HCC. This signature distinguished HCC from surrounding tissue and from other tumor types, and was independent of risk factors. However, aberrant methylation of an independent subset of promoters was associated with tumor progression and etiological risk factors (HBV or HCV infection and alcohol consumption). Interestingly, distinct methylation of an independent panel of gene promoters was strongly correlated with survival after cancer therapy.

Conclusion

Our study shows that HCC tumors exhibit specific DNA methylation signatures associated with major risk factors and tumor progression stage, with potential clinical applications in diagnosis and prognosis.     

Influence of ammonium and nitrate supply on growth,nitrate reductase activity and N-use efficiency in a natural hybrid pine and its parents

Aims Selection of tree species with a high capacity to assimilate N and efficiently utilize N resources would facilitate the success of initial tree seedling establishment in infertile soils. The preference for N forms was tested using three pine species (Pinus densata, Pinus tabuliformis and Pinus yunnanensis). Pinus densata is a natural diploid hybrid between P. tabuliformis and P. yunnanensis .Methods Seedlings of three pine species were supplied with nitrate-N, ammonium-N (at two different pH regimes) or combined ammonium and nitrate as a nitrogen source in perlite culture in a controlled environment.Important findings Seedlings of P. densata had higher total biomass and net photosynthesis when supplied with nitrate-N and ammonium nitrate than with ammonium-N. In parental species, total biomass and net photosynthesis for P. yunnanensis seedlings was higher in ammonium-N than in nitrate-N, whereas the other parental species P. tabuliformis had the highest total biomass among species for all treatments except ammonium with CaCO 3. Most morphological traits in P. densata seedlings were intermediate between its two parental species. However, N-use efficiency and photosynthetic N-use efficiency of P. densata significantly exceeded both parents when supplied with nitrate-N and ammonium nitrate. The results suggested that the diploid hybrid tree species P. densata has a preference for nitrate and is not well adapted to ammonium-N as a sole nitrogen source regardless of the growth medium pH. Based on changes in environmental conditions, such as predicted future temperature increases in high altitude areas associated with climate change, P. densata is likely to be increasingly competitive and have wide adaptation in high altitude regions.     

Supramolecular organization of photosynthetic membrane proteins in the chlorosome-containing bacterium Chloroflexus aurantiacus

The arrangement of core antenna complexes (B808-866-RC) in the cytoplasmic membrane of filamentous phototrophic bacterium Chloroflexus aurantiacus was studied by electron microscopy in cultures from different light conditions. A typical nearest-neighbor center-to-center distance of ~18 nm was found, implying less protein crowding compared to membranes of purple bacteria. A mean RC:chlorosome ratio of 11 was estimated for the occupancy of the membrane directly underneath each chlorosome, based on analysis of chlorosome dimensions and core complex distribution. Also presented are results of single-particle analysis of core complexes embedded in the native membrane.     

DNA Methylation Characteristics of Primary Melanomas with Distinct Biological Behaviour

In melanoma, the presence of promoter related hypermethylation has previously been reported, however, no methylation-based distinction has been drawn among the diverse melanoma subtypes. Here, we investigated DNA methylation changes associated with melanoma progression and links between methylation patterns and other types of somatic alterations, including the most frequent mutations and DNA copy number changes. Our results revealed that the methylome, presenting in early stage samples and associated with the BRAF^V600E mutation, gradually decreased in the medium and late stages of the disease. An inverse relationship among the other predefined groups and promoter methylation was also revealed except for histologic subtype, whereas the more aggressive, nodular subtype melanomas exhibited hypermethylation as well. The Breslow thickness, which is a continuous variable, allowed for the most precise insight into how promoter methylation decreases from stage to stage. Integrating our methylation results with a high-throughput copy number alteration dataset, local correlations were detected in the MYB and EYA4 genes. With regard to the effects of DNA hypermethylation on melanoma patients'' survival, correcting for clinical cofounders, only the KIT gene was associated with a lower overall survival rate. In this study, we demonstrate the strong influence of promoter localized DNA methylation changes on melanoma initiation and show how hypermethylation decreases in melanomas associated with less favourable clinical outcomes. Furthermore, we establish the methylation pattern as part of an integrated apparatus of somatic DNA alterations.     

The analogs of oxytocin and D-homoarginine vasopressin with bulky substituted phenylalanine in position 2

Solid phase technique on p-methylbenzhydrylamine resin wasused for the synthesis of eight analogs of oxytocin and 8-D-homoarginine vasopressin with the non-coded amino acids L- or D-2,3,4,5,6-pentamethylphenylalanine and L- or D-4-phenylphenylalanine in position 2. The preparation of theabove mentioned non-coded amino acids is described as well.All eight analogs were found to be potent inhibitors ofoxytocin activity in the uterotonic in vitro test in theabsence of Mg²⁺ ions. In the uterotonic test invitro in the presence of Mg²⁺ and in the test invivo, their potency is strongly decreased or completelyabolished. The substances are also weak pressor inhibitors.The L or D configuration does not seem to influence theactivity significantly.     

Chickpea facilitates phosphorus uptake by intercropped wheat from an organic phosphorus source

Pot experiments were conducted to investigate interspecific complementation in utilization of phytate and FePO₄ by plants in the wheat (Triticum aestivum L.)/chickpea (Cicer arietinum L.) intercropping under sterile and non-sterile conditions. The pots were separated into two compartments by either a solid root barrier to eliminate root contact and solute movement, by a nylon mesh (30 M) to prevent root contact but permit solute exchange, or not separated between the compartments. Wheat plants were grown in one compartment and chickpea in the other. Two P sources were tested at 60 mg P kg^–1 soil (sodium phytate or FePO₄). Under non-sterile conditions, the biomass of wheat was significantly greater when the roots were intermingled with chickpea than when the roots were separated from chickpea roots by a solid root barrier or nylon mesh. When phytate–P was applied, P concentrations in wheat (2.9 g kg^–1 in shoots and 1.4 g kg^–1 in roots) without root barrier between the two species were higher than those in the treatments with nylon mesh or with the solid root barrier separation (1.9 g kg^–1 in shoots and 1.0 g kg^–1 in roots). In contrast, P concentrations in wheat supplied with FePO₄ were similar between the root separation treatments. There was no significant difference in P uptake by chickpea between the P sources or between the root separation treatments, except that P uptake was greater in the phytate treatment with the root barrier. Total P uptake from phytate was increased by 25% without root separation compared to the root separation treatments. Under sterile conditions and supply of phytate–P, the biomass of wheat was doubled when the roots were intermingled with chickpea and increased by a third with the nylon mesh separation compared to that with the solid root barrier. Biomass production in wheat at various treatments correlated with P concentration in shoot. Biomass production and P concentration in chickpea were unaffected by root separation. Total P uptake by plants was 68% greater with root intermingling and 37% greater with nylon mesh separation than that with the solid root barrier. The results suggest that chickpea roots facilitate P utilization from the organic P by wheat.     

Pigment configuration in the light-harvesting protein of the xanthophyte alga <Emphasis Type="Italic">Xanthonema debile</Emphasis>

Proper biogenesis and maintenance of photosynthetic thylakoid membrane complexes are essential for the photosynthetic light reactions. A thylakoid lumenal protein, Psb27, plays a vital role in assembly or/and maintenance of photosystem II (PSII). In cyanobacteria, it is a small lipoprotein docked to the lumenal side of PSII, and functions in the assembly of the Mn₄Ca cluster and in the PSII repair cycle. However, Psb27 from Arabidopsis thaliana is not a lipoprotein, and it is involved in PSII repair and acclimation to fluctuating light stress, suggesting a functional divergence between Arabidopsis Psb27 and cyanobacterial Psb27s. To gain a better understanding of Psb27 from higher plants, we determined the crystal structure of Arabidopsis Psb27 by X-ray crystallography at a resolution of 1.85 Å. The structure of Arabidopsis Psb27 is a four-helix bundle, similar to its orthologues from cyanobacteria. However, there are several structural differences between Arabidopsis Psb27 and cyanobacterial Psb27s concerning the overall molecular shape, the N- and C-terminal structures, and the surface charge. These differences suggest that Psb27 from higher plants and cyanobacteria may function differently.     

Sulfhydryl groups in root-cell plasma membranes of wheat genotypes differing in Zn efficiency

Sulfhydryl groups were quantified in root-cell plasma membranes of two genotypes of wheat ( Triticum aestivum cv. Warigal and T. turgidum conv. durum cv. Durati) differing in Zn efficiency. Smaller amounts of 5,5'-dithio-bis(2-nitrobenzoic acid)-reactive sulfhydryl groups were found in Zn-deficient than in Zn-sufficient roots; and also in Zn-inefficient genotype Durati compared to Zn-efficient Warigal, regardless of Zn supply. Upon transfer of 15-day-old Zn-deficient plants into solutions containing various Zn²⁺ activities, a Zn-dependent increase in the amount of reactive sulfhydryl groups was evident in roots of both genotypes, but occurred only in Warigal when 20-day-old plants were used, indicating irreversible physiological damage in Durati plants due to prolonged Zn deficiency. Upon transfer into solutions of increasing Zn²⁺ activities, the increase in total Zn concentration in roots was about an order of magnitude smaller than the increase in amounts of reactive sulfhydryl groups in the roots of both genotypes, suggesting that, in wheat roots, a relatively small amount of Zn is required for preventing oxidation of sulfhydryl groups into disulfides. The amount of reactive sulfhydryl groups in the roots is positively related to Zn efficiency of wheat genotypes and may be one of the mechanisms that, under conditions of Zn deficiency, allow better growth and productivity of Zn-efficient genotypes in comparison to Zninefficient ones.