Proteomics of colorectal cancer: Overview of discovery studies and identification of commonly identified cancer-associated proteins and candidate CRC serum markers

Colorectal cancer (CRC) is a common cause of cancer-related mortality in the developed world. Improved methods for early detection and disease management are urgently needed. Many efforts in the past 5 years have been devoted to protein biomarker discovery for early detection of CRC. Here, we discuss identity-based studies employing tandem mass spectrometry that analyzed clinical material as well as model systems. Through meta-analysis we provide a list of CRC-associated tissue proteins discovered in multiple studies, with the greater majority being 2D gel-based discoveries coupled to MS/MS. So far only a limited number of CRC-associated proteins have been validated in serum for non-invasive testing for CRC. This list includes several intracellular and nuclear proteins that a priori would not have been considered candidate biomarkers based on their predicted subcellular localization. Finally, we highlight promising new directions that combine targeted analyses of subcellular proteomes, like the cell surface, secretome, exosome, and nuclear matrix, with nanoLC-MS/MS-based proteomics. We anticipate that in the near future, these novel mass spectrometry-based in-depth approaches will uncover many novel, specific CRC marker candidates in clinical tissues and that their targeted validation with multi-reaction monitoring MS will speed up development of non-invasive tests in feces and serum/plasma.     

Identifying object categories from event-related EEG: toward decoding of conceptual representations

Multivariate pattern analysis is a technique that allows the decoding of conceptual information such as the semantic category of a perceived object from neuroimaging data. Impressive single-trial classification results have been reported in studies that used fMRI. Here, we investigate the possibility to identify conceptual representations from event-related EEG based on the presentation of an object in different modalities: its spoken name, its visual representation and its written name. We used Bayesian logistic regression with a multivariate Laplace prior for classification. Marked differences in classification performance were observed for the tested modalities. Highest accuracies (89% correctly classified trials) were attained when classifying object drawings. In auditory and orthographical modalities, results were lower though still significant for some subjects. The employed classification method allowed for a precise temporal localization of the features that contributed to the performance of the classifier for three modalities. These findings could help to further understand the mechanisms underlying conceptual representations. The study also provides a first step towards the use of concept decoding in the context of real-time brain-computer interface applications.     

Synaesthetic Colour in the Brain: Beyond Colour Areas. A Functional Magnetic Resonance Imaging Study of Synaesthetes and Matched Controls

Background

In synaesthesia, sensations in a particular modality cause additional experiences in a second, unstimulated modality (e.g., letters elicit colour). Understanding how synaesthesia is mediated in the brain can help to understand normal processes of perceptual awareness and multisensory integration. In several neuroimaging studies, enhanced brain activity for grapheme-colour synaesthesia has been found in ventral-occipital areas that are also involved in real colour processing. Our question was whether the neural correlates of synaesthetically induced colour and real colour experience are truly shared.

Methodology/Principal Findings

First, in a free viewing functional magnetic resonance imaging (fMRI) experiment, we located main effects of synaesthesia in left superior parietal lobule and in colour related areas. In the left superior parietal lobe, individual differences between synaesthetes (projector-associator distinction) also influenced brain activity, confirming the importance of the left superior parietal lobe for synaesthesia. Next, we applied a repetition suppression paradigm in fMRI, in which a decrease in the BOLD (blood-oxygenated-level-dependent) response is generally observed for repeated stimuli. We hypothesized that synaesthetically induced colours would lead to a reduction in BOLD response for subsequently presented real colours, if the neural correlates were overlapping. We did find BOLD suppression effects induced by synaesthesia, but not within the colour areas.

Conclusions/Significance

Because synaesthetically induced colours were not able to suppress BOLD effects for real colour, we conclude that the neural correlates of synaesthetic colour experience and real colour experience are not fully shared. We propose that synaesthetic colour experiences are mediated by higher-order visual pathways that lie beyond the scope of classical, ventral-occipital visual areas. Feedback from these areas, in which the left parietal cortex is likely to play an important role, may induce V4 activation and the percept of synaesthetic colour.     

Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues

Background: Altered nuclear and genomic structure and function are hallmarks of cancer cells. Research into nuclear proteins in human tissues could uncover novel molecular processes in cancer. Here, we examine biochemical tissue fractions containing chromatin-binding (CB) proteins in the context of colorectal cancer (CRC) progression. Methods: CB protein-containing fractions were biochemically extracted from human colorectal tissues, including carcinomas with chromosomal instability (CIN), carcinomas with microsatellite instability (MIN), and adenomas. The CB proteins were subjected to label-free LC–MS/MS and the data were analyzed by bioinformatics. Results: Over 1700 proteins were identified in the CB fraction from colonic tissues, including 938 proteins associated with nuclear annotation. Of the latter, 169 proteins were differential between adenomas and carcinomas. In this adenoma-versus-carcinoma comparison, apart from specific changes in components of the splicing and protein translational machineries, we also identified significant changes in several proteins associated with chromatin-directed functions. Furthermore, several key cell cycle proteins as well as those involved in cellular stress were increased, whereas specific components of chromosome segregation and DNA recombination/repair systems were decreased. Conclusions: Our study identifies proteomic changes at the subnuclear level that are associated with CRC and may be further investigated. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.     

Copper affects the enzymes of the ascorbate-glutathione cycle and its related metabolites in the roots of Phaseolus vulgaris

The involvement of the ascorbate-glutathione cycle in the defence against Cu-induced oxidative stress was studied in the roots of Phaseolus vulgaris L. cv. Limburgse vroege. All the enzymes of this cycle [ascorbate peroxidase (APOD), EC 1.11.1.11; monodehydroascorbate reductase (MDHAR), EC 1.6.5.4; dehydroascorbate reductase (DHAR), EC 1.8.5.1; glutathione reductase (GR), EC 1.6.4.2] were increased, and the total ascorbate and glutathione pools rose after a 15 μ M root Cu treatment. In the first hours after the start of the experiment, the accumulation of dehydroascorbate (DHA), formed as a result of a Cu-mediated direct oxidation of ascorbate (AA), was limited by a non-enzymatic reduction using glutathione (GSH) as the reductant. At 24 h, the enzyme capacities of both DHAR and GR were increased to maintain the redox status of the AA and GSH pools. After 72 h of Cu application, the DHAR capacity was inhibited and MDHAR was responsible for maintaining the AA pool in its reduced form. Although the GR capacity was enhanced after 72 h in the treated plants, the GSSG/GSH ratio was increased. This could be due to direct participation of GSH in the detoxification of Cu through reduction and complexation.     

Effects of Pb-EDTA and EDTA on oxidative stress reactions and mineral uptake in Phaseolus vulgaris

Sequestration of Pb by synthetic chelates has been reported to increase bioavailability, uptake, and translocation of this metal in plants. In this work the potential phytotoxic effects of Pb-EDTA were investigated in Phaseolus vulgaris L. cv. Limburgse vroege plants grown on hydroponics. Addition of 50 µ M Pb-EDTA to the nutrient solution caused a significant induction of syringaldazine peroxidase (SPOD; EC 1.11.1.7) in roots and primary leaves and guaiacol peroxidase (GPOD; EC 1.11.1.7) in leaves. Addition of 100 µ M Pb-EDTA further exacerbated ascorbate peroxidase (APOD; EC 1.11.1.11), GPOD, dehydroascorbate reductase (DHAR; EC 1.8.5.1), glutathione reductase (GR; EC 1.6.4.2) and malic enzyme (ME; EC 1.1.1.40) in roots and APOD and ME in primary leaves. Addition of 200 µ M Pb-EDTA also induced DHAR in leaves. This induction of peroxidases (SPOD, GPOD, APOD), enzymes of the ascorbate-glutathione cycle (DHAR, GR in roots) and of an NADP⁺ reducing enzyme in roots and primary leaves indicates that oxidative stress has been initiated. At 200 µ M Pb-EDTA, chlorophyll a and b content in leaves was significantly reduced while visible effects on root morphology and shoot length were observed, while no significant morphological effects were found in the leaves, confirming the sensitive character of the measured enzymes as plant stress indicators. Elevation of the Pb-EDTA concentration in the growth medium significantly reduced the content of Ca, Fe, Mn and Zn taken up by plants, probably due to ion leakage as a result of observed toxicity. Addition of up to 200 µ M EDTA increased chelation of divalent cations in nutrient solution resulting in reduced plant uptake of Zn, Cu, Fe and Mn. This did not result in phytotoxicity.     

Clutch size: a major sex ratio determinant in fig pollinating wasps?

Under local mate competition, sex ratio theory predicts that increasing numbers of ovipositing females (foundresses) on a site should lead to higher proportions of males in their broods. Fig pollinators have confirmed this prediction. It is also predicted that with decreasing clutch size, solitary foundresses should produce increasing proportions of sons. We show this to be true. Further, when several females compete, brood size decreases. As a result, the proportion of males increases, and this could provide a mechanistic explanation of sex ratio response to numbers of colonizing females. Therefore, sex ratio data on fig wasps need to be reassessed to determine whether females 'count' other foundresses, as is generally accepted, or whether they simply 'count' the number of eggs that they lay.     

Plant-associated bacteria and their role in the success or failure of metal phytoextraction projects: first observations of a field-related experiment

Phytoextraction has been reported as an economically and ecologically sound alternative for the remediation of metal-contaminated soils. Willow is a metal phytoextractor of interest because it allows to combine a gradual contaminant removal with production of biomass that can be valorized in different ways. In this work two willow clones growing on a metal-contaminated site were selected: ‘Belgisch Rood’ (BR) with a moderate metal extraction capacity and ‘Tora’ (TO) with a twice as high metal accumulation. All cultivable bacteria associated with both willow clones were isolated and identified using 16SrDNA ARDRA analysis followed by 16SrDNA sequencing. Further all isolated bacteria were investigated for characteristics that might promote plant growth (production of siderophores, organic acids and indol acetic acid) and for their metal resistance. The genotypic and phenotypic characterization of the isolated bacteria showed that the TO endophytic bacterial population is more diverse and contains a higher percentage of metal-resistant plant growth promoting bacteria than the endophytic population associated with BR. We hypothesize that the difference in the metal accumulation capacity between BR and TO clones might be at least partly related to differences in characteristics of their associated bacterial population.