Available online at www.sciencedirect.com Profiling techniques in nutrition and health research Martin Kussmann 1 , Serge Rezzi 1 and Hannelore Daniel 2 Nutrition sciences apply transcriptomics, proteomics and metabolomics to molecularly assess nutritional adaptations. Transcriptomics can generate a holistic overview on molecular changes to dietary interventions. Proteomics is most challenging because of the higher complexity of proteomes as compared to transcriptomes and metabolomes. However, it delivers not only markers but also targets of intervention, such as enzymes or transporters, and it is the platform of choice for discovering bioactive food proteins and peptides. Metabolomics is a tool for metabolic characterization of individuals and can deliver metabolic endpoints possibly related to health or disease. Omics in nutrition should be deployed in an integrated fashion to elucidate biomarkers for defining an individual’s susceptibility to diet in nutritional interventions and for assessing food ingredient efficacy. Addresses 1 BioAnalytical Science Department, Nestle ´ Research Center, Nestec Ltd., Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland 2 Molecular Nutrition Unit, Technical University of Munich, Am Forum 5, 85350 Freising Weihenstephan, Germany Corresponding author: Kussmann, Martin (serge.rezzi@rdls.nestle.com), Rezzi, Serge (daniel@wzw.tum.de) and Daniel, Hannelore (daniel@wzw.tum.de) Current Opinion in Biotechnology 2008, 19:83–99 This review comes from a themed issue on Food Biotechnology Edited by Hannelore Daniel and Martin Kussmann Available online 2nd April 2008 0958-1669/$ – see front matter # 2008 Elsevier Ltd. All rights reserved. DOI 10.1016/j.copbio.2008.02.003 Introduction Food stuffs contain macronutrients (carbohydrates, lipids and proteins) and micronutrients (vitamins, minerals, trace elements) that exhibit effects at RNA, protein and metabolite level in a cell or organism when exposed to these food components (Figure 1). The corresponding profiling technologies, namely transcriptomics (gene expression analysis), proteomics (protein expression analysis) and metabolomics (metabolite profiling) are applied to better understand and assess these effects in a holistic fashion (Figure 1). We will use ‘nutritional genomics’ as the collective term that covers the three sub-disciplines of transcriptomics, proteomics and metabo- lomics and describe the use of medium to high throughput profiling technologies to assess the response of a cell or an organism to a dietary treatment or particular foods or food constituents. Every nutritional process relies on the inter- play of a large number of proteins encoded by the respective mRNA molecules that are expressed in a certain cell, organ or organism (Figure 1). Alterations of mRNA levels and in turn of the corresponding protein levels (although this not necessarily changes in parallel) are critical parameters in controlling the flux of a nutrient or metabolite through a biochemical pathway. Nutrients and non-nutrient components of foods, diets and lifestyle can affect essentially every step in the flow of genetic information from gene expression to protein synthesis and protein degradation and thereby alter metabolic functionality in the most complex ways. The key ques- tion is, whether these genomics technologies, combined with advanced data analysis and interpretation tools, allow a reconstruction and understanding of these sensing and signal integration mechanisms and their multidimen- sional wiring to better define human nutrition in health and disease. Transcriptomics in nutrition and food sciences Microarray-based transcriptome analysis may be con- sidered the first mature genome-wide profiling technol- ogy. Consequently, it is also used most widely and applications of transcriptomics in nutritional studies seem unlimited when it comes to basic and preclinical research in either cell culture systems or animal models. The mRNA profiling techniques have the potential to easily identify specific transcript changes that respond to a given nutrient, non-nutrient compound, treatment or diet in a well defined experimental setting. This might not mean that the changes in mRNA level can be taken as a causal marker, it might rather be a pattern of expressed mRNAs that changes in a characteristic and reproducible way. Since the technology has the character of a screening process covering thousands of potentially affected indicators of the metabolic status simultaneously it also reveals quite often totally unexpected findings. Chip-based technologies for mRNA profiling The different array platforms available use different probes with either short or long oligonucleotides or cDNA, they have different production procedures and they use different labelling methods. As a more general requirement, arrays must possess probes that hybridize with high sensitivity and specificity. Commercial plat- forms such as those of Affymetrix and Agilent rely on the in situ synthesis of probes. Affymetrix oligonucleotide arrays consist of 25-mer probes while those of Agilent use longer 60-mer probes. Short oligonucleotides can www.sciencedirect.com Current Opinion in Biotechnology 2008, 19:83–99