Inhibition of histone-deacetylase activity by short-chain fatty acids and some polyphenol metabolites formed in the colon

Colorectal cancer is the most abundant cause of cancer mortality in the Western world. Nutrition and the microbial flora are considered to have a marked influence on the risk of colorectal cancer, the formation of butyrate and other short-chain fatty acids (SCFAs) possibly playing a major role as chemopreventive products of microbial fermentation in the colon. In this study, we investigated the effects of butyrate, other SCFAs, and of a number of phenolic SCFA and trans-cinnamic acid derivatives formed during the intestinal degradation of polyphenolic constituents of fruits and vegetables on global histone deacetylase (HDAC) activity in nuclear extracts from colon carcinoma cell cultures using tert-butoxycarbonyl-lysine (acetylated)-4-amino-7-methylcoumarin (Boc-Lys(Ac)-AMC) as substrate. Inhibition of HDAC activity, e.g., by butyrate, is related to a suppression of malignant transformation and a stimulation of apoptosis of precancerous colonic cells. In nuclear extracts from HT-29 human colon carcinoma cells, butyrate was found to be the most potent HDAC inhibitor (IC(50)=0.09 mM), while other SCFAs such as propionate were less potent. In the same assay, p-coumaric acid (IC(50)=0.19 mM), 3-(4-OH-phenyl)-propionate (IC(50)=0.62 mM) and caffeic acid (IC(50)=0.85 mM) were the most potent HDAC inhibitors among the polyphenol metabolites tested. Interestingly, butyrate was also the most potent HDAC inhibitor in a whole-cell HeLa Mad 38-based reporter gene assay, while all polyphenol metabolites and all other SCFAs tested were much less potent; some were completely inactive. The findings suggest that butyrate plays an outstanding role as endogenous HDAC inhibitor in the colon, and that other SCFAs and HDAC-inhibitory polyphenol metabolites present in the colon seem to play a much smaller role, probably because of their limited levels, their marked cytotoxicity and/or their limited intracellular availability.     

Protein and energy value of vinasse for pigs

A vinasse, originating as the condensed molasses residue from the microbial production of citric acid, was chemically analyzed and given to growing pigs to determine its protein and energy value. It contained, per kg dry matter (62.6%), 185 g crude protein, 538 g N-free extracts, 48 g total sugar, 277 g ash and 12.8 MJ gross energy. Ammonia, betaine and amino acids (about half glutamic acid) accounted for 3.5, 9.1 and 28.6%, respectively, of the crude-protein N. In a 25-day balance trial with the final 10 days as collection period, ten pigs initially weighing 33 kg were pair-fed daily an average of about 1 kg of dry matter of either a basal diet (95% ground barley plus 5% cellulose) or of a mixed diet composed of, on dry basis, 77% basal diet plus 23% vinasse. Partial digestibility of components in the vinasse was: organic matter, 52%; crude protein, 45%; N-free extract, 58%; ash, 83%; and gross energy, 42%. Average daily gain and N retention were not different between dietary groups. The vinasse contained, per kg dry matter, 5.40 MJ DE and 3.61 MJ ME compared with 14.96 MJ DE and 14.48 MJ ME for the dry basal diet. The conclusion is that this vinasse, according to its low protein and energy value, can provide only a small percentage of the daily ration for pigs.     

A role for ABIL3 in plant cell morphogenesis

Actin nucleation facilitated by the ARP2/3 complex plays a central role in plant cell shape development. The molecular characterization of the distorted class of trichome mutants has recently revealed the SCAR/WAVE complex as an essential upstream activator of ARP2/3 function in plants. The SCAR/WAVE complex is conserved from animals to plants and, generally, is composed of the five subunits SCAR/WAVE, PIR121, NAP125, BRICK and ABI. In plants, four of the five subunits have been shown to participate in trichome and pavement morphogenesis. Plant ABI‐like proteins (ABIL), however, which constitute a small four‐member protein family in Arabidopsis thaliana, have not been characterized functionally, so far. Here we demonstrate that microRNA knock‐down of the ABIL3 gene leads to a distorted trichome phenotype reminiscent of ARP2/3 mutant phenotypes and consistent with a crucial role of the ABIL3 protein in an ARP2/3‐activating SCAR/WAVE complex. In contrast to ARP2/3 mutants, however, the ABIL3 knock‐down stimulated cell elongation in the root, indicating distinct functions of the ABIL3 protein in different tissues. Furthermore, we provide evidence that ABIL3 associates with microtubules in vivo, opening up the intriguing possibility that ABI‐like proteins have a function in linking SCAR/WAVE‐dependent actin nucleation with organization of the microtubule cytoskeleton.     

Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas

Background

Renal oncocytomas (ROs) are benign epithelial tumors of the kidney whereas chromophobe renal cell carcinoma (chRCCs) are malignant renal tumors. The latter constitute 5–7% of renal neoplasias. ROs and chRCCs show pronounced molecular and histological similarities, which renders their differentiation demanding. We aimed for the differential proteome profiling of ROs and early-stage chRCCs in order to better understand distinguishing protein patterns.

Methods

We employed formalin-fixed, paraffin-embedded samples (six RO cases, six chRCC cases) together with isotopic triplex dimethylation and a pooled reference standard to enable cohort-wide quantitative comparison. For lysosomal-associated membrane protein 1 (LAMP1) and integrin alpha-V (ITGAV) we performed corroborative immunohistochemistry (IHC) in an extended cohort of 42 RO cases and 31 chRCC cases.

Results

At 1% false discovery rate, we identified?>?3900 proteins, of which?>?2400 proteins were consistently quantified in at least four RO and four chRCC cases. The proteomic expression profiling discriminated ROs and chRCCs and highlighted established features such as accumulation of mitochondrial proteins in ROs together with emphasizing the accumulation of endo-lysosomal proteins in chRCCs. In line with the proteomic data, IHC showed enrichment of LAMP1 in chRCC and of ITGAV in RO.

Conclusion

We present one of the first differential proteome profiling studies on ROs and chRCCs and highlight differential abundance of LAMP1 and ITGAV in these renal tumors.

     

Blm10 binds to pre-activated proteasome core particles with open gate conformation

Blm10 is bound to the yeast proteasome core particle, a crucial protease of eukaryotic cells [corrected]. Two gates, at both ends of the CP, control the access of protein substrates to the catalytic cavity of the CP. Normally, substrate access is auto-inhibited by a closed gate conformation unless regulatory complexes are bound to the CP and translocate protein substrates in an ATP-dependent manner. Here, we provide evidence that Blm10 recognizes pre-activated open gate CPs, which are assumed to exist in an equilibrium with inactive closed gate CP. Consequently, single-capped Blm10-CP shows peptide hydrolysis activity. Under conditions of disturbed CP assembly, as well as in open gate mutants, pre-activated CP or constitutively active CP, respectively, prevail. Then, Blm10 sequesters disordered and open gate CP by forming double-capped Blm10(2)-CP in which peptide hydrolysis activity is repressed. We conclude that Blm10 distinguishes between gate conformations and regulates the activation of CP.     

Sex-specific aspects of tumor therapy

There is increasing evidence that sex-specific differences in toxicity profiles and outcome after radiotherapy are accumulating in medical oncology, and that treatment strategies may require some modification. Furthermore, sex-specific differences in the sensitivity to genotoxic and therapeutical agents are also of general concern for risk estimation. This review is focussed on the specific influence of sex on these endpoints covering both a clinical and a biological point of view. In this paper, the literature was systematically reviewed with respect to sex-specific differences in tumor and normal tissue sensitivity after exposure to ionizing radiation, as well as to the relevant underlying molecular and cellular mechanisms. Although a number of data on sex-specific differences are available and remarkable differences on clinical, molecular, and cellular levels have been reported, a firm conclusion on any existing sex-specific differences is not yet possible. Future studies are required and should be focussed on this aspect of individual radiosensitivity.     

A Bayesian Network View on Nested Effects Models

Nested effects models (NEMs) are a class of probabilistic models that were designed to reconstruct a hidden signalling structure from a large set of observable effects caused by active interventions into the signalling pathway. We give a more flexible formulation of NEMs in the language of Bayesian networks. Our framework constitutes a natural generalization of the original NEM model, since it explicitly states the assumptions that are tacitly underlying the original version. Our approach gives rise to new learning methods for NEMs, which have been implemented in the /Bioconductor package nem. We validate these methods in a simulation study and apply them to a synthetic lethality dataset in yeast.