Identification of biomarkers for the initiation of apoptosis in human preneoplastic colonocytes by proteome analysis

Highly pathogenic natural monoclonal antibody B4-IgM recognizes a post-translational modification comprised of acetylated N-terminal methionine followed by aspartic or glutamic acid

The natural monoclonal antibody B4-IgM recognizes murine annexin 4 (mAn4) and exacerbates ischemia-reperfusion injury in many mouse models. During apoptosis, the intracellular mAn4 protein translocates to the membrane surface, remaining attached to the outer membrane leaflet where it is recognized by the anti-mAn4 B4-IgM antibody. B4-IgM does not recognize human annexin 4 (hAn4). However, the B4-IgM antibody epitope was detected by Western blot of unknown human proteins and by flow cytometry on all studied human cell lines undergoing apoptosis and on a minor subset of healthy cells. The B4-IgM antibody also recognizes the epitope on necrotic cells in cytoplasmic proteins, apparently entering through pores large enough to allow natural antibodies to penetrate the cells and bind to the epitope expressed on self-proteins. Using proteomics and site-directed mutagenesis, we found that B4-IgM binds to an epitope with post-translationally modified acetylated N-terminal methionine, followed by either glutamic or aspartic acid. The epitope is not induced by apoptosis or injury because this modification can also occur during protein translation. This finding reveals an additional novel mechanism whereby injured cells are detected by natural antibodies that initiate pathogenic complement activation through the recognition of epitopes that are shared across multiple proteins found in variable cell lines.

Applications and Pharmacological Properties of Cactus Pear (Opuntia spp.) Peel: A Review

Nowadays, there is a growing interest in the exploitation of by-products from fruits and vegetables, generated from industrial processing or human feeding. Residues of popularly consumed fruits such as orange, lemon, banana, pomegranate, among others, have been widely described and studied; however, cactus pear (Opuntia spp.) residues, as a locally consumed product, have been forgotten. The whole fruit can be divided into the edible portion (pulp) and the non-edible portion (seeds and peel). Several studies mainly focus on the characteristics of the edible portion or in the whole fruit, ignoring by-products such as peels, which are rich in compounds such as phenols, flavonoids and dietary fiber; they have also been proposed as an alternative source of lipids, carbohydrates and natural colorants. Some uses of the peel have been reported as a food additives, food supplements, as a source of pectins and for wastewater treatment; however, there have not been any deep investigations of the characteristics and potential uses of the cactus pear peel (CPP). The aim of the present paper is to provide an overview of the current research on CPP. CPP has many bio-active compounds that may provide health benefits and may also be useful in pharmaceutical, food and manufacturing industries; however, greater research is needed in order to gain thorough knowledge of the possibilities of this by-product.

Proteomics study of silver nanoparticles on Caco-2 cells

Silver nanoparticles (AgNPs) have been incorporated into several consumer products. While these advances in technology are promising and exciting, the effects of these nanoparticles have not equally been studied. Due to the size, AgNPs can penetrate the body through oral exposure and reach the gastrointestinal tract. The present study was designed as a comparative proteomic analysis of Caco-2 cells, used as an in vitro model of the small intestine, exposed to 30 nm citrate stabilized-silver nanoparticles (AgNPs) for 24 or 72 h. Using two complementary proteomic approaches, 2D gel-based and label-free mass spectrometry, we present insight into the effects of AgNPs at proteins level. Exposure of 1 or 10 μg/mL AgNPs to Caco-2 cells resulted in 56 and 88 altered proteins at 24 h and 72 h respectively, by 2D gel-based technique. Ten of these proteins were found to be common between the two time-points. Using label-free mass spectrometry technique, 291 and 179 altered proteins were found at 24 h and 72 h, of which 24 were in common. Analysis of the proteomes showed several major biological processes altered, from which, cell cycle, cell morphology, cellular function and maintenance were the most affected.

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Comparison between 2D gel-based vs label-free MS based proteomics study

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Significant changes in the protein profiles of Caco-2 cells exposed to AgNPs.

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Contribute to understand the mechanisms of action of AgNPs

Effects of silver nanoparticles and ions on a co-culture model for the gastrointestinal epithelium

Background

The increased incorporation of silver nanoparticles (Ag NPs) into consumer products makes the characterization of potential risk for humans and other organisms essential. The oral route is an important uptake route for NPs, therefore the study of the gastrointestinal tract in respect to NP uptake and toxicity is very timely. The aim of the present study was to evaluate the effects of Ag NPs and ions on a Caco-2/TC7:HT29-MTX intestinal co-culture model with mucus secretion, which constitutes an important protective barrier to exogenous agents in vivo and may strongly influence particle uptake.

Methods

The presence of the mucus layer was confirmed with staining techniques (alcian blue and toluidine blue). Mono and co-cultures of Caco-2/TC7 and HT29-MTX cells were exposed to Ag NPs (Ag 20 and 200 nm) and AgNO₃ and viability (alamar blue), ROS induction (DCFH-DA assay) and IL-8 release (ELISA) were measured. The particle agglomeration in the media was evaluated with DLS and the ion release with ultrafiltration and ICP-MS. The effects of the Ag NPs and AgNO₃ on cells in co-culture were studied at a proteome level with two-dimensional difference in gel electrophoresis (2D-DIGE) followed by Matrix Assisted Laser Desorption Ionization - Time Of Flight/ Time Of Flight (MALDI-TOF/TOF) mass spectrometry (MS). Intracellular localization was assessed with NanoSIMS and TEM.

Results

The presence of mucus layer led to protection against ROS and decrease in IL-8 release. Both Ag 20 and 200 nm NPs were taken up by the cells and Ag NPs 20 nm were mainly localized in organelles with high sulfur content. A dose- and size-dependent increase in IL-8 release was observed with a lack of cytotoxicity and oxidative stress. Sixty one differentially abundant proteins were identified involved in cytoskeleton arrangement and cell cycle, oxidative stress, apoptosis, metabolism/detoxification and stress.

Conclusions

The presence of mucus layer had an impact on modulating the induced toxicity of NPs. NP-specific effects were observed for uptake, pro-inflammatory response and changes at the proteome level. The low level of overlap between differentially abundant proteins observed in both Ag NPs and AgNO₃ treated co-culture suggests size-dependent responses that cannot only be attributed to soluble Ag.

Electronic supplementary material

The online version of this article (doi:10.1186/s12989-016-0117-9) contains supplementary material, which is available to authorized users.

Approaches that ascertain the role of dietary compounds in colonic cancer cells

Preventive approaches against cancer have not been fully developed and applied. For example, the incidence of some types of cancer, including colon cancer, is highly dependent upon lifestyle, and therefore, amenable to prevention. Among the lifestyle factors, diet strongly affects the incidence of colon cancer; however, there are no definitive dietary recommendations that protect against this malignancy. The association between diet-derived bioactives and development of colonic neoplasms will remain ill defined if we do not take into account: (1) the identity of the metabolites present in the colonic lumen; (2) their concentrations in the colon; and (3) the effect of the colonic contents on the function of individual bioactives. We review two approaches that address these questions: the use of fecal water and in vitro models of the human colon. Compared to treatment with individual diet-derived compounds, the exposure of colon cancer cells to samples from fecal water or human colon simulators mimics closer the in vitro conditions and allows for more reliable studies on the effects of diet on colon cancer development. The rationale and the advantages of these strategies are discussed from the perspective of a specific question on how to analyze the combined effect of two types of bioactives, butyrate and polyphenol metabolites, on colon cancer cells.

Site-specific anticancer effects of dietary flavonoid quercetin

Food-derived flavonoid quercetin, widely distributed in onions, apples, and tea, is able to inhibit growth of various cancer cells indicating that this compound can be considered as a good candidate for anticancer therapy. Although the exact mechanism of this action is not thoroughly understood, behaving as antioxidant and/or prooxidant as well as modulating different intracellular signalling cascades may all play a certain role. Such inhibitory activity of quercetin has been shown to depend first of all on cell lines and cancer types; however, no comprehensive site-specific analysis of this effect has been published. In this review article, cytotoxicity constants of quercetin measured in various human malignant cell lines of different origin were compiled from literature and a clear cancer selective action was demonstrated. The most sensitive malignant sites for quercetin revealed to be cancers of blood, brain, lung, uterine, and salivary gland as well as melanoma whereas cytotoxic activity was higher in more aggressive cells compared to the slowly growing cells showing that the most harmful cells for the organism are probably targeted. More research is needed to overcome the issues of poor water solubility and relatively low bioavailability of quercetin as the major obstacles limiting its clinical use.

Potential markers of preeclampsia--a review

Preeclampsia is a leading cause of maternal and fetal/neonatal mortality and morbidity worldwide. The early identification of patients with an increased risk for preeclampsia is therefore one of the most important goals in obstetrics. The availability of highly sensitive and specific physiologic and biochemical markers would allow not only the detection of patients at risk but also permit a close surveillance, an exact diagnosis, timely intervention (e.g. lung maturation), as well as simplified recruitment for future studies looking at therapeutic medications and additional prospective markers. Today, several markers may offer the potential to be used, most likely in a combinatory analysis, as predictors or diagnostic tools. We present here the current knowledge on the biology of preeclampsia and review several biochemical markers which may be used to monitor preeclampsia in a future, that, we hope, is not to distant from today.

Pathogenic natural antibodies recognizing annexin IV are required to develop intestinal ischemia-reperfusion injury

Intestinal ischemia-reperfusion (IR) injury is initiated when natural IgM Abs recognize neo-epitopes that are revealed on ischemic cells. The target molecules and mechanisms whereby these neo-epitopes become accessible to recognition are not well understood. Proposing that isolated intestinal epithelial cells (IEC) may carry IR-related neo-epitopes, we used in vitro IEC binding assays to screen hybridomas created from B cells of unmanipulated wild-type C57BL/6 mice. We identified a novel IgM mAb (mAb B4) that reacted with the surface of IEC by flow cytometric analysis and was alone capable of causing complement activation, neutrophil recruitment and intestinal injury in otherwise IR-resistant Rag1(-/-) mice. mAb B4 was found to specifically recognize mouse annexin IV. Preinjection of recombinant annexin IV blocked IR injury in wild-type C57BL/6 mice, demonstrating the requirement for recognition of this protein to develop IR injury in the context of a complex natural Ab repertoire. Humans were also found to exhibit IgM natural Abs that recognize annexin IV. These data in toto identify annexin IV as a key ischemia-related target Ag that is recognized by natural Abs in a pathologic process required in vivo to develop intestinal IR injury.

Characterization of proteomic and metabolomic responses to dietary factors and supplements

Over the past decade there has been a renewed interest in research and development of both dietary and nutritional supplements. Significant advancements have been made in the scientific assessment of the quality, safety, and efficacy of these products because of the strong interest in and financial support of these projects. As research in both fields continues to advance, opportunities to use new and innovative research technologies and methodologies, such as proteomics and metabolomics, are critical for the future progress of the science. The purpose of the symposium was to begin the process of communicating new innovative proteomic and metabolomic methodologies that may be applied by researchers in both the nutrition and the natural product communities. This symposium highlighted 2 proteomic approaches, protein fingerprinting in complex mixtures with peptoid microarrays and top-down mass spectrometry for annotation of gene products. Likewise, an overview of the methodologies used in metabolomic profiling of natural products was presented, and an illustration of an integrated metabolomics approach in nutrition research was highlighted.

Proteomics in nutrition research: principles, technologies and applications

The global profiling of the whole protein complement of the genome expressed in a particular cell or organ, or in plasma or serum, makes it possible to identify biomarkers that respond to alterations in diet or to treatment, and that may have predictive value for the modelling of biological processes. Proteomics has not yet been applied on a large scale in nutritional studies, yet it has advantages over transcriptome profiling techniques in that it directly assesses the entities that carry out the biological functions. The present review summarizes the different approaches in proteomics research, with special emphasis on the current technical ‘workhorses’: two-dimensional (2D)-PAGE with immobilized pH gradients and protein identification by MS. Using a work-flow approach, we provide information and advice on sample handling and preparation, protein solubilization and pre-fractionation, protein separation by 2D-PAGE, detection and quantification via computer-assisted analysis of gels, and protein identification and characterization techniques by means of MS. Examples from nutritional studies employing proteomics are provided to demonstrate not only the advantages but also the limitations of current proteome analysis platforms.

Effects of dietary flavonoids on apoptotic pathways related to cancer chemoprevention

Epidemiological studies have described the beneficial effects of dietary polyphenols (flavonoids) on the reduction of the risk of chronic diseases, including cancer. Moreover, it has been shown that flavonoids, such as quercetin in apples, epigallocatechin-3-gallate in green tea and genistein in soya, induce apoptosis. This programmed cell death plays a critical role in physiological functions, but there is underlying dysregulation of apoptosis in numerous pathological situations such as Parkinson's disease, Alzheimer's disease and cancer. At the molecular level, flavonoids have been reported to modulate a number of key elements in cellular signal transduction pathways linked to the apoptotic process (caspases and bcl-2 genes), but that regulation and induction of apoptosis are unclear. The aim of this review is to provide insights into the molecular basis of the potential chemopreventive activities of representative flavonoids, with emphasis on their ability to control intracellular signaling cascades responsible for regulating apoptosis, a relevant target in cancer-preventive approach.

Proteome alterations in human host cells infected with coxsackievirus B3

Coxsackievirus B3 (CVB3) is a common factor in human myocarditis. The interplay between host factors and virus components is crucial for the fate of the infected cells. Despite that, host protein responses, which characterize CVB3-induced diseases, have not yet been determined in detail. To investigate the nature of modified protein patterns in infected human cells compared with uninfected cells, two-dimensional gel electrophoresis in combination with matrix-assisted laser desorption/ionization-mass spectrometry were used. The regulated proteins, e.g. nucleophosmin (nucleolar protein B23), lamin, the RNA-binding protein UNR and the p38 mitogen-activated protein kinase, were sorted according to their functional groups and interpreted in the context of the myocarditis process.

Cyclic changes and hormonal regulation of annexin IV mRNA and protein in human endometrium

Annexin IV (ANXA4) belongs to a ubiquitous family of Ca(2+)-dependent phospholipid-binding proteins. ANXA4 has been shown to be involved in a range of physiological functions including ion channel regulation, exocytosis and Ca(2+)-dependent signal transduction. The aims of this study were to fully characterize ANXA4 mRNA and protein in human endometrium during the menstrual cycle and to investigate the hormonal regulation of ANXA4. ANXA4 mRNA expression was quantified by real-time PCR in fresh endometrial tissue from cycling women, and protein expression was analysed by immunohistochemistry and western blotting. Hormonal regulation of ANXA4 transcription and translation was investigated using an endometrial explant system. ANXA4 mRNA was significantly up-regulated during mid-secretory (MS) and late-secretory (LS) phases compared with proliferative phases during the menstrual cycle. ANXA4 protein was localized to glandular and luminal epithelium and was present in high levels throughout the menstrual cycle except during early-secretory (ES) phase, when it was significantly reduced. Our data also show that, in proliferative explants, progesterone significantly increased the ANXA4 mRNA and protein after 48h in culture. Estrogen did not have any significant effects. This is the first study to show that ANXA4 transcription and translation are regulated by progesterone and suggests that ANXA4 may be important in regulating ion and water transport across the endometrial epithelium.

Cactus pear: a natural product in cancer chemoprevention

BACKGROUND

Cancer chemoprevention is a new approach in cancer prevention, in which chemical agents are used to prevent cancer in normal and/or high-risk populations. Although chemoprevention has shown promise in some epithelial cancers, currently available preventive agents are limited and the agents are costly, generally with side effects. Natural products, such as grape seed, green tea, and certain herbs have demonstrated anti-cancer effects. To find a natural product that can be used in chemoprevention of cancer, we tested Arizona cactus fruit solution, the aqueous extracts of cactus pear, for its anti-cancer effects in cultured cells and in an animal model.

METHOD

Aqueous extracts of cactus pear were used to treat immortalized ovarian and cervical epithelial cells, as well as ovarian, cervical, and bladder cancer cells. Aqueous extracts of cactus pear were used at six concentrations (0, 0.5, 1, 5, 10 or 25%) to treat cells for 1, 3, or 5 days. Growth inhibition, apoptosis induction, and cell cycle changes were analyzed in the cultured cells; the suppression of tumor growth in nude mice was evaluated and compared with the effect of a synthetic retinoid N-(4-hydroxyphernyl) retinamide (4-HPR), which is currently used as a chemoprevention agent. Immunohistochemistry staining of tissue samples from animal tumors was performed to examine the gene expression.

RESULTS

Cells exposed to cactus pear extracts had a significant increase in apoptosis and growth inhibition in both immortalized epithelial cells and cancer cells in a dose- and time-dependent manner. It also affected cell cycle of cancer cells by increasing G1 and decreasing G2 and S phases. Both 4-HPR and cactus pear extracts significantly suppressed tumor growth in nude mice, increased annexin IV expression, and decreased VEGF expression.

CONCLUSION

Arizona cactus pear extracts effectively inhibited cell growth in several different immortalized and cancer cell cultures, suppressed tumor growth in nude mice, and modulated expression of tumor-related genes. These effects were comparable with those caused by a synthetic retinoid currently used in chemoprevention trials. The mechanism of the anti-cancer effects of cactus pear extracts needs to be further studied.

Effects of increased cellular zinc levels on gene and protein expression in HT-29 cells

High cellular zinc concentrations lead to impairments in ATP synthesis and cell cycle control particularly in neurons and epithelial cells. The molecular basis for these dysfunctions is still not fully elucidated. Here we analyzed the effects of a high zinc exposure (10 ppm) on gene and protein expression in the human epithelial cell line HT-29. Of the 1176 genes analyzed with cDNA arrays, nine differentially expressed genes were identified. Proteome analysis based on 1310 detected proteins identified 11 molecular targets. Most of the identified genes/proteins have not been linked to cellular zinc status before (e.g. PEC-60, R-ras3). More than half of the targets participate in ATP production or stress response. Therefore, it appears that higher zinc concentrations mediate their effects mainly via impairments in cellular energy metabolism and stress response.

The effects of quercetin on SW480 human colon carcinoma cells: a proteomic study

Background

High fruit and vegetable intake is known to reduce the risk of colon cancer. To improve understanding of this phenomenon the action of different phytochemicals on colon cells has been examined. One such compound is quercetin that belongs to the group known as flavonoids. The purpose of this study was to determine the influence of quercetin on the proteome of the SW480 human colon adenocarcinoma cell line, specifically to identify proteins that could be the molecular targets of quercetin in its amelioration of the progression of colon cancer. To this end, two-dimensional gel electrophoresis and mass spectrometry were used to identify proteins that underwent a change in expression following treatment of the cells with 20 μM quercetin. This could elucidate how quercetin may reduce the progression of colon cancer.

Results

Quercetin treatment of the SW480 human colon cancer cells was found to result in the decreased expression of three proteins and the increased expression of one protein. The identified proteins with decreased expression were type II cytoskeletal 8 keratin and NADH dehydrogenase Fe-S protein 3. The other protein with decreased expression was not identified. The protein with increased expression belonged to the annexin family.

Conclusion

Several proteins were determined to have altered expression following treatment with quercetin. Such changes in the levels of these particular proteins could underlie the chemo-protective action of quercetin towards colon cancer.

Transcriptome and proteome analysis identifies the pathways that increase hepatic lipid accumulation in zinc-deficient rats

For identification of the underlying molecular changes in hepatic lipid metabolism in zinc deficiency, rats were force-fed a zinc-deficient diet. Subsequently DNA-microarray and proteome profiling was performed in combination with hepatic lipid analysis. Of 6200 target sequences analyzed, 268 transcripts showed altered expression levels in livers of zinc-deficient rats, with 43 genes thereof related to hepatic lipid metabolism. Northern blot analysis and quantitative real-time RT-PCR were employed to confirm changes in mRNA levels. Proteins involved in lipid metabolism were identified by proteome analysis. Functional gene clusters with uniform changes in transcript levels suggested that the pathways required for lipolysis and mitochondrial as well as peroxisomal fatty acid degradation were downregulated, whereas those needed for de novo fatty acid synthesis and triglyceride assembly were increased. Subsequent enzymatic analysis of liver tissues confirmed an almost 40% greater triacylglycerol concentration in zinc-depleted rats, as well as an altered fatty acid composition of the lipid fraction as determined by gas chromatography. Liver lipids of zinc-deficient rats had significantly greater proportions of cis-9-oleic acid, cis-11-vaccenic acid, caprylic acid, myristic acid, alpha-linolenic acid, and eicosapentaenoic acid, and significantly less stearic and arachidonic acids. These alterations in hepatic metabolism are discussed in the context of changes in mRNA and protein levels of enzymes and transporters responsible for fatty acid metabolism, sequestration, and their transcriptional control.

Nutrient-gene interactions: a single nutrient and hundreds of target genes

Based on the effects of a selective experimental zinc deficiency in a rodent model we explore the use of transcriptome profiling for assessing nutrient-gene interactions in the liver at the molecular and cellular levels. Zinc deficiency caused pleiotropic alterations in mRNA/protein levels of hundreds of genes. In the context of observed metabolic alterations in hepatic metabolism, possible mechanisms are discussed for how a low zinc status may be sensed and transmitted into changes in various metabolic pathways. However, it also becomes obvious that analysis of such complex nutrient-gene interactions beyond the descriptional level is a real challenge for systems biology.