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Nutriproteomics and Proteogenomics: Cultivating Two Novel Hybrid Fields of Personalized Medicine with Added Societal Value

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Nutriproteomics and Proteogenomics: Cultivating Two Novel Hybrid Fields of Personalized Medicine with Added Societal Value 240 Current Pharmacogenomics and Personalized Medicine, 2010, 8, 240-244 Editorial Nutriproteomics and Proteogenomics: Cultivating Two Novel Hybrid Fields of Personalized Medicine with Added Societal Value Vural Ozdemir1,*, Jean Armengaud2, Laurette Dubé3, Ramy Karam Aziz4 and Bartha M. Knoppers1 1Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada; 2Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Institut de Biologie Environnementale et Biotechnologie (IBEB), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Bagnols-sur-Cèze, F-30207, France; 3Desautels Faculty of Management, McGill University and the McGill World Platform (MWP) for Health and Economic Convergence, Montreal, QC, Canada; 4Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt Keywords: Biomarkers, biotechnology foresight, gene-centric human proteome project, nutriproteomics, personalized nutri- tion, population biobanks, prospective policy, proteogenomics. 1. NUTRIPROTEOMICS: A NEW SUBSPECIALTY IN proteins, and discerning the mechanisms by which proteome PERSONALIZED MEDICINE variation impacts nutrition related health outcomes. Kuss- mann notes that nutriproteomics science sits on a metapro- Personalized medicine requires diagnostics that enable teomics approach representing a synthesis of information customization of health interventions such as drugs, vac- from three different proteome levels: host, food and resident cines, stem cell therapy and nutrition [1-6]. It is important to microbes. While food (from animal, plant, or microbial approach personalized medicine with this broader outlook, sources) and host proteomes have been intensively studied in rather than a narrow focus on drug therapy, as nutrition and the past, proteomes of human-associated resident microbes, other health interventions influence health [7]. Such global i.e., the intestinal microbial metaproteome, have received vision is also needed in order to integrate information from relatively less attention [10]. Hence, nutriproteomics pre- multiple levels of the biological hierarchy from genome to sents an opportunity for personalized medicine to integrate proteome to metabolome, and ways in which these biological proteomics information from microbiome, host and food. parts interact with each other, the environment, and society more generally [8]. 2. ANTICIPATING THE NUTRIPROTEOMICS In the past, nutrition research and public health programs FUTURE(S) have focused on adequate access to food or alleviation of Nutrition represents a fundamental and ever present envi- nutritional deficiencies. This framework, however, has ronmental exposure that is essential to sustain cellular life shifted considerably over the past decade. Recognition of and population health. Hence, anticipating the future trajec- population heterogeneity in nutritional and adverse responses tories of nutriproteomics is of substantial interest both to to food led to a greater emphasis on understanding the mo- innovators and to the end-users of this knowledge in person- lecular basis of this variability and by extension, on the pos- alized medicine. Health technology assessment (HTA) is a sibility of nutritional interventions customized at a subpopu- widely used tool to support decisions on the future of tech- lation level. nologies in health care, public policy and business since the In the December issue of the CPPM, Kussmann intro- 1970s. More recently, HTA evolved beyond deterministic duces a new subfield of personalized medicine research: nu- analyses of “impacts” of a new technology. Modern HTA tritional proteomics or nutriproteomics [9]. This emerging does not assume that technologies or their social environ- application of proteomics involves the characterization ment are necessarily static [11]. Instead, we are increasingly and quantification of food-derived bioactive peptides and witnessing a model based on a dynamic co-evolution of technology and society, or real-time technology assessment [12]. Traditional HTA questions such as “Do we adopt/reject *Address correspondence to this author at the Centre of Genomics a technology, given that it is now well-developed and ma- and Policy, Department of Human Genetics, Faculty of Medicine, McGill ture?” are being replaced with “How can a new technology University, 740 Dr. Penfield, Suite 5200, Montreal, QC, Canada H3A 1A4; Tel: (514) 398-6920; Fax: (514) 398-8954; and its applications be co-designed and governed collabora- E-mail: [email protected] tively early on, together with innovators and anticipated end- 1875-6921/10 $55.00+.00 © 2010 Bentham Science Publishers Ltd. Editorial Current Pharmacogenomics and Personalized Medicine, 2010, Vol. 8, No. 4 241 users?” This signals an upstream shift in HTA to the stage of offer new perspectives for exploiting proteomics data that technology design before its applications enter the society. In will be generated through the HPP [19]. effect, this presents at the same time an important opportu- While vigorous debates on whether the HPP should be nity to negotiate a social contract between science and soci- gene- or protein-centric are expected [14, 20], the call made ety, and to steer the biotechnology future(s) towards those for an international HPP brings about formidable traction to that are likely to have desirable and sustainable impacts on the field of proteomics and nutriproteomics. This project global public health. Hence, modern HTA efforts underscore might also draw the genomics and proteomics communities the co-construction of innovations and their social context. much closer. Both communities share a complementary vi- Insofar as the current context of personalized medicine sion on data intensive 21st century science [8, 21, 22] that innovations is concerned, the rise of nutriproteomics coin- aims to understand the human biology and the interacting cides with two related, and potentially transformational, data environmental-societal factors at a systems level, for ad- intensive biotechnology initiatives: vances in diagnostic, preventive, prognostic and therapeutic end-points. Conceivably, the HPP will also stimulate spin- (1) the recent proposal for a gene-centric Human Proteome off novel proteomics platforms capable of higher throughput Project (HPP) [13, 14] and, analyses, as with genomics technologies after the HGP, and (2) the new field of proteogenomics [15]. thus drive down the cost of proteomics applications for per- sonalized medicine in the future. In this concise editorial commentary, we discuss how nutriproteomics, the HPP and proteogenomics might together 4. PROTEOGENOMICS: A PRODUCTIVE ALLI- cultivate a favourable ground for a productive alliance be- ANCE OF PROTEOMICS AND GENOMICS tween genomics and proteomics [16], and for novel strate- Genome annotation involves finding and delineating gies to study complex nutritional endpoints such as obesity structural genes and attributing a biological function to them. and healthy eating [17]. This is important not only for the human genome but also for 3. TOWARDS A GENE-CENTRIC HUMAN PRO- genomes from microbial pathogens and non-pathogens that TEOME PROJECT are becoming available as efforts to map the human micro- biome are accelerating [10]. Genome annotation, especially At the protein level, we still have scant knowledge of the assigning functions to genes and consistently classifying 20,300 predicted protein-coding human genes discovered these functions using a controlled vocabulary, is an arduous through the Human Genome Project (HGP). For the proteins and dynamic process that improves over time as knowledge encoded by most of these genes, the abundance, distribution, and understanding of gene products (e.g., proteins) accumu- subcellular localization, post-translational characteristics, late. To this end, proteogenomics is a new alliance of ge- interaction networks, and function are still poorly under- nomics and proteomics that substantially benefited the anno- stood. Recently, a group of researchers under the umbrella of tation of genomes [15, 16, 23]. Proteogenomics involves the Human Proteome Organization (HUPO) proposed a fed- high-throughput identification and characterization of pro- erated international effort to map the protein complement of teins by extra-large shotgun mass spectrometry approaches the human genome, a gene-centric HPP [13]. Given the and the integration of these data with genomic data. In es- enormous complexity of the human proteome and its varia- sence, proteomics provides orthogonal data for genome an- tion in each person over time, normal physiology and disease notation, as a complement to the DNA-centric evidence used in different cell types, the HPP is being conceived as a sys- to predict protein-coding sequences and gene function, or the tematic effort to deliver on reasonable and achievable end- RNA-centric evidence revealing transcribed loci. These or- points. Accordingly, this group of proteomics researchers thogonal data will be integrated as essential parts of auto- aims “to ensure that, for each predicted protein-coding gene, mated genome annotation pipelines (e.g., RAST), especially at least one of its major representative proteins will be char- as the number of sequenced genomes increases exponentially acterized in the context of its major anatomical sites of ex- [24]. Notably, proteogenomics analyses of the bacterium pression, its abundance, and its interacting protein partners”
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