Proteomics at the Center of Nutrigenomics: Comprehensive Molecular Understanding of Dietary Health Effects
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Nutrition 25 (2009) 1085–1093 www.nutritionjrnl.com Review Proteomics at the center of nutrigenomics: Comprehensive molecular understanding of dietary health effects Martin Kussmann, Ph.D.* and Michael Affolter, Ph.D. Functional Genomics Group, Department of BioAnalytical Sciences, Nestle´Research Center, Lausanne, Switzerland Manuscript received May 29, 2009; accepted May 31, 2009. Abstract Apart from the air we breathe, food is the only physical matter we take into our body during our life. Nutrition exhibits therefore the most important life-long environmental impact on human health. Food components interact with our body at system, organ, cellular, and molecular levels. These dietary com- ponents come in complex mixtures, in which not only the presence and concentrations of a single com- pound but also interactions of multiple compounds determine ingredient bioavailability and bioefficacy. Modern nutritional and health research focuses on promoting health, preventing or delay- ing the onset of disease, and optimizing performance. Deciphering the molecular interplay between food and health requires therefore holistic approaches because nutritional improvement of certain health aspects must not be compromised by deterioration of others. In other words, in nutrition, we have to get everything right. Proteomics is a central platform in nutrigenomics that describes how our genome expresses itself as a response to diet. Nutrigenetics deals with our genetic predisposition and susceptibility toward diet and helps stratify subject cohorts and discern responders from non-responders. Epigenetics represent DNA sequence-unrelated biochemical modifications of DNA itself and DNA-binding proteins and appears to provide a format for life-long or even transgeneration imprinting of metabolism. Proteomics in nutrition can identify and quantify bioactive proteins and peptides and addresses questions of nutritional bioefficacy. In this review, we focus on these latter as- pects, update the reader on technologic developments, and review major applications. Ó 2009 Published by Elsevier Inc. Keywords: Proteomics; Nutrition; Health; Biomarker; Nutrigenomics; Nutrigenetics Introduction Proteomics is a central platform in nutrigenomics that describes how our genome expresses itself as a response to Food components interact with our body at system, organ, diet [4]. Nutrigenetics deals with our genetic predisposition cellular, and molecular levels. These dietary components and susceptibility toward diet [5] and helps stratify subject come in complex mixtures, in which not only the presence cohorts and discern responders from non-responders [6]. Epi- and concentrations of a single compound but also interactions genetics represent DNA sequence-unrelated biochemical of multiple compounds determine ingredient bioavailability modifications of DNA itself and DNA-binding proteins and and bioefficacy [1]. appears to provide a format for life-long or even transgener- Modern nutritional and health research focuses on pro- ation imprinting of metabolism [7,8]. Proteomics in nutrition moting health, preventing or delaying the onset of disease, can identify and quantify bioactive proteins and peptides and and optimizing performance [2]. Deciphering the molecular addresses questions of nutritional bioefficacy [9,10]. interplay between food and health requires therefore holistic The interplay between nutrition and health has been approaches because nutritional improvement of certain known for centuries: the Greek doctor Hippocrates (fourth health aspects must not be compromised by deterioration of century B.C.) can be seen as the father of ‘‘functional others [3]. food,’’ because he recommended using food as medicine and vice versa. Another example of such long-term experi- *Corresponding author. Tel.: þ41-21-785-9572; fax: þ41-21-785-9486. ence is the record of traditional Chinese medicine: Sun Si- E-mail address: [email protected] (M. Kussmann). Miao, a famous doctor of the Tang dynasty (seventh century 0899-9007/09/$ – see front matter Ó 2009 Published by Elsevier Inc. doi:10.1016/j.nut.2009.05.022 1086 M. Kussmann and M. Affolter / Nutrition 25 (2009) 1085–1093 A.D.), stated that, ‘‘When a person is sick, the doctor should multiple-stage fragmentation for ion traps; high selectivity first regulate the patient’s diet and lifestyle.’’ for triple-Q; high sensitivity and speed for ToF; and very The new era of nutritional research translates this rather high mass accuracy and resolution for orbitrap and FT-ICR. empirical knowledge to evidence-based molecular science, Current top-end proteomic machines are orbitrap [15] and because food components interact with our body at system, FT-ICR instruments [16], which rely on frequency readout organ, cellular, and molecular levels [11]. Modern nutritional of oscillating ions rather than ToF- or scanning-based analysis. and health research focuses on promoting health, preventing The major remaining analytical challenge is not mass ac- or delaying the onset of disease, and optimizing performance curacy (today down to subparts per million), mass resolution [11]. (today up to several hundred thousand), or absolute sensitiv- Dietary components come in complex mixtures, in which ity (today down to a picomolar range), but the dynamic range not only the presence and concentrations of a single com- of protein concentrations (e.g., estimated 1012 in human pound but also interactions of multiple compounds influence blood) [17]. Current MS-based proteomic platforms can de- food compound bioavailability and bioefficacy [1]. Hence, liver a dynamic range of 104. This means that the remaining, the necessity of developing and applying comprehensive as such inaccessible, low-abundant proteome has to be ad- analytical methods to reveal bioactive ingredients and their dressed by depletion of the most abundant proteins (e.g., action becomes evident [12]. by the commercially available multiple affinity removal sys- Proteomics is a central platform in elucidating these tem that specifically removes the top 7 or even 14 plasma pro- molecular events in nutrition: it can identify and quantify bio- teins) [18] or by selective enrichment of low-abundant active proteins and peptides and addresses questions of nutri- proteins (e.g., by the immobilized metal affinity chromatog- tional bioefficacy [9]. In this article, we focus on these latter raphy or titanium dioxide techniques for phosphoproteins aspects, update the reader on technologic developments, and [19] or lectins [20] or the cell-surface capture technique for review major applications: we summarize mass spectrometry glycoproteins [21]). All these biochemical depletion and (MS)-rooted proteomic techniques for protein identification enrichment resins and columns have matured a great deal and quantification and go through a selection of nutritional and come now in robust formats. intervention and bioefficacy studies assessed by proteomic After depletion and/or enrichment, usually further prese- means. paration measurements are taken at the protein or peptide Proteins are the key actors in virtually all biological pro- level, based on two-dimensional (2D) gels or on liquid chro- cesses in the human body—they are the ‘‘molecular robots’’ matography (LC), or on hybrid approaches (Gel-LC). Fig- that do all the work. Hence, because we want to gain a more ure 1 summarizes these proteomic workflows. comprehensive understanding of this machinery and further Gel-based protein separation methods have the advantage develop the concept of nutritional systems biology, proteo- of physically preserving the protein context and generating mics is at the center of this concerted action. real protein images. However, they have limited dynamic range, bias toward the more easily soluble proteins, and Proteomics technology a low degree of automation with, in consequence, low throughput. The most advanced method for 2D protein sepa- Protein identification ration is differential imaging gel electrophoresis [22], which relies on multiplexed staining and coprocessing of one con- Any proteomic study, be it in a nutritional or other frame- trol plus a maximum of two case samples. Protein spots work, commences with a protein survey of what can be have then to be detected, excised, digested with trypsin, ‘‘seen’’ in a given sample and condition. Identifying proteins and amended to LC-MS/MS. at a large scale and with high throughput is a mass spectro- Complementary to the gels and in view of an increasing de- metric business. Figure 1 outlines proteomic workflows for mand for throughput and speed, (multi)dimensional LC the ‘‘discovery mode.’’ setups have been coupled online to MS analysis, with simple Mass spectrometers can identify proteins and peptides by reversed-phase columns and combined strong cation ex- determination of their exact masses and generating informa- change-reversed phase systems being the most frequently ap- tion on the amino acid sequences. Today, the main ionization plied. These workflows run under the terms MudPIT methods deployed are electrospray [13] and matrix-assisted la- (multidimensional protein identification technology) or shot- ser desorption [14], which can put large, fragile biomolecules gun proteomics [23]. One major difference compared with gel such as proteins and peptides rapidly and gently into gas phase approaches is that the protein context is physically sacrificed and ionize them while preserving their integrity. These ion by upstream tryptic digestion of the protein mixture and sub- sources