Systems Biology of Personalized Nutrition: Feature Article
Systems Biology of Personalized Nutrition: Feature Article
Systems Biology of Personalized Nutrition: Feature Article
Ben van Ommen, Tim van den Broek, Iris de Hoogh, Marjan van Erk, Eugene van Someren,
Tanja Rouhani-Rankouhi, Joshua C. Anthony, Koen Hogenelst, Wilrike Pasman, André Boorsma,
and Suzan Wopereis
Affiliations: B. van Ommen, T. van den Broek, I. de Hoogh, M. van Erk, E. van Someren, T. Rouhani-Rankouhi, K. Hogenelst, W. Pasman,
A. Boorsma, and S. Wopereis are with TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands.
J.C. Anthony is with Habit LLC, Oakland, California, USA.
Correspondence: B. van Ommen, TNO, Utrechtseweg 48, Postbox 360, 3700 AJ Zeist, the Netherlands. Email: ben.vanommen@tno.nl.
Key words: flexibility, nutrigenetics, nutrigenomics, personalized nutrition, systems biology.
C The Author(s) 2017. Published by Oxford University Press on behalf of the International Life Sciences Institute.
V
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doi: 10.1093/nutrit/nux029
Nutrition ReviewsV Vol. 75(8):579–599
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Table 1 Examples of personal goals in relation to personal nutrition
Goal Definition
Weight management Maintaining (or attaining) an ideal body weight and/or body shaping that ties into heart, muscle, brain, and
metabolic health
Metabolic health Keeping metabolism healthy today and tomorrow
Cholesterol Reducing and optimizing the balance between high-density lipoprotein and low-density lipoprotein choles-
terol in individuals in whom this is disturbed
Blood pressure Reducing blood pressure in individuals who have elevated blood pressure
Heart health Keeping the heart healthy today and tomorrow
Muscle Having muscle mass and muscle functional abilities. This is the physiological basis or underpinning of the
consumer goal of “strength”
Endurance Sustaining energy to meet the challenges of the day (eg, energy to do that report at work, energy to play
soccer with your children after work)
have a specific nutrition component. Only recently, sci- Finally, this review demonstrates that macronutrient,
entific evidence has shown that advances in analytical micronutrient, and non-nutrient recommendations can
technologies, data science, molecular physiology, and be optimized at the individual level, depending on a
nutritional knowledge may allow the subgrouping of person’s biological characteristics and specific goals.
populations to be refined to a more personal level. This
has resulted in the definition and scientific substantia- PERSONALIZED NUTRITION IN THE ERA OF
tion of a range of personalized health and performance LARGE-SCALE BIOLOGY
goals. Often, these goals extend beyond prevention
and/or mitigation of chronic disease and include multi- Public health recommendations for nutrition and diet
ple aspects of well-being, such as mood, attention, en- are based on averages of population data. However,
durance, and weight maintenance, as well as well-being individuals who adhere to these recommendations will
equivalents of medical conditions (maintenance of glu- differ in their response because of the inherent varia-
cose control, normal blood pressure, healthy levels of tions in and complexity of individual genetic makeups
serum lipids and low-density lipoprotein [LDL] and that interact with a host of environmental stimuli.
high-density lipoprotein [HDL] cholesterols, etc). Overall, the so-called omics revolution provides a solid
Indeed, with respect to nutrition, the boundaries be- framework for a systems-based approach to personal-
tween medical treatments, illness prevention strategies, ized nutrition research. There are, however, limitations
and strategies to achieve optimal health have become to the application of the current framework of evidence
artificial and are a legal hindrance to best nutritional based on randomized controlled trials, which are
practice. For example, the mechanisms of glycemic designed to minimize variation across study population
control and the nutritional approaches to optimize groups, to these new opportunities. In contrast, an ap-
metabolic health and cure type 2 diabetes are almost proach to personalized research requires that individual
identical, yet nutritional interventions are underused variation be embraced, thus necessitating a different ex-
in medical practice. Already in 2002, the Diabetes perimental approach. Indeed, enough inter-individual
Prevention Program established by the US National variation is available and can be quantified to fine-tune
Institute of Diabetes and Digestive and Kidney the genome–exome–phenome relationships. Until re-
Diseases provided evidence that a multiyear lifestyle cently, this biological variation, now exposed by exten-
modification program was more effective than metfor- sive and accurate phenotyping, was ignored (dismissed
min treatment in reducing the incidence of diabetes in as confounders) or avoided (minimized through stratifi-
high-risk persons.1,2 cation). Tools to translate these genotypic and pheno-
This article describes biological mechanisms from a typic variations into personalized recommendations
systems perspective and outlines how the biology of using alternative research approaches, such as n ¼ 1 re-
personalized nutrition can be translated into recom- search paradigms, are now available.3
mendations for achieving specific health and perfor- Over the past 2 decades, various technological revo-
mance goals for individuals (Table 1). The concept of lutions have provided the building blocks for a systems
“systems flexibility” is introduced as an overarching physiology approach. The time is approaching when
biological mechanism, and a number of relevant exam- personal genomes, thousands of plasma proteins and
ples are examined in the context of metabolic health. metabolites can be scrutinized affordably, and detailed
muscle adipose
vasculature
gut
organs
liver pancreas
triglycerides
folate B12 choline
K
dairy leafy Meat fish
carnine nutrients
fruit vegetables egg (connected in diets)
carbs Grains Mg
protein
&nuts
fiber legumes
Figure 1 A systems biology view on personalized nutrition. Four interacting layers are used to demonstrate the connection between
personal nutrition–based consumer goals (top layer) and nutrients (bottom layer). The 2 middle layers (the organ and process layers)
connect nutrients to goals and represent the detailing of the biological processes involved. These 2 layers are extended in Figure 2.
Abbreviations: K, potassium; Mg, magnesium.
within the organ where loss of flexibility occurs. For ex- flexibility is impaired in obese individuals with type 2
ample, the failure of peripheral adipose tissue to ade- diabetes24 and likely contributes to the selective accu-
quately absorb glucose or convert it into fatty acids may mulation of saturated fatty acids.25 Figure 2 summarizes
lead to the accumulation of hepatic lipids.15,16 the major processes within and between liver, muscle,
Subsequently, other organs (muscle, liver) may also be- pancreas, and adipose tissue involved in the mainte-
come insulin resistant. Several factors can cause insulin nance of plasma glucose homeostasis. It shows several
resistance, including nutrition (overnutrition or, in examples of mechanisms related to the loss of metabolic
some cases, micronutritional inadequacies) and disease. flexibility, which can result in liver steatosis and other
Genetics may also contribute to the development of dis- metabolic impairments. Thus, many processes are con-
ease.17–20 Insulin resistance can also cause increased ac- nected to form a metabolic system in which all parts
cumulation of hepatic triglycerides, ultimately resulting must function optimally and in which malfunctioning
in hepatic steatosis and fatty liver disease.21 (loss of flexibility) of one of the processes may become
Accumulation of hepatic triglycerides can be caused by manifest in other processes or organs. Furthermore, dif-
adipose tissue malfunctioning; it can also be caused by a ferent mechanisms may be impaired in different indi-
shortage of choline resulting from genetic disorders, in- viduals with the same disease. Changes in strategies for
cluding those affecting phosphatidylethanolamine N- handling energy open avenues for personalized
methyltransferase (PEMT) —an enzyme involved in the “systems interventions,” either by modifying the quan-
hepatic biosynthesis of phosphatidylcholine.22 tity, timing, and source of energy consumed, or by opti-
Alternatively, low dietary intake of carnitine, which is mizing the processes involved, through the
essential for shuttling fatty acids into the mitochondria, manipulation of nutrients or other lifestyle components.
may contribute to fatty liver as a result of poor fatty In other words, although impaired phenotypic flexibil-
acid oxidation.23 ity may contribute to morbidities, the opposite is also
Both adipose tissue insulin resistance and hepatic true: regaining or optimizing phenotypic flexibility is
insulin resistance affect systemic triglyceride handling the basis of prevention and cure of metabolic diseases.
and metabolic flexibility (the capacity to switch from Interestingly, the concept of systems flexibility may be
glucose to fatty acids as fuel) in muscle. Metabolic valid for both the health/disease trajectory and the aging
trajectory. Many processes involved in aging and in- glucose tolerance test is used clinically to quantify the
creased frailty (energy/glucose/insulin homeostasis, plasma glucose response upon absorption of 75 g of glu-
protein homeostasis, redox homeostasis, mitochondrial cose and provides quantitative information on various
homeostasis, stress resistance, inflammation control) aspects of insulin sensitivity and glucose handling. This
are part of the systems flexibility concept.26,27 concept was extended by adding more analytical param-
In summary, systems flexibility is centrally posi- eters (levels of insulin, inflammatory markers, fatty
tioned in health, disease, and, possibly, aging, and inter- acids, triglycerides, etc) and other stressors (various
individual variations may have multiple causes and lipid/carbohydrate/protein formulations). The science,
consequences. Systems flexibility is a combination of all technology, and applicability of these stress response
of the interacting systems, each of which may have a ge- biomarkers in nutrition research has been extensively
nome component, and a response to environmental fac- reviewed by Stroeve et al.28
tors. Often, single parameters of flexibility, such as The application of both an oral glucose tolerance test
glucose flexibility, are composites of many underlying and a standardized mixed-meal challenge test to compare
processes, each possibly having individual characteris- processes between healthy and metabolically impaired
tics. It is, therefore, important to observe, quantify, and individuals (ie, those with type 2 diabetes) revealed a large
intervene on a systems level and not only on the basis number of biological processes that were different between
of single parameters. the 2 groups (S.W., unpublished data, 2017). The same 2
challenge tests accurately quantified health differences
QUANTIFICATION OF SYSTEMS FLEXIBILITY: within a cohort of 100 healthy individuals ranging in age
BIOMARKERS OF STRESS RESPONSE and fat percentage, substantiating the claim that these bio-
markers can indeed be used to quantify health. This study
Traditionally, plasma biomarkers are measured under used stress response biomarker panels comprising 120
homeostatic (overnight fasting) conditions. If system measured markers that could quantify all relevant systems
flexibility is indeed important to health, the quantifica- flexibility processes. A growing number of nutritional in-
tion of flexibility and its use as a biomarker is relevant. tervention studies, including challenge tests, are being per-
Flexibility can be quantified by using tolerance, chal- formed. A database that focuses on nutritional
lenge, or stress tests. Further, there should be a clear intervention studies of systems flexibility has been estab-
distinction between how markers behave in response to lished, the Nutritional Phenotype Database (http://www.
a challenge under conditions of health versus condi- dbnp.org/). Eventually, the use of a challenge test that
tions of disease. A number of relevant biomarkers exist quantifies systems flexibility could become standard pro-
and are used in tolerance tests. For example, the oral cedure in health diagnostics.29
Lipid flexibility
Adipose insulin sensivity
• Adipokine producon
• Lipoprotein producon
• Muscle insulin sensivity
• Ketogenesis ** **
• beta-oxidaon ******* ** • gluconeogenesis
• Lipolysis
Carnine, choline • insulin sensivity
• incren producon
• bile producon
• insulin sensivity
• Disposion index
• Metabolic flexibility
* *
* ******** *** *
***** * *** * *
Figure 3 The “health space” concept to visualize aspects of systems flexibility, the involvement of specific biological processes, and
the effect of personalized nutritional interventions on these processes. The 3-dimensional space is created by 3 distinct axes, on pur-
pose defined to represent biologically relevant processes (this is in contrast with normal multivariate statistical approaches such as principle
component analysis, where the axes are purely defined on statistical grounds). Each of the axes is constructed from the systems flexibility re-
sponse biomarker profiles connected to the processes mentioned with each axis (see Stroeve et al28 for a detailed explanation of the relation-
ship between biomarkers and biological processes). The multivariate statistical approach is explained in Bouwman et al.30 The effect of
hypothetical nutritional intervention studies is demonstrated by the arrows. Abbreviations: DHA, docosahexaenoic acid; EPA, eicosapentaenoic
acid; Mg, magnesium; Se, selenium; Vit E, vitamin E; Vit K, vitamin K.
A key question, then, is how to define and measure of biomarker panels. Until recently, these large bio-
the state of optimal systems flexibility. This could be marker panels have been too costly to be used outside
achieved in part by using single-parameter methods like of research projects. However, the cost of both geno-
the oral glucose tolerance test, which can be used to de- typic and phenotypic biomarker panels is decreasing
termine a curve derived from optimal homeostatic (fast- rapidly, and it is now possible to assess large research
ing) plasma glucose concentration, optimal plasma cohorts, patient populations, and even consumer
glucose peak concentration and time, optimal time to groups on a routine basis, allowing new disruptive
return to homeostasis, etc. This method can be used if developments in healthcare, as described elsewhere.29,31
sufficient data from a range of health, disease, and age Nevertheless, many questions remain: (1) Is “optimal
conditions are available to establish the comparison be- systems flexibility” equal for all? (2) Are individual data
tween the measured outcome and the desired health points needed? If so, what determines individual differ-
outcome. However, this method, underestimates the ences, and how can this be quantified? and (3) Is
complexity of a systems-based approach because it dis- “optimal systems flexibility” itself flexible (ie, how
regards so many other processes involved in systems should the bandwidth of optimal systems flexibility be
flexibility. To address this complexity, an emerging con- defined)? For example, does the definition of “optimal”
cept to visualize optimal systems flexibility is the “health vary, depending on an individual’s life stage, health
space.”30 Essentially, a 3-dimensional space is created goals, or priorities?
by using predefined axes that represent biological pro-
cesses relevant to different aspects of systems flexibility, SYSTEMS FLEXIBILITY AND NUTRITION: OPTIMIZING
each constructed from multiple biomarkers using mul- EACH PROCESS INVOLVED IN SYSTEMS FLEXIBILITY
tivariate statistical methods. The axes can be tailored to
the scope of the intervention. Figure 328,30 provides an ex- Because multiple biological processes distributed over
ample, tailored to the topic of this review, with the 3 axes various organs, each of which might function subopti-
constructed as carbohydrate flexibility, lipid flexibility, and mally, are involved in systems flexibility, interventions
inflammatory stress. To support the advancement of new that optimize these individual processes need to be
health space models, detailed information about organ designed. Different interventions targeting the same
and process flexibility can be obtained through a number outcome are possible. Upon detailed analysis, results
Renopathy
Stroke
Nephropathy
gut
IBD Brain
inflammaon
disorders
β-cell Pathology
Cardiac Heart Myocardial
dysfuncon failure infacons gluc Risk factor
Figure 6 A systems flexibility view in the context of personalized nutrition. The inner part of the figure represents the metabolic inflam-
matory part (yellow boxes) connected to risk factors of the metabolic syndrome (red boxes), which is termed phenotypic flexibility (Van
Ommen et al29,64). Imbalance or loss of flexibility leads to one or more pathologies (blue boxes). This system is connected to the outer circle
of neurohormonal processes, which impact the system flexibility (green boxes). A number of nutrients are shown where they interfere with
this flexibility scheme. Abbreviations: gluc, glucose; IBD, inflammatory bowel disease; IR, insulin resistance; LDL, low-density lipoprotein; Se, se-
lenium; Zn, zinc.
depends on the physiological context. To translate the inflammation, decreases with intake of both vitamins E
above information into personalized dietary recom- and D.97,98 Vitamin D has been shown to inhibit nu-
mendations, it may be useful to determine the specific clear factor kappa B (NF-jB) pathway–dependent tran-
insulin-dependent systems flexibility subtype of an indi- scriptional activation through activation of IjB-a,
vidual (as depicted in Figure 3) together with the indi- which may explain changes in CRP production.99
vidual’s vitamin D, magnesium, and vitamin K levels. Vitamin E decreases inflammation in several ways, in-
Individuals with decreased b-cell function may be ad- cluding through activating protein kinase C a and sub-
vised to take (a higher dose of) vitamin K, vitamin D, sequently inhibiting NF-jB and through inhibiting the
and magnesium. Individuals with the muscle insulin re- release of interleukin 1b (IL-1b) from monocytes.100,101
sistance phenotype may benefit from extra vitamin D, Meta-analyses have suggested an inverse relationship
magnesium, and epigallocatechin gallate, whereas non- between magnesium intake and chronic inflammation.
obese, postmenopausal female individuals with liver in- Magnesium deficiency might contribute to elevated
sulin resistance may benefit from soy isoflavones. CRP concentrations by activating macrophages via the
N-methyl-D-aspartate receptor and subsequently releas-
Inflammation ing interleukin 6 (IL-6) and tumor necrosis factor a
(TNF-a).102,103 Furthermore, a large cross-sectional
Chronic low-grade inflammation is involved in many study in the United States showed that flavonoid intake
pathologies,94 its modulation can be quantified by vari- is inversely related to CRP levels in adults.104
ous types of markers,95 and many dietary components The ability of long-chain n-3 fatty acids derived
can alter it.96 C-reactive protein (CRP), a biomarker of from the essential fatty acid alpha-linolenic acid to