Functional genomics and proteomics applied to the study of nutritional metabolism

Proteomics analysis indicated the protein expression pattern related to the development of fetal conotruncal defects

Abnormal development of embryonic conus arteriosus could lead to conotruncal defects in fetal heart, and increase the incidence of fetal congenital heart disease. Tetralogy of Fallot (TOF) is one of the most common forms of congenital heart disease. It may be helpful for us to solve this clinical problem through exploring the molecular mechanisms of development in embryonic congenital heart disease. Proteomics has attracted much attention in understanding the development of human diseases during the past decades. However, there is still little information about the relationship between protein expression pattern and TOF. In this study, we aimed to explore the potential linkage of proteomics and TOF development. Briefly, 121 differentially expressed proteins were identified from a TOF group, compared with a control group. The expression levels of 34 of these proteins were significantly different (>1.5 absolute fold change, p < 0.05) between the two groups. Gene ontology (GO) and pathway analysis showed that these proteins were mainly associated with carbon metabolism, biosynthesis of antibodies, positive regulation of transcription from RNA polymerase II promoter, nucleus, ATP binding, and so on. The ingenuity pathway analysis (IPA) results indicated that 435 of upstream regulators were identified of these differentially expressed proteins, which might be involved in the development of TOF. Data of string analysis showed the protein-protein interaction network among the differentially expressed proteins and regulators, which are related to TOF. In conclusion, our study explored the protein expression pattern of TOF, which might provide new insights into understanding the mechanism of TOF development and afford potential targets for TOF diagnosis and therapy.

Proteome alterations induced in human white blood cells by consumption of Brussels sprouts: Results of a pilot intervention study

Epidemiological studies indicate a correlation of cruciferous vegetables consumption with reduced incidence of cancer. This study was designed to investigate molecular mechanisms, which may help to understand the beneficial effects of Brussels sprout consumption. In order to avoid the limitations of in vitro model systems, we performed a dietary intervention study with five participants. We investigated, whether sprout consumption affects the proteome profile of primary white blood cells. In order to achieve maximal sensitivity in detecting specific adaptive proteome alterations, we metabolically labelled freshly isolated cells in the presence of (35) S-methionine/cysteine and performed autoradiographic quantification of protein synthesis. Proteins were separated by 2-DE and spots of interest were cut out, digested and identified by MS. After the intervention, we found a significant up-regulation of the synthesis of manganese superoxide dismutase (1.56-fold) and significant down-regulation of the synthesis of heat shock 70 kDa protein (hsp70; 2.27-fold). Both proteins play a role in malignant transformation of cells. Hsp-70 is involved in the regulation of apoptosis, which leads to elimination of cancer cells, while SOD plays a key role in protection against reactive oxygen species mediated effects. Our findings indicate that the alteration of the synthesis of these proteins may be involved in the anticarcinogenic effects of cruciferous vegetables, which was observed in earlier laboratory studies with animals.

Use of conventional and -omics based methods for health claims of dietary antioxidants: a critical overview

This article describes the principles and limitations of methods used to investigate reactive oxygen species (ROS) protective properties of dietary constituents and is aimed at providing a better understanding of the requirements for science based health claims of antioxidant (AO) effects of foods. A number of currently used biochemical measurements aimed of determining the total antioxidant capacity and oxidised lipids and proteins are carried out under unphysiological conditions and are prone to artefact formation. Probably the most reliable approaches are measurements of isoprostanes as a parameter of lipid peroxidation and determination of oxidative DNA damage. Also the design of the experimental models has a strong impact on the reliability of AO studies: the common strategy is the identification of AO by in vitro screening with cell lines. This approach is based on the assumption that protection towards ROS is due to scavenging, but recent findings indicate that activation of transcription factors which regulate genes involved in antioxidant defence plays a key role in the mode of action of AO. These processes are not adequately represented in cell lines. Another shortcoming of in vitro experiments is that AO are metabolised in vivo and that most cell lines are lacking enzymes which catalyse these reactions. Compounds with large molecular configurations (chlorophylls, anthocyans and polyphenolics) are potent AO in vitro, but weak or no effects were observed in animal/human studies with realistic doses as they are poorly absorbed. The development of -omics approaches will improve the scientific basis for health claims. The evaluation of results from microarray and proteomics studies shows that it is not possible to establish a general signature of alterations of transcription and protein patterns by AO. However, it was shown that alterations of gene expression and protein levels caused by experimentally induced oxidative stress and ROS related diseases can be normalised by dietary AO.

Thermally oxidized dietary fat upregulates the expression of target genes of PPAR alpha in rat liver

Oxidized fats affect animal metabolism in several ways. To gain a comprehensive understanding of the molecular mechanisms underlying the effects of dietary oxidized fats in rats at varying dietary vitamin E concentrations, the gene expression profile of the liver was monitored with an array containing 1176 binding sites for cDNAs. Rats were fed diets with a fresh fat and vitamin E concentrations of 25 or 250 mg alpha-tocopherol/kg (FF25, FF250 rats) or a fat heated at 50 degrees C for 38 d, with vitamin E concentrations of 25 or 250 mg alpha-tocopherol/kg (OF25, OF250 rats) for 63 d. Differences in gene expression were considered to be significant at a ratio of at least 1.4. In the OF25 rats, the expression of 47 genes was altered; in the OF250 rats, the expression of 37 genes was altered, and in the FF250 rats, the expression of 21 genes was altered compared with FF25 rats. In both OF25 and OF250 rats, a series of target genes of the peroxisome proliferator-activated receptor alpha (PPAR alpha) was upregulated. Determination of gene expression of acyl CoA oxidase and activity of catalase confirmed that oxidized fats caused peroxisome proliferation in the liver. In OF25 and OF250 rats, there was also upregulation of 12 and 5 genes involved in xenobiotic metabolism and stress response, of 7 and 7 genes involved in protein metabolism, of 5 and 2 genes encoding intracellular effectors or modulators and of 5 and 6 genes, respectively, encoding activators or repressors of transcription or translation. In conclusion, this study provides indirect evidence that dietary oxidized fats cause an activation of the PPAR alpha, irrespective of the dietary vitamin E concentration. Identification of several other differentially regulated genes may be helpful to understand the effects of oxidized fats on animal metabolism.

Human nutrition and food research: opportunities and challenges in the post-genomic era

Sequencing of the human genome has opened the door to the most exciting new era for nutritional science. It is now possible to study the underlying mechanisms for diet-health relationships, and in the near future dietary advice (and possibly tailored food products) for promoting optimal health could be provided on an individual basis, in relation to genotype and lifestyle. The role of food in human evolution is briefly reviewed, from palaeolithic times to modern-day hunter-gatherer societies. The aetiology of 'diseases of modern civilization', such as diabetes, heart disease and cancer, and the effect of changes in dietary patterns are discussed. The risk of disease is often associated with common single nucleotide polymorphisms, but the effect is dependent on dietary intake and nutritional status, and is often more apparent in intervention studies employing a metabolic challenge. To understand the link between diet and health, nutritional research must cover a broad range of areas, from molecular to whole body studies, and is an excellent example of integrative biology, requiring a systems biology approach. The annual cost to the National Health Service of diet-related diseases is estimated to be in excess of 15 billion, and although diet is a key component of any preventative strategy, it is not given the prominence it deserves. For example, less than 1% of the pound 1.6 billion budget for coronary heart disease is spent on prevention. The polygenic and multifactorial nature of chronic diseases requires substantial resources but the potential rewards, in terms of quality of life and economics, are enormous. It is timely therefore to consider investing in a long-term coordinated national programme for nutrition research, combining nutritional genomics with established approaches, to improve the health of individuals and of the nation.

Diet, Nutrition, and Cancer Prevention: The Postgenomic Era

The genomic era of human nutrition is upon us: the human genome and several plant genomes have been characterized, and genetically modified foods are now abundantly available in the marketplace. The link between diet and cancer is well established, and new genomic technologies have made possible the investigation of nutritional modulation of the carcinogenesis pathway with nutrients, micronutrients, and phytochemicals. Current study of nutrient-modulated carcinogenesis involves exploring the effect of nutrients on DNA damage and repair mechanisms; DNA methylation, which influences gene expression and cellular phenotypes; antioxidant rearranging and oxidative stress; target receptors and signal transduction pathways; cell cycle controls and check points; apoptosis; and antiangiogenic processes. With nutritional genomics, proteomics, and metabolomics, scientists are able to simultaneously elucidate the biological effects of dietary constituents on cell function and global gene expression. This generation of new knowledge on nutrient-gene interactions provides the justification for a research framework for diet and cancer prevention that is focused on identifying and developing new biomarkers as well as a novel and contemporary paradigm for dietary intervention.

Evaluation of the effects of the dietary intake of proteins and amino acids by DNA microarray technology

The DNA microarray technique has been increasingly utilized in various fields of life sciences. It allows us to analyze the expression levels of thousands of genes simultaneously. The high productivity will facilitate the evaluation of changes in amino acid metabolism and their consequences in response to dietary proteins and amino acids. We compared the expression profiles by the GeneChip system in the liver and other tissues among three groups of rats fed with a 12% casein, a 12% gluten or a protein-free diet. Feeding the gluten or the protein-free diet up- or down-regulated a few hundred genes in the liver compared to the casein diet. Although some of the genes were already known to respond to changes in the protein nutritional state, the majority was newly identified responders. This paper also discusses the possibility of a use this technology for safety evaluation of excessive intake of dietary components, especially of amino acids.

The 10 basic requirements for a scientific paper reporting antioxidant, antimutagenic or anticarcinogenic potential of test substances in in vitro experiments and animal studies in vivo

There is increasing evidence that chemicals/test substances cannot only have adverse effects, but that there are many substances that can (also) have a beneficial effect on health. As this journal regularly publishes papers in this area and has every intention in continuing to do so in the near future, it has become essential that studies reported in this journal reflect an adequate level of scientific scrutiny. Therefore a set of essential characteristics of studies has been defined. These basic requirements are default properties rather than non-negotiables: deviations are possible and useful, provided they can be justified on scientific grounds. The 10 basic requirements for a scientific paper reporting antioxidant, antimutagenic or anticarcinogenic potential of test substances in in vitro experiments and animal studies in vivo concern the following areas: (1) Hypothesis-driven study design; (2) The nature of the test substance; (3) Valid and invalid test systems; (4) The selection of dose levels and gender; (5) Reversal of the effects induced by oxidants, carcinogens and mutagens; (6) Route of administration; (7) Number and validity of test variables; (8) Repeatability and reproducibility; (9) Statistics; and (10) Quality Assurance.

Proteomics: general strategies and application to nutritionally relevant proteins

Proteomics as a subset of applied genomics technologies will be a key area of biology during the first decade or two of the new Millennium, and that it will have major impact, both directly and indirectly, on nutritional science. The aim of this review is to summarize information about general strategies of proteome and its application to important food proteins (plant, animal, and microbial). Methods are also described for protein separation, identification and determination. This article covers papers published within the last decade.

The use of genetic modification technologies in the discovery of genes affecting production traits and disease resistance in animals

Genetic modification technologies, developed initially in laboratory strains of selected bacteria and viruses, are essential tools for understanding the genomes of livestock. These tools allow researchers to: isolate, sequence and characterise any livestock gene; locate genes on chromosomes; follow the inheritance of any gene and/or chromosomal region in any pedigree; detect phenotypic variation due to, or associated with, variation in the DNA sequence of a gene and identify the genetic alteration causing this. Most of the many thousands of genes identified in livestock vary between individuals. Finding the best type of the key genes affecting animal productivity is an exciting and a daunting task. It is only possible with the use of laboratory-based genetic modification techniques. This review will briefly describe the technologies now in use and, using local examples, show how molecular geneticists are using these to help identify genetic alterations and breed healthier or more productive animals. As with any new technology, a new language evolves to describe new products and processes. The new language makes communication easier between participants in the field but more difficult for others to understand the technology. A glossary of terms has therefore been added to this review to help readers less familiar with molecular genetics.

Genomic interrogation of mechanism(s) underlying cellular responses to toxicants

Assessment of the impact of xenobiotic exposure on human health and disease progression is complex. Knowledge of mode(s) of action, including mechanism(s) contributing to toxicity and disease progression, is valuable for evaluating compounds. Toxicogenomics, the subdiscipline which merges genomics with toxicology, holds the promise to contributing significantly toward the goal of elucidating mechanism(s) by studying genome-wide effects of xenobiotics. Global gene expression profiling, revolutionized by microarray technology and a crucial aspect of a toxicogenomic study, allows measuring transcriptional modulation of thousands of genes following exposure to a xenobiotic. We use our results from previous studies on compounds representing two different classes of xenobiotics (barbiturate and peroxisome proliferator) to discuss the application of computational approaches for analyzing microarray data to elucidate mechanism(s) underlying cellular responses to toxicants. In particular, our laboratory demonstrated that chemical-specific patterns of gene expression can be revealed using cDNA microarrays. Transcript profiling provides discrimination between classes of toxicants, as well as, genome-wide insight into mechanism(s) of toxicity and disease progression. Ultimately, the expectation is that novel approaches for predicting xenobiotic toxicity in humans will emerge from such information.

Dietary protein quantity and quality affect rat hepatic gene expression

To gain a comprehensive understanding of the molecular mechanisms underlying the effects of dietary protein on alternations in physiologic and pathologic status, the GeneChip microarray system was used to investigate the consequences of two different states of protein malnutrition on gene expression in rat liver. Expressions of 281 genes were increased or decreased by twofold or more by treatment with a protein-free diet for 1 wk compared with control rats fed a casein diet. Similarly, 111 genes were affected in rats fed a wheat gluten diet compared with those fed the casein diet. Although some of the genes identified were known to respond to protein nutrition, a majority were newly identified as responders to protein nutritional status. Interesting findings included the drastic changes in the levels of genes for Id (inhibitor of DNA binding) proteins, which are involved in the regulation of multiple genes, and of a set of genes in the pathway of cholesterol biosynthesis and disposal. This study represents a step toward a more global understanding of gene expression changes in states of protein malnutrition.

Calorific restriction: can we extrapolate from animals to humans?

Dietary restriction in animals results in a dramatic reduction of cancer incidence. Several attempts have been made to extrapolate this observation to the human situation. Recent developments in our knowledge of gene-dietary interactions, particularly in relation to vitamins, have been taken into account in a new examination of the likely effects of dietary restriction in humans, but this is a relatively new area of research. Epidemiological studies in relation to diet have also been considered, but probably need to be refined further because of the subtle effects of dietary interactions. Until more detailed information is available the extrapolation can still only be made with the utmost caution.