Proteomics and Systems Biology: Current and Future Applications in the Nutritional Sciences

Abstract

In the last decade, advances in genomics, proteomics, and metabolomics have yielded large-scale datasets that have driven an interest in global analyses, with the objective of understanding biological systems as a whole. Systems biology integrates computational modeling and experimental biology to predict and characterize the dynamic properties of biological systems, which are viewed as complex signaling networks. Whereas the systems analysis of disease-perturbed networks holds promise for identification of drug targets for therapy, equally the identified critical network nodes may be targeted through nutritional intervention in either a preventative or therapeutic fashion. As such, in the context of the nutritional sciences, it is envisioned that systems analysis of normal and nutrient-perturbed signaling networks in combination with knowledge of underlying genetic polymorphisms will lead to a future in which the health of individuals will be improved through predictive and preventative nutrition. Although high-throughput transcriptomic microarray data were initially most readily available and amenable to systems analysis, recent technological and methodological advances in MS have contributed to a linear increase in proteomic investigations. It is now commonplace for combined proteomic technologies to generate complex, multi-faceted datasets, and these will be the keystone of future systems biology research. This review will define systems biology, outline current proteomic methodologies, highlight successful applications of proteomics in nutrition research, and discuss the challenges for future applications of systems biology approaches in the nutritional sciences.

Asthma, allergy, and responses to methyl donor supplements and nutrients

“…While some of the reports reviewed above 47, 50, 51, 60, 61, 63, 66 investigated other nutrients or foods, these were studied individually and no consideration was given to the relationships between each of these nutrients. While studies of diet patterns 67, 68 address this issue to a certain extent, pathway-based or systems-based analyses 69 might help dissect the complex interrelationships between individual nutrients.…”

“…Given that these nutrients are intricately related in pathways (Figure 1), future studies need to include analyses of multiple nutrients. Furthermore, given the complexities of the one-carbon metabolism pathway, analyses including a systems-based approach or pathway analyses may further our understanding of the role of dietary methyl donors in the development of atopic disease 69 .…”

Molecular Nutrition Research—The Modern Way Of Performing Nutritional Science

“…Several review articles on the use of proteomics in nutrition research have been published [85,86,87]. The focus has been on identifying new health biomarkers and bioactive peptides in foods.…”

Recent advances in nutrition, genes and brain health

“…Studies on the role of nutrition in health and disease now involve genomics, epigenomics, post-translational modifications, proteomics, metabolomics and systems biology (13)(14)(15)(16)(17) . Moreover, comprehensive analyses of genetic variability are advancing understanding of individual differences in responses to nutrition.…”