A defined diet for pre-adult Drosophila melanogaster

Drosophila melanogaster is unique among animal models because it has a fully defined synthetic diet available to study nutrient-gene interactions. However, use of this diet is limited to adult studies due to impaired larval development and survival. Here, we provide an adjusted formula that reduces the developmental period, restores fat levels, enhances body mass, and fully rescues survivorship without compromise to adult lifespan. To demonstrate an application of this formula, we explored pre-adult diet compositions of therapeutic potential in a model of an inherited metabolic disorder affecting the metabolism of branched-chain amino acids. We reveal rapid, specific, and predictable nutrient effects on the disease state consistent with observations from mouse and patient studies. Together, our diet provides a powerful means with which to examine the interplay between diet and metabolism across all life stages in an animal model.

Tracing vitamins on the long non-coding lane of the transcriptome: vitamin regulation of LncRNAs

A major revelation of genome-scale biological studies in the post-genomic era has been that two-thirds of human genes do not encode proteins. The majority of non-coding RNA transcripts in humans are long non-coding RNA (lncRNA) molecules, non-protein-coding regulatory transcripts with sizes greater than 500 nucleotides. LncRNAs are involved in nearly every aspect of cellular physiology, playing fundamental regulatory roles both in normal cells and in disease. As result, they are functionally linked to multiple human diseases, from cancer to autoimmune, inflammatory, and neurological disorders. Numerous human conditions and diseases stem from gene-environment interactions; in this regard, a wealth of reports demonstrate that the intake of specific and essential nutrients, including vitamins, shapes our transcriptome, with corresponding impacts on health. Vitamins command a vast array of biological activities, acting as coenzymes, antioxidants, hormones, and regulating cellular proliferation and coagulation. Emerging evidence suggests that vitamins and lncRNAs are interconnected through several regulatory axes. This type of interaction is expected, since lncRNA has been implicated in sensing the environment in eukaryotes, conceptually similar to riboswitches and other RNAs that act as molecular sensors in prokaryotes. In this review, we summarize the peer-reviewed literature to date that has reported specific functional linkages between vitamins and lncRNAs, with an emphasis on mammalian models and humans, while providing a brief overview of the source, metabolism, and function of the vitamins most frequently investigated within the context of lncRNA molecular mechanisms, and discussing the published research findings that document specific connections between vitamins and lncRNAs.

Maternal dietary choline levels cause transcriptome shift due to genotype-by-diet interactions in rainbow trout (Oncorhynchus mykiss)

The objective of this study was to identify metabolic regulatory mechanisms affected by choline availability in rainbow trout (Oncorhynchus mykiss) broodstock diets associated with increased offspring growth performance. Three customized diets were formulated to have different levels of choline: (a) 0 % choline supplementation (Low Choline: 2065 ppm choline), (b) 0.6 % choline supplementation (Medium Choline: 5657 ppm choline), and (c) 1.2 % choline supplementation (High Choline: 9248 ppm choline). Six all-female rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning at 22 months post-hatch; their offspring were fed a commercial diet. Experimental broodstock diet did not affect overall choline, fatty acid, or amino acid content in the oocytes (p > 0.05), apart from tyrosine (p ≤ 0.05). Offspring body weights from the High and Low Choline diets did not differ from those in the Medium Choline diet (p > 0.05); however, family-by-diet and sire-by-diet interactions on offspring growth were detected (p ≤ 0.05). The High Choline diet did not improve growth performance in the six broodstock families at final harvest (520-days post-hatch, or dph). Numerous genes associated with muscle development and lipid metabolism were identified as affected by broodstock diet, including myosin, troponin C, and fatty acid binding proteins, which were associated with key signaling pathways of lipid metabolism, muscle cell development, muscle cell proliferation, and muscle cell differentiation. These findings indicate that supplementing broodstock diets with choline does regulate expression of genes related to growth and nutrient partitioning but does not lead to growth benefits in rainbow trout families selected for disease resistance.

The genomic landscape of chronic obstructive pulmonary disease: Insights from nutrigenomics

Chronic obstructivе pulmonary disеasе (COPD), a rеspiratory disеasе, is influenced by a combination of gеnеtic and еnvironmеntal factors. Thе fiеld of nutrigеnomics, which studiеs thе intеrplay bеtwееn diеt and gеnеs, provides valuable insights into thе gеnomic landscapе of COPD and its implications for production and managеmеnt. This rеviеw providеs a comprеhеnsivе ovеrviеw of thе gеnеtic aspеcts of COPD and thе rolе of nutrigеnomics in advancing our undеrstanding of thе undеrlying mеchanisms. Through studies of gеnomе-widе associations, researchers have identified gеnеtic factors that contribute to suscеptibility to COPD. Thеsе gеnеs arе associatеd with oxidativе strеss, inflammation, and antioxidant dеfеnsе mеchanisms. Nutrigеnomics rеsеarch is currеntly invеstigating how diеtary componеnts interact with gеnеtic variations to modulatе thе dеvеlopmеnt of COPD. Antioxidants, omеga-3 fatty acids and vitamin D havе dеmonstratеd potеntial bеnеfits in rеducing inflammation, improving lung function, and minimizing еxacеrbations in patients with COPD. Therefore, there are sеvеral challеngеs that must be added to the nutrigеnomic rеsеarch. The challenges include thе nееd for largеr clinical trials, adding hеtеrogеnеity and validating biomarkеrs. In the tеrms of futurе dirеctions, prеcision nutrition, gеnе-basеd thеrapiеs, biomarkеr dеvеlopmеnt, intеgration of multi-omics data, systеms biology analysis, longitudinal studiеs, and public hеalth implications arе important arеas to еxplorе. Pеrsonalizеd nutritional intеrvеntions based on an individual's gеnеtic profilе hold grеat promisе for optimizing COPD managеmеnt. In conclusion, nutrigеnomics provides valuable insights into the gеnomic landscapе of COPD and its intеraction with the disease. This knowlеdgе can guidе thе dеvеlopmеnt of pеrsonalizеd diеtary stratеgiеs and gеnе-basеd thеrapiеs for thе prеvеntion and managеmеnt of COPD. Howеvеr, morе rеsеarch is nееdеd to validatе thеsе findings, dеvеlop еffеctivе intеrvеntions, and implеmеnt thеm еffеctivеly in clinical practicе to improvе thе quality of lifе for pеoplе with COPD.

A crossover randomized controlled trial examining the effects of black seed (Nigella sativa) supplementation on IL-1β, IL-6 and leptin, and insulin parameters in overweight and obese women

BACKGROUND

Nigella sativa (NS) oil has been found to have advantageous benefits in the management of inflammation and obesity. This study investigated the effect of NS supplementation on blood mRNA expressions and serum levels of IL-1β, IL-6, leptin, and insulin concentrations in overweight/obese women.

METHODS

In a crossover design, participants were randomized to receive either NS supplements(2000 mg/day) or placebo for 2 durations(8 weeks). With between-subject and within-subject components and interactions, a repeated-measure ANOVA model was used considering the treatment, time, and the carryover effects. Cohen's d(d) was used to measure the magnitude of the effects.

RESULTS

Forty-six eligible participants were included. NS supplementation significantly reduced the mRNA expressions(d=-0.68, P = 0.03) and serum levels of IL-1β with medium-high effect sizes(d=-1.6, P < 0.001). Significant reductions with large effect sizes were observed in the gene expression and serum levels of IL-6(d=-1.8, d=-0.78, respectively; P < 0.01) and Leptin(d=-1.9, d=-0.89, respectively; P < 0.01, serum leptin P carryover < 0.001). Despite the meaningful carryover effect for serum leptin, results remained significant following the first intervention period analysis(P < 0.001). A significant but low effect size decrease in serum insulin was observed(d=-0.3, P = 0.02).

CONCLUSIONS

The clinical significance of present findings regarding improvements in obesity-related pro-inflammatory markers must be interpreted with caution due to some observed medium-low effect sizes.

TRIAL REGISTRATION

IRCT20180430039475N1 (Date:25/6/2018).

Triangulating nutrigenomics, metabolomics and microbiomics toward personalized nutrition and healthy living

The unique physiological and genetic characteristics of individuals influence their reactions to different dietary constituents and nutrients. This notion is the foundation of personalized nutrition. The field of nutrigenetics has witnessed significant progress in understanding the impact of genetic variants on macronutrient and micronutrient levels and the individual's responsiveness to dietary intake. These variants hold significant value in facilitating the development of personalized nutritional interventions, thereby enabling the effective translation from conventional dietary guidelines to genome-guided nutrition. Nevertheless, certain obstacles could impede the extensive implementation of individualized nutrition, which is still in its infancy, such as the polygenic nature of nutrition-related pathologies. Consequently, many disorders are susceptible to the collective influence of multiple genes and environmental interplay, wherein each gene exerts a moderate to modest effect. Furthermore, it is widely accepted that diseases emerge because of the intricate interplay between genetic predisposition and external environmental influences. In the context of this specific paradigm, the utilization of advanced "omic" technologies, including epigenomics, transcriptomics, proteomics, metabolomics, and microbiome analysis, in conjunction with comprehensive phenotyping, has the potential to unveil hitherto undisclosed hereditary elements and interactions between genes and the environment. This review aims to provide up-to-date information regarding the fundamentals of personalized nutrition, specifically emphasizing the complex triangulation interplay among microbiota, dietary metabolites, and genes. Furthermore, it highlights the intestinal microbiota's unique makeup, its influence on nutrigenomics, and the tailoring of dietary suggestions. Finally, this article provides an overview of genotyping versus microbiomics, focusing on investigating the potential applications of this knowledge in the context of tailored dietary plans that aim to improve human well-being and overall health.

Nutrigenomics and redox regulation: Concepts relating to the Special Issue on nutrigenomics

During our whole lifespan, from conception to death, the epigenomes of all tissues and cell types of our body integrate signals from the environment. This includes signals derived from our diet and the uptake of macro- and micronutrients. In most cases, this leads only to transient changes, but some effects of this epigenome programming process are persistent and can even be transferred to the next generation. Both epigenetic programming and redox processes are affected by the individual choice of diet and other lifestyle decisions like physical activity. The nutrient-gene communication pathways have adapted during human evolution and are essential for maintaining health. However, when they are maladaptive, such as in long-term obesity, they significantly contribute to diseases like type 2 diabetes and cancer. The field of nutrigenomics investigates nutrition-related signal transduction pathways and their effect on gene expression involving interactions both with the genome and the epigenomes. Several of these diet-(epi)genome interactions and the involved signal transduction cascades are redox-regulated. Examples include the effects of the NAD+/NADH ratio, vitamin C levels and secondary metabolites of dietary molecules from plants on the acetylation and methylation state of the epigenome as well as on gene expression through redox-sensitive pathways via the transcription factors NFE2L2 and FOXO. In this review, we summarize and extend on these topics as well as those discussed in the articles of this Special Issue and take them into the context of redox biology.

Nutrigenomics and microbiome shaping the future of personalized medicine: a review article

The relationship between nutrition and genes has long been hinted at and sometimes plainly associated with certain diseases. Now, after many years of research and coincidental findings, it is believed that this relationship, termed "Nutrigenomics," is certainly a factor of major importance in various conditions. In this review article, we discuss nutrigenomics, starting with basics definitions and enzymatic functions and ending with its palpable association with cancer. Now, diet is basically what we eat on a daily basis. Everything that enters through our alimentary tract ends up broken down to minute molecules and amino acids. These molecules interact with our microbiome and genome in discreet ways. For instance, we demonstrate how proper intake of probiotics enhances beneficial bacteria and may alleviate IBS and prevent colorectal cancer on the long term. We also show how a diet rich in folic acid is essential for methylenetetrahydrofolate reductase (MTHFR) function, which lowers risk of colorectal cancer. Also, we discuss how certain diets were associated with development of certain cancers. For example, red and processed meat are highly associated with colorectal and prostate cancer, salty diets with stomach cancer, and obesity with breast cancer. The modification of these diets significantly lowered the risk and improved prognosis of these cancers among many others. We also examined how micronutrients had a role in cancer prevention, as vitamin A and C exert anti-carcinogenic effects through their function as antioxidants. In addition, we show how folic acid prevent DNA mutations by enhancing protein methylation processes. Finally, after a systematic review of myriad articles on the etiology and prevention of cancer, we think that diet should be a crucial feature in cancer prevention and treatment programs. In the future, healthy diets and micronutrients may even be able to successively alter the liability to genetic mutations that result in cancer. It also will play a role in boosting treatment and improving prognosis of diagnosed cancers.

Strategies to fortify the nutritional values of polished rice by implanting selective traits from brown rice: A nutrigenomics-based approach

Whole-grain cereals are important components of a healthy diet. It reduces the risk of many deadly diseases like cardiovascular diseases, diabetes, cancer, etc. Brown rice is an example of whole grain food, which is highly nutritious due to the presence of various bioactive compounds (flavonoids, phenolics, vitamins, phytosterols, oils, etc.) associated with the rice bran layer of brown rice. White rice is devoid of the nutritious rice bran layer and thus lacks the bioactive compounds which are the major attractants of brown rice. Therefore, to confer health benefits to the public at large, the nutrigenomic potential of white rice may be improved by integrating the phytochemicals associated with the rice bran layer of brown rice into it via biofortification processes like conventional breeding, agronomic practices, metabolic engineering, CRISPR/Cas9 technology, and RNAi techniques. Thus, this review article focuses on improving the nutritional qualities of white/polished rice through biofortification processes, utilizing new breeding technologies (NBTs).

Nutrigenomics: SNPs correlated to physical activity, response to chiropractic treatment, mood and sleep

Abstract

Nutrigenomics, a rapidly evolving field that bridges genetics and nutrition, explores the intricate interactions between an individual's genetic makeup and how they respond to nutrients. At its core, this discipline focuses on investigating Single Nucleotide Polymorphisms (SNPs), the most common genetic variations, which significantly influence a person's physiological status, mood regulation, and sleep patterns, thus playing a pivotal role in a wide range of health out-comes. Through decoding their functional implications, researchers are able to uncover genetic factors that impact physical fitness, pain perception, and susceptibility to mood disorders and sleep disruptions. The integration of nutrigenomics into healthcare holds the promise of transformative interventions that cater to individual well-being. Notable studies shed light on the connection between SNPs and personalized responses to exercise, as well as vulnerability to mood disorders and sleep disturbances. Understanding the intricate interplay between genetics and nutrition informs targeted dietary approaches, molding individual health trajectories. As research advances, the convergence of genetics and nourishment is on the brink of reshaping healthcare, ushering in an era of personalized health management that enhances overall life quality. Nutrigenomics charts a path toward tailored nutritional strategies, fundamentally reshaping our approach to health preservation and preventive measures.

Nutrigenomics: SNPs Correlated to Lipid and Carbohydrate Metabolism

Background

Nutrigenomics - the study of the interactions between genetics and nutrition - has emerged as a pivotal field in personalized nutrition. Among various genetic variations, single-nucleotide polymorphisms (SNPs) have been extensively studied for their probable relationship with metabolic traits.

Methods

Throughout this review, we have employed a targeted research approach, carefully handpicking the most representative and relevant articles on the subject. Our methodology involved a systematic review of the scientific literature to ensure a comprehensive and accurate overview of the available sources.

Results

SNPs have demonstrated a significant influence on lipid metabolism, by impacting genes that encode for enzymes involved in lipid synthesis, transport, and storage. Furthermore, they have the ability to affect enzymes in glycolysis and insulin signaling pathways: in a way, they can influence the risk of type 2 diabetes. Thanks to recent advances in genotyping technologies, we now know numerous SNPs linked to lipid and carbohydrate metabolism. The large-scale studies on this topic have unveiled the potential of personalized dietary recommendations based on an individual's genetic makeup. Personalized nutritional interventions hold promise to mitigate the risk of various chronic diseases; however, translating these scientific insights into actionable dietary guidelines is still challenging.

Conclusions

As the field of nutrigenomics continues to evolve, collaborations between geneticists, nutritionists, and healthcare providers are essential to harness the power of genetic information for improving metabolic health. By unraveling the genetic basis of metabolic responses to diet, this field holds the potential to revolutionize how we approach dietary recommendations and preventive healthcare practices.

Nutrigenomics: SNPs correlated to Food Preferences and Susceptibilities

Background

Nutrigenomics explores the intricate interplay between single nucleotide polymorphisms (SNPs), food preferences, and susceptibilities.

Methods

This study delves into the influence of SNPs on food sensitivities, allergies, tyramine intolerance, and taste preferences. Genetic factors intricately shape physiological reactions to dietary elements, with polymorphisms contributing to diverse sensitivities and immune responses.

Results

Tyramine intolerance, arising from metabolic inefficiencies, unveils genetic markers exerting influence on enzyme function. SNPs transcend genetic diversity by exerting substantial impact on food sensitivities/allergies, with specific variants correlating to heightened susceptibilities. Genes accountable for digesting food components play pivotal roles. Given the rising prevalence of food sensitivities/allergies, understanding genetic foundations becomes paramount. In the realm of taste and food preferences, SNPs sculpt perception and choice, yielding variances in taste perception and preferences for sweetness, bitterness, and umami. This genetic medley extends its reach to encompass wider health implications.

Conclusions

In this review article, we have focused on how polymorphisms wield significant sway over physiological responses, sensitivities, and dietary inclinations. Unraveling these intricate relationships illuminates the path to personalized nutrition, potentially revolutionizing tailored recommendations and interventions.

Nutrigenomics: SNPs correlated to detoxification, antioxidant capacity and longevity

Abstract

Nutritional genomics, also known as nutrigenomics, is the study of how a person's diet and genes interact with each other. The field of nutrigenomics aims to explain how common nutrients, food additives and preservatives can change the body's genetic balance towards either health or sickness. This study reviews the effects of SNPs on detoxification, antioxidant capacity, and longevity. SNPs are mutations that only change one nucleotide at a specific site in the DNA. Specific SNPs have been associated to a variety of biological processes, including detoxification, antioxidant capacity, and longevity. This article mainly focuses on the following genes: SOD2, AS3MT, CYP1A2, and ADO-RA2A (detoxification); LEPR, TCF7L2, KCNJ11, AMY1, and UCP3 (antioxidant capacity); FOXO3 and BPIFB4 (longevity). This review underlines that many genes-among which FOXO3, TCF7L2, LEPR, CYP1A2, ADORA2A, and SOD2-have a unique effect on a person's health, susceptibility to disease, and general well-being. Due to their important roles in numerous biological processes and their implications for health, these genes have undergone intensive research. Examining the SNPs in these genes can provide insight into how genetic variants affect individuals' responses to their environment, their likelihood of developing certain diseases, and their general state of health.

New insights into the nutritional genomics of adult-onset riboflavin-responsive diseases

Riboflavin, or vitamin B2, is an essential nutrient that serves as a precursor to flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). The binding of the FAD and/or FMN cofactors to flavoproteins is critical for regulating their assembly and activity. There are over 90 proteins in the human flavoproteome that regulate a diverse array of biochemical pathways including mitochondrial metabolism, riboflavin transport, ubiquinone and FAD synthesis, antioxidant signalling, one-carbon metabolism, nitric oxide signalling and peroxisome oxidative metabolism. The identification of patients with genetic variants in flavoprotein genes that lead to adult-onset pathologies remains a major diagnostic challenge. However, once identified, many patients with adult-onset inborn errors of metabolism demonstrate remarkable responses to riboflavin therapy. We review the structure:function relationships of mutant flavoproteins and propose new mechanistic insights into adult-onset riboflavin-responsive pathologies and metabolic dysregulations that apply to multiple biochemical pathways. We further address the vexing issue of how the inheritance of genetic variants in flavoprotein genes leads to an adult-onset disease with complex symptomologies and varying severities. We also propose a broad clinical framework that may not only improve the current diagnostic rates, but also facilitate a personalized approach to riboflavin therapy that is low cost, safe and lead to transformative outcomes in many patients.

The Influence of Single Nucleotide Polymorphisms On Body Weight Trajectory After Bariatric Surgery: A Systematic Review

PURPOSE OF REVIEW

To conduct a systematic review to summarize the results of studies on this subject and to identify whether single nucleotide polymorphisms (SNPs) are good prognostic markers for body weight trajectory after bariatric surgery.

RECENT FINDINGS

A considerable number of events can influence the body weight trajectory after bariatric surgery, and in the post-genomic era, genetic factors have been explored. This study is registered with PROSPERO (CRD42021240903). SNPs positively associated with poor weight loss after bariatric surgery were rs17702901, rs9939609, rs1360780, rs1126535, rs1137101, rs17782313, rs490683, and rs659366. Alternatively, SNPs rs2229616, rs5282087, rs490683, rs9819506, rs4771122, rs9939609, rs4846567, rs9930506, rs3813929, rs738409, rs696217, rs660339, rs659366, rs6265, rs1801260, and rs2419621 predicted a higher weight loss after bariatric surgery. Six studies performed with a genetic risk score (GRS) model presented significant associations between GRS and outcomes following bariatric surgery. This systematic review shows that, different SNPs and genetic models could be good predictors for body weight trajectory after bariatric surgery. Based on the results of the selected studies for this Systematic Review is possible to select SNPs and metabolic pathways of interest for the GRS construction to predict the outcome of bariatric surgery to be applied in future studies.

Transcriptome-based nutrigenomics analysis reveals the roles of dietary taurine in the muscle growth of juvenile turbot (Scophthalmus maximus)

The present study explored transcriptomics and gene regulation variations in the muscle of turbot fed with dietary taurine. A 70-day feeding trial was conducted using turbot (initial body weight: 3.66 ± 0.02 g) fed with different levels of dietary taurine: 0 % (C), 0.4 % (T2), 1.2 % (T4) and 2.0 % (T6). Two methods were used to analyze and verify the taurine effects on muscle growth: (1) real-time quantitative PCR (qRT-PCR) for the key muscle growth-related genes and (2) transcriptomic analysis by next-generation sequencing (NGS). The results showed that 1.2 % of dietary taurine supplementation significantly increased the expression of muscle growth stimulatory genes, including TauT, myoD, Myf5, myogenin and follistatin. And also, the 1.2 % level significantly decreased the expression of the muscle growth-restricting gene (myostatin). Meanwhile, transcriptomics analysis found that 1.2 % dietary taurine supplementation significantly increased the number of up-regulated genes linked to metabolic pathways. In contrast, taurine significantly enriched the actin cytoskeleton and metabolic pathways in the T4 and T2 groups, respectively. These findings align with the gene ontology (GO) analysis, which indicated a higher number of cellular component (CC) gene expressions at a 1.2 % of dietary taurine compared to a 0.4 % of dietary taurine supplementation. In conclusion, dietary taurine had positive impacts on the growth-stimulatory genes. Moreover, 1.2 % of dietary taurine supplementation is important to the metabolic pathway enrichment.

Nutrigenomics of inward rectifier potassium channels

Inwardly rectifying potassium (Kir) channels play a key role in maintaining the resting membrane potential and supporting potassium homeostasis. There are many variants of Kir channels, which are usually tetramers in which the main subunit has two trans-membrane helices attached to two N- and C-terminal cytoplasmic tails with a pore-forming loop in between that contains the selectivity filter. These channels have domains that are strongly modulated by molecules present in nutrients found in different diets, such as phosphoinositols, polyamines and Mg²⁺. These molecules can impact these channels directly or indirectly, either allosterically by modulation of enzymes or via the regulation of channel expression. A particular type of these channels is coupled to cell metabolism and inhibited by ATP (KATP channels, essential for insulin release and for the pathogenesis of metabolic diseases like diabetes mellitus). Genomic changes in Kir channels have a significant impact on metabolism, such as conditioning the nutrients and electrolytes that an individual can take. Thus, the nutrigenomics of ion channels is an important emerging field in which we are attempting to understand how nutrients and diets can affect the activity and expression of ion channels and how genomic changes in such channels may be the basis for pathological conditions that limit nutrition and electrolyte intake. In this contribution we briefly review Kir channels, discuss their nutrigenomics, characterize how different components in the diet affect their function and expression, and suggest how their genomic changes lead to pathological phenotypes that affect diet and electrolyte intake.

Translation of nutrigenomic research for personalised and precision nutrition for cancer prevention and for cancer survivors

Personalised and precision nutrition uses information on individual characteristics and responses to nutrients, foods and dietary patterns to develop targeted nutritional advice that is more effective in improving the diet and health of each individual. Moving away from the conventional 'one size fits all', such targeted intervention approaches may pave the way to better population health, including lower burden of non-communicable diseases. To date, most personalised and precision nutrition approaches have been focussed on tackling obesity and cardiometabolic diseases with limited efforts directed to cancer prevention and for cancer survivors. Advances in understanding the biological basis of cancer and of the role played by diet in cancer prevention and in survival after cancer diagnosis, mean that it is timely to test and to apply such personalised and precision nutrition approaches in the cancer area. This endeavour can take advantage of the enhanced understanding of interactions between dietary factors, individual genotype and the gut microbiome that impact on risk of, and survival after, cancer diagnosis. Translation of these basic research into public health action should include real-time acquisition of nutrigenomic and related data and use of AI-based data integration methods in systems approaches that can be scaled up using mobile devices.

Adipose tissue angiogenesis genes are down-regulated by grape polyphenols supplementation during a human overfeeding trial

The adaptive response to overfeeding is associated with profound modifications of gene expression in adipose tissue to support lipid storage and weight gain. The objective of this study was to assess in healthy lean men whether a supplementation with polyphenols could interact with these molecular adaptations. Abdominal subcutaneous adipose tissue biopsies were sampled from 42 subjects participating to an overfeeding protocol providing an excess of 50% of their total energy expenditure for 31 days, and who were supplemented with 2 g/day of grape polyphenols or a placebo. Gene expression profiling was performed by RNA sequencing. Overfeeding led to a modification of the expression of 163 and 352 genes in the placebo and polyphenol groups, respectively. The GO functions of these genes were mostly involved in lipid metabolism, followed by genes involved in adipose tissue remodeling and expansion. In response to overfeeding, 812 genes were differentially regulated between groups. Among them, a set of 41 genes were related to angiogenesis and were downregulated in the polyphenol group. Immunohistochemistry targeting PECAM1, as endothelial cell marker, confirmed reduced angiogenesis in this group. Finally, quercetin and isorhamnetin, two polyphenol species enriched in the plasma of the volunteers submitted to the polyphenols, were found to inhibit human umbilical vein endothelial cells migration in vitro. Polyphenol supplementation do not prevent the regulation of genes related to lipid metabolism in human adipose tissue during overfeeding, but impact the angiogenesis pathways. This may potentially contribute to a protection against adipose tissue expansion during dynamic phase of weight gain.

Nutrigenomics in the context of evolution

Nutrigenomics describes the interaction between nutrients and our genome. Since the origin of our species most of these nutrient-gene communication pathways have not changed. However, our genome experienced over the past 50,000 years a number of evolutionary pressures, which are based on the migration to new environments concerning geography and climate, the transition from hunter-gatherers to farmers including the zoonotic transfer of many pathogenic microbes and the rather recent change of societies to a preferentially sedentary lifestyle and the dominance of Western diet. Human populations responded to these challenges not only by specific anthropometric adaptations, such as skin color and body stature, but also through diversity in dietary intake and different resistance to complex diseases like the metabolic syndrome, cancer and immune disorders. The genetic basis of this adaptation process has been investigated by whole genome genotyping and sequencing including that of DNA extracted from ancient bones. In addition to genomic changes, also the programming of epigenomes in pre- and postnatal phases of life has an important contribution to the response to environmental changes. Thus, insight into the variation of our (epi)genome in the context of our individual's risk for developing complex diseases, helps to understand the evolutionary basis how and why we become ill. This review will discuss the relation of diet, modern environment and our (epi)genome including aspects of redox biology. This has numerous implications for the interpretation of the risks for disease and their prevention.

Effect of different doses of cholecalciferol and calcidiol on meat quality parameters and skeletal muscle transcriptome profiles in swine

Skeletal muscle tissue is one of the potential targets for vitamin D actions. There are indications that vitamin D supplementation to swine has a positive effect on meat quality. However, these issues need further study, especially in terms of response to the use of different forms of vitamin D. We carried out a multi-purpose study to compare the effects of cholecalciferol and calcidiol on meat quality and muscle tissue transcriptome. Meat quality assessment and gene expression analysis were performed on longissimus dorsi samples collected from swine fed grower/finisher diets containing 2000 IU cholecalciferol/1500 IU cholecalciferol per kg (n = 8), 3000 IU cholecalciferol/2500 IU cholecalciferol per kg (n = 10), 2000 IU cholecalciferol +1000 IU calcidiol/1500 IU cholecaliferol +1000 IU calcidiol per kg (n = 8), and 2000 IU calcidiol/1500 IU calcidiol per kg (n = 8). The results suggest that increasing the dose of cholecalciferol and using calcidiol in the diet of finishers may improve meat texture parameters (shear force P = 0,014, toughness P = 0,048, cohesiveness P = 0,017, resilience P = 0,002). Shear force (68.46 N-51.42 N) and toughness (145.85 N-114.52 N) decreased the most under the effect of increasing cholecalciferol dosage. In turn, cohesiveness (0.60 N-0.65 N) and resilience (0.23 N-0.28 N) increased most strongly under the use of cholecalciferol+calcidiol. Moreover, the results indicate no significant effect of increasing cholecalciferol dose and use calcidiol in the swine diet on muscle tissue transcriptome.

Current challenges and future implications of exploiting the omics data into nutrigenetics and nutrigenomics for personalized diagnosis and nutrition-based care

Nutrigenetics and nutrigenomics, combined with the omics technologies, are a demanding and an increasingly important field in personalizing nutrition-based care to understand an individual's response to nutrition-guided therapy. Omics is defined as the analysis of the large data sets of the biological system featuring transcriptomics, proteomics, and metabolomics and providing new insights into cell regulation. The effect of combining nutrigenetics and nutrigenomics with omics will give insight into molecular analysis, as human nutrition requirements vary per individual. Omics measures modest intraindividual variability and is critical to exploit these data for use in the development of precision nutrition. Omics, combined with nutrigenetics and nutrigenomics, is instrumental in the creation of goals for improving the accuracy of nutrition evaluations. Although dietary-based therapies are provided for various clinical conditions such as inborn errors of metabolism, limited advancement has been done to expand the omics data for a more mechanistic understanding of cellular networks dependent on nutrition-based expression and overall regulation of genes. The greatest challenge remains in the clinical sector to integrate the current data available, overcome the well-established limits of self-reported methods in research, and provide omics data, combined with nutrigenetics and nutrigenomics research, for each individual. Hence, the future seems promising if a design for personalized, nutrition-based diagnosis and care can be implemented practically in the health care sector.

- Invited Review - Factors affecting beef quality and nutrigenomics of intramuscular adipose tissue deposition

Beef quality is characterized by marbling (marbling degree and marbling fineness), physiochemical (shear force, meat color, fat color, texture, and maturity), and sensory (tenderness, flavor, juiciness, taste, odor, and appearance) traits. This paper summarizes and addresses beef-quality characteristics and the beef-grading systems in Korea, Japan, the USA, and Australia. This paper summarizes recent research progresses on the genetic and nutritional factors that affect beef quality. Intramuscular (i.m.) adipose tissue deposition or marbling is a major determinant of beef quality. This paper addresses the mechanisms of i.m. adipose tissue deposition focused on adipogenesis and lipogenesis. We also address selected signaling pathways associated with i.m. adipose tissue deposition. Nutrients contribute to the cellular response and phenotypes through gene expression and metabolism. This paper addresses control of gene expression through several nutrients (carbohydrates, fat/fatty acids, vitamins, etc.) for i.m. adipose tissue deposition. Several transcription factors responsible for gene expression via nutrients are addressed. We introduce the concept of genome-based precision feeding in Korean cattle.

Molecular mechanisms underlying hypertensive effect of fructose and the preventive properties of inulin - Global transcriptomic analysis in rat aorta

BACKGROUND AND AIMS

Excessive intake of fructose is a significant contributor in the development of hypertension and pathogenesis of cardiometabolic diseases. We previously showed that dietary inulin can prevent fructose-induced hypertension in rats. Nevertheless, molecular mechanisms of both fructose and inulin in aorta remain unknown. The aim of this study was to identify global transcriptomic changes in aorta in rats on fructose-based diet or partial substitution of dietary fructose with inulin.

METHODS AND RESULTS

At the end of study periods, aortas were isolated, RNA extracted, and transcriptomics performed using microarrays followed by in-dept bioinformatic analyses. We observed that fructose-based diet affected the expression of over 1700 genes involved in the regulation of vascular functions, cell signaling, and cellular metabolism. Partial substitution of dietary fructose with inulin affected the expression of over 1300 genes regulating endothelial and vascular functions, including relaxin signaling pathway, immune/inflammatory response, or cellular metabolism. Bioinformatic analyses revealed transcription factors, such as Junb or Nr4a2, and miRNAs, such as miR-206, miR-137 or miR-375, as potential transcriptional and post-transcriptional regulators of identified differentially expressed genes. Genes identified following both diets are associated with development of cardiovascular diseases, hypertension, immune system diseases and metabolic diseases. Moreover, a negative correlation between the expression profiles obtained by fructose-based diet and that by partial substitution of dietary fructose with inulin was observed.

CONCLUSION

Our study showed that fructose can significantly impact global transcriptomic profile in aorta, changes that can be counteracted by inulin and which present relevant molecular mechanisms underlying its anti-hypertensive property.

Mechanistic insights into dietary (poly)phenols and vascular dysfunction-related diseases using multi-omics and integrative approaches: Machine learning as a next challenge in nutrition research

Dietary (poly)phenols have been extensively studied for their vasculoprotective effects and consequently their role in preventing or delaying onsets of cardiovascular and metabolic diseases. Even though early studies have ascribed the vasculoprotective properties of (poly)phenols primarily on their putative free radical scavenging properties, recent data indicate that in biological systems, (poly)phenols act primarily through genomic and epigenomic mechanisms. The molecular mechanisms underlying their health properties are still not well identified, mainly due to the use of physiologically non-relevant conditions (native molecules or extracts at high concentrations, rather than circulating metabolites), but also due to the use of targeted genomic approaches aiming to evaluate the effect only on few specific genes, thus preventing to decipher detailed molecular mechanisms involved. The use of state-of-the-art untargeted analytical methods represents a significant breakthrough in nutrigenomics, as these methods enable detailed insights into the effects at each specific omics level. Moreover, the implementation of multi-omics approaches allows integration of different levels of regulation of cellular functions, to obtain a comprehensive picture of the molecular mechanisms of action of (poly)phenols. In combination with bioinformatics and the methods of machine learning, multi-omics has potential to make a huge contribution to the nutrition science. The aim of this review is to provide an overview of the use of the omics, multi-omics, and integrative approaches in studying the vasculoprotective properties of dietary (poly)phenols and address the potentials for use of the machine learning in nutrigenomics.

What do we know about nutrient-based strategies targeting molecular mechanisms associated with obesity-related fatty liver disease?

Obesity is a risk factor for developing nonalcoholic fatty liver disease (NAFLD), and the associated molecular mechanisms could be targeted with nutrient-based strategies. Therefore, it is necessary to review the current mechanisms to propose further treatments. Obesity facilitates the onset of insulin resistance, lipidic abnormalities, hepatic fat accumulation, lipid peroxidation, mitochondrial dysfunction, excessive reactive oxygen species (ROS) production, and inflammation, all related to further steatosis progression and fibrosis. Microbiota alterations can also influence liver disease by the translocation of pathogenic bacteria, energy extraction from short chain fatty acids (SCFAs), intestinal suppression of the expression of fasting-induced adipose factor (FIAF), reduction of bile acids, and altered choline metabolism. There are also genetic polymorphisms in metabolic proteins that predispose to a higher risk of liver diseases, such as those found in the patatin-like phospholipase domain-containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), membrane-bound O-acyltransferase domain-containing 7 (MBOAT7) or also known as lysophosphatidylinositol acyltransferase 1 (LPIAT1), transmembrane channel-like 4 genes (TMC4), fat mass and obesity-associated protein (FTO), the b Klotho (KLB) and carboxylesterase (CES1). No clear dietary guidelines target all mechanisms related to NAFLD development and progression. However, energy and carbohydrate intake restriction, regular physical exercise, supplementation of antioxidants, and restoration of gut microbiota seem to have beneficial effects on the new proposed features of NAFLD.

Sex differences in vitamin D metabolism, serum levels and action

The ubiquity of vitamin D metabolising enzymes and vitamin D receptors in mammalian organisms suggests that vitamin D has pleiotropic effects. There are quite a few studies indicating the anticancer, cardioprotective and antidiabetic effects of vitamin D; however, the best-documented actions of vitamin D are the regulation of Ca-phosphate balance and its effect on immune function.Vitamin D levels in organisms are modulated by many environmental and non-environmental factors. One potential factor that may influence vitamin D levels and effects is the sex of the individuals studied. This review focuses on the scientific evidence indicating different synthesis and metabolism of vitamin D in females and males, mainly from PubMed database sources. The article verifies the sex differences in vitamin D levels reported around the world. Moreover, the different effects of vitamin D on the musculoskeletal, cardiovascular, nervous and immune systems, as well as cancer in males and females, were discussed.Most studies addressing sex differences in vitamin D levels and effects are observational studies with conflicting results. Therefore, carefully designed clinical trials and experiments on animal models should be carried out to determine the role of non-environmental factors that may differentiate vitamin D levels in females and males.

Is Habitual Dietary Intake of Fats Associated with Apelin Gene Expression in Visceral and Subcutaneous Adipose Tissues and Its Serum Levels in Obese Adults?

INTRODUCTION

Apelin could be one of the last protective defenses before developing obesity-related disorders, including insulin resistance, type 2 diabetes, and hypertension, which can be modified by dietary intake. The present study investigated the association of habitual intake of total fatty acids (TFAs), saturated-, monounsaturated-, polyunsaturated FAs, n-3, and n-6 FAs with Apelin expression in visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT).

METHODS

We obtained VAT and SAT from 168 participants (64 nonobese and 104 obese) who had undergone open abdominal surgery. Dietary intake information was gathered with a valid and reliable food frequency questionnaire. The mRNA expression of the Apelin gene was analyzed by real-time PCR.

RESULTS

Apelin serum levels were increased in the obese subjects compared to the nonobese group (p = 0.016). The SAT and VAT Apelin mRNA levels were significantly elevated in the obese participants compared to the nonobese ones (p < 0.05). Based on BMI status, only obese subjects indicated a positive association between SAT and VAT Apelin expression and TFA intake (p < 0.001). However, this association was observed between SAT and VAT Apelin gene expression and polyunsaturated fatty acid (PUFA) and n-3 FA intakes in both obese and nonobese groups (p < 0.05).

CONCLUSION

High Apelin gene expression was associated with TFA intake in obese subjects in both fat tissues. However, habitual intake of PUFA and n-3 FA was associated with Apelin gene expression in obese and nonobese individuals. Our results indicate a determinative role of the quality and quantity of FA intake on adipose tissue.

Emergence of nutrigenomics and dietary components as a complementary therapy in cancer prevention

Cancer is an illness characterized by abnormal cell development and the capability to infiltrate or spread to rest of the body. A tumor is the term for this abnormal growth that develops in solid tissues like an organ, muscle, or bone and can spread to other parts of the body through the blood and lymphatic systems. Nutrition is a critical and immortal environmental component in the development of all living organisms encoding the relationship between a person's nutrition and their genes. Nutrients have the ability to modify gene expression and persuade alterations in DNA and protein molecules which is researched scientifically in nutrigenomics. These interactions have a significant impact on the pharmacokinetic properties of bioactive dietary components as well as their site of action/molecular targets. Nutrigenomics encompasses nutrigenetics, epigenetics, and transcriptomics as well as other "omic" disciplines like proteomics and metabolomics to explain the vast disparities in cancer risk among people with roughly similar life style. Clinical trials and researches have evidenced that alternation of dietary habits is potentially one of the key approaches for reducing cancer risk in an individual. In this article, we will target how nutrigenomics and functional food work as preventive therapy in reducing the risk of cancer.

Nutritional and genetic determinants of essential hypertension among adult respondents of the 2013 national nutrition survey, Philippines: a preliminary observational study

Preventive strategies for hypertension and its sequelae require an understanding of their predisposing conditions and recognition of at-risk individuals. Several factors, both genetic and nongenetic, are influential, and likely vary in their effects across ethnicities. This study aimed to identify dietary, lifestyle-related differences and genetic variants associated with hypertension in Filipinos. The study included 147 adult Filipino respondents of the 2013 Philippine National Nutrition Survey living in the National Capital Region. Data on the socio-demographic profile and selected lifestyle factors were obtained via face-to-face interviews. Blood pressure, anthropometric and biochemical indicators of health were determined using standard procedures. Hypertension incidence was determined following American College of Cardiology/American Heart Association guideline. Genotyping utilized the customized Illumina Golden Gate genotyping array, with subsequent allele and genotypic association analytics. Genetic variant effects were adjusted to clinical parameters via logistic regression. Between those with and without hypertension, there was relatively higher intake of dietary protein, fat but not carbohydrates in the latter (P<.05). Of note, other established risk factors for hypertension, such as high lipid levels and fasting blood sugar, were consistently frequently seen among hypertensive respondents. Of the gene markers, 3 SNPs (rs10492602 of APOC [3' UTR], rs12721054 of CYP2C19 [exon] and rs4244285 [intergenic between PCDH17-DIAPH3 locus]) remained significant after multivariable logistic regression. The study highlights that both nutrition and genetic information may contribute to hypertension among Filipinos. This could guide public health initiatives to identify Filipinos susceptible to hypertension and recommend control strategies in lowering its morbidity rate.

Integrating nutriepigenomics in Parkinson's disease management: New promising strategy in the omics era

Parkinson's disease (PD) is the most prevalent brain motor disorder and is frequently regarded as an idiopathic and sporadic disease due to its unclear etiology. Although the pathological mechanisms of PD have already been investigated at various omics levels, no disease-modifying drugs are currently available. At the moment, treatments can only provide symptomatic relief to control or improve motor symptoms. Parkinson's disease is a multifactorial disease, the development and progression of which are influenced by multiple factors, including the genetic markups and the environment. As an indispensable component of our daily life, nutrition is considered one of the most robust environmental factors affecting our health. Consequently, depending on our dietary habits, nutrition can either induce or reduce our susceptibility to PD. Epigenetic mechanisms regulate gene expression through DNA methylation, histone modifications, and non-coding RNAs (ncRNAs) activity. Accumulating evidence from nutriepigenomics studies has reported altered epigenetic mechanisms in clinical and pre-clinical PD models, and the potential role of nutrition in modifying the changes. In addition, through nutrigenetics and nutrigenomics studies, the diet-gene, and gene-diet interactions concerning PD development and progression have been investigated. Herein, current findings on the roles of nutrition in epigenetic mechanisms underpinning PD development and progression are discussed. Recent advancements in the multi-omics approach in PD nutrition research are also underlined. The ability of nutrients to influence epigenetic mechanisms and the availability of multi-omics applications compel the immediate use of personalized nutrition as adjuvant therapy for PD.

Genome Tectonics: Linking Dynamic Genome Organization with Cellular Nutrients

BACKGROUND

Our daily intake of food provides nutrients for the maintenance of health, growth, and development. The field of nutrigenomics aims to link dietary intake/nutrients to changes in epigenetic status and gene expression.

SUMMARY

Although the relationship between our diet and our genes in under intense investigation, there is still a significant aspect of our genome that has received little attention with regard to this. In the past 15 years, the importance of genome organization has become increasingly evident, with research identifying small-scale local changes to large segments of the genome dynamically repositioning within the nucleus in response to/or mediating change in gene expression. The discovery of these dynamic processes and organization maybe as significant as dynamic plate tectonics is to geology, there is little information tying genome organization to specific nutrients or dietary intake.

KEY MESSAGES

Here, we detail key principles of genome organization and structure, with emphasis on genome folding and organization, and link how these contribute to our future understand of nutrigenomics.

Nutrigenomics: Perceptions of South African Dietitians and General Practitioners

INTRODUCTION

Although investigations into the emerging field of nutrigenomics are relatively limited and more research in this field is required, experts agree that there is potential for it to be incorporated into health care practice. If health care professionals can promote healthy dietary behavior based on nutrigenomic testing, it can assist in addressing the health consequences of poor diet and lightning the strain on the South African health care system.

METHODS

Registered dietitians (RDs) and general practitioners (GPs) registered with the Health Professions Council of South Africa (HPCSA) who obtained their qualification in South Africa (SA) were eligible to participate in this cross-sectional study. Participants were identified using convenience and snowball sampling. A self-administered electronic survey using EvaSys Software® was completed by those that agreed to participate.

RESULTS

Nearly all RDs (97.3%), but less than a third of GPs (30.4%), had heard of the term nutrigenomics. Approximately three-quarters of RDs (74.7%) and GPs (73.9%) had or would personally consider undergoing genetic testing. More than 40% (43.5%) of RDs ranked direct-to-consumer genetic testing companies as the most equipped, while 31.8% of GPs ranked RDs as the most equipped to provide patients with nutrigenomic services. Both RDs and GPs ranked similar reasons as "strongly agree" for why consumers were motivated to make use of nutrigenomic services, which included "motivated by a desire to prevent or manage disease" (56.7%), "prevent a disease based on family history" (65.9%), "control health outcomes based on family history" (54.9%), and "improve overall health-related quality of life" (48.6%). Cost concerns were reported as the greatest barrier to implementing nutrigenomic services (75.7%). Other barriers included confidentiality issues (47.8%) and moral concerns (37.3%). Greater individualization of diet prescription (66.5%), stronger foundations for nutrition recommendations (62.4%), and dietary prescriptions that would manage or prevent certain diseases more effectively (59.0%) were all perceived as benefits of including nutrigenomics in practice.

CONCLUSION

This study identified perceived consumer motivators and barriers that might affect the willingness to seek nutrigenomic services in SA. In addition, the need for more nutrigenomic training opportunities, including the planning of personalized diets based on genetic testing results and interpretation of results, was confirmed. However, both RDs and GPs felt that the emerging field of nutrigenomics needs further development before it can be applied effectively in routine private and public health care in SA.

Vitamin D binding protein gene polymorphisms are associated with lower plasma 25-hydroxy-cholecalciferol concentrations in Ethiopian lactating women

Ethiopian women have been reported to have low plasma 25-hydroxy-cholecalciferol (25(OH)D) concentrations despite an abundance of sunshine. Low dietary vitamin D intake, limited skin exposure to sun, and genetics are among factors suggested to affect vitamin D status in this population. In this study (Clinical Trial NCT02210884), we hypothesized that polymorphisms in the vitamin D binding protein (VDBP) gene (rs7041, rs4588) are associated with reduced plasma 25(OH)D concentrations in Ethiopian women. Lactating Ethiopian women (n = 110) were randomly assigned to weekly administration of vitamin D3 (15,000 IU) or a placebo. Plasma 25(OH)D was measured at baseline (within 2 weeks of delivery, before supplementation) and at 3, 6, and 12 months after delivery. Associations between VDBP polymorphism status for rs7041 and rs4588 and plasma 25(OH)D were determined by analysis of variance and multiple linear and logistic regressions. Multiple linear regression with maternal age as a covariate revealed that rs7041 is associated with reduced plasma 25(OH)D (P = .021) and more risk alleles at rs7041 and rs4588 are associated with reduced plasma 25(OH)D (P = .017). Logistic regression models for vitamin D insufficiency showed that additional risk alleles for rs7041 and rs4588 are associated with increased odds ratios (OR = 1.66; 95% CI, 1.10-2.62; P = .019) for plasma 25(OH)D below 40 nmol/L. Supplementation increased plasma 25(OH)D at 3 months in women with fewer risk alleles and across all genotypes at 6 and 12 months. VDBP polymorphisms may contribute to vitamin D insufficiency in Ethiopian lactating women. Furthermore, VDBP polymorphisms may blunt short-term responses to vitamin D supplementation and require longer periods of intervention.

A review of the Mediterranean diet and nutritional genomics in relation to cancer in women

Cancer is the leading cause of death among women all over the world. Female tissue-specific cancers are the most commonly diagnosed among women and account for most cancer-related deaths. The main risk factors for women's cancer are hereditary factors, specific exposure to dangerous chemicals, disorders such as hormone imbalance, and lifestyle. High body mass index, low physical activity, low intake of fruit and vegetables, smoking, excessive alcohol consumption, lack of cancer screening and treatment are the most common risk factors. Nutrigenetics and nutrigenomics are both part of nutritional genomics. Nutrigenetics is how a person's body reacts to nutrients based on his/her genotype. It can be used to create a personalized diet, maintain a person's health, avoid disease, and if necessary to sustain therapy. Nutrigenomics studies the impact of nutrition on gene expression and the epigenomic, proteomic, transcriptomic and metabolomic effects of dietary intake. There is evidence that diet matters for different women's cancers, and is related to cancer progression, survival and treatment. The optimum combination for cancer prevention is a diet rich in vitamins and fibre, with low meat consumption, low milk intake and moderate use of alcohol. The Mediterranean diet looks to be an optimal diet with a good nutrition pattern, qualifying it as a therapy to prescribe.

Polymorphisms, diet and nutrigenomics

Every human being possesses an exclusive nutritional blueprint inside their genes. Bioactive food components and nutrients affect the expression of such genes. Nutrigenomics is the science that analyzes gene-nutrient interactions (nutrigenetics), which can lead to the development of personalized nutritional recommendations to maintain optimal health and prevent disease. Genomic diversity among various ethnic groups might affect nutrients bioavailability as well as their metabolism. Nutrigenomics combines different branches of science including nutrition, bioinformatics, genomics, molecular biology, molecular medicine, and epidemiology. Genes regulate intake and metabolism of different nutrients, while nutrients positively or negatively influence the expression of a number of genes; testing of specific genetic polymorphisms may therefore become a useful tool to manage weight loss and to fully understand gene-nutrient interactions. Indeed, several approaches are used to study gene-nutrient interactions: epigenetics, the study of genome modification not related to changes in nucleotide sequence; transcriptomics, the study of tissue-specific and time-specific RNA transcripts; proteomics, the study of proteins involved in biological processes; and metabolomics, the study of changes of primary and secondary metabolites in body fluids and tissues. Hence, the use of nutrigenomics to improve and optimize a healthy, balanced diet in clinical settings could be an effective approach for long-term lifestyle changes that might lead to consistent weight loss and improve quality of life.

Nutrigenomics in crustaceans: Current status and future prospects

In aquaculture, nutrigenomics or "nutritional genomics" is concerned with studying the impacts of nutrients and food ingredients on gene expressions and understanding the interactions that may occur between nutrients and dietary bioactive ingredients with the genome and cellular molecules of the treated aquatic animals at the molecular levels that will, in turn, mediate gene expression. This concept will throw light on or provide important information to recognize better how specific nutrients may influence the overall health status of aquatic organisms. In crustaceans, it is well known that the nutritional requirements vary among different species. Thus, studying the nutrigenomics in different crustacean species is of significant importance. Of interest, recognition of the actual mechanisms that may be associated with the effects of the nutrients on the immune responses of crustaceans will provide clear outstanding protection, build a solid immune system, and also decrease the possibilities of the emergence of infectious diseases in the culture systems. Similarly, the growth, molting, lipid metabolism, antioxidant capacity, and reproduction could be effectively enhanced by using specific nutrients. In the area of crustacean research, nutrigenomics has been rapidly grown for addressing several aspects related to the influences of nutrients on crustacean development. Several researchers have studied the relationships between several functional genes and their expression profile with several physiological functions of crustaceans. They found a close association between the effects of optimal feeding with efficient production, growth, reproduction development, and health status of several crustacean species. Moreover, they illustrated that regulation of the gene expression in individual cells by different nutrients and formulated feeds could improve the growth development and immunity-boosting of several crustacean species. The present review will spotlight on such relationships between the dietary nutrients and expression of genes linked with growth, metabolism, molting, antioxidant, reproduction, and immunity of several crustacean species. The literature included in this review article will provide references and future outlooks for the upcoming research plans. This will contribute positively for maintaining the sustainability of the sector of the crustacean industry.

The role of nutrition in harnessing the immune system: a potential approach to prevent cancer

Cancer is a vital barrier to increase the life expectancy and the foremost cause of death globally. The initial diagnosis and proper management of cancer can expand the survival rate of individuals. This review provides an in-depth investigation of cancer causes symptoms, types of cancer, and worldwide distribution of cancer. The relation between nutrition (i.e., various food items) and cancer is also emphasized to offer a framework of nutrition management in different cancer types. The microbiota is closely associated with the occurrence of cancer. Thus, genomics of intestinal microbes and nutrigenomics have been discussed based on the reported meta-analysis studies. A dramatic increase in cancer rates has been observed due to intake of alcohol, microbial infections, and deficiency of nutrition. Malnutrition is a substantial problem in cancer patients linked with improper treatment and increased morbidity. The detail studies of cancer and nutrigenomics are an eminent approach to comprehend the relation between microbes and the consumption of certain food types which can further reduce the cancer risk. The incorporation of specific nutrients and probiotics improved the gut microbial health, increased life expectancy, and also decreased the incidence of tumorigenesis in individuals.

Wheat germ oil vitamin E cytoprotective effect and its nutrigenomics signature in human hepatocyte lipotoxicity

Wheat germ oil (WGO) is rich in α-tocopherol (vitamin E, VE), a vitamin that has long been suggested to exert hepatoprotective effects. In this study, this function of WGO-VE and its transcriptomics fingerprint were investigated in comparison with RRR-α-tocopherol and all-rac-α-tocopherol (nVE and sVE, respectively), in human liver cells treated with oleic acid (OA) to develop steatosis and lipotoxicity. Used in chemoprevention mode, all the VE formulations afforded significant reduction of the OA-induced steatosis and its consequent impact on lipotoxicity indicators, including ROS production and efflux (as H₂O₂), and apoptotic and necrotic cell death. A trend toward a better control of lipotoxicity was observed for WGO-VE and nVE compared to sVE. Gene microarray data demonstrated that these effects of VE formulations were associated with significantly different responses of the cellular transcriptome to compensate for the modifications of OA treatment, including the downregulation of cellular homeostasis genes and the induction of genes associated with defects of liver cell metabolism, fibrosis and inflammation, liver disease and cancer. Ingenuity Pathway Analysis data showed that WGO-VE modulated genes associated with liver carcinogenesis and steatosis, whereas nVE modulated genes involved in liver cell metabolism and viability biofunctions; sVE did not significantly modulate any gene dataset relevant to such biofunctions. In conclusion, WGO-VE prevents lipotoxicity in human liver cells modulating genes that differ from those affected by the natural or synthetic forms of pure VE. These differences can be captured by precision nutrition tools, reflecting the molecular complexity of this VE-rich extract and its potential in preventing specific cues of hepatocellular lipotoxicity.

Immune responses to prebiotics in farmed salmonid fish: How transcriptomic approaches help interpret responses

Within aquaculture, prebiotics are composed of complex carbohydrate molecules that cannot be digested by the fish directly but are metabolised by the microbial communities within the host gut, with the desire that "healthy" bacterial species are promoted with subsequently improved performance of the fish, there are likely some direct responses of intestinal cells to these dietary components. The sources and processing of prebiotics, which fall under the overarching theme of "functional feeds" are highly varied between species and types of prebiotics administered. How these feeds exert their effect, and the host responses are hard to determine, but new technologies and the development of high-throughput technologies (omics) are enabling the mechanisms and methods of action to be further understood. The recent advances in the availability of 'omics' technologies with the transition from single gene assays to microarray and RNA-seq in fish health have enabled novel functional ingredients to be analysed. This review will focus on recent studies on targeted gene expression and 'omics' technologies to characterize immune responses. Comparisons between the immunomodulatory effect of different prebiotics have been made and specific examples of how transcriptomics techniques have been used to identify immune responses to prebiotics are given.

Haptoglobin polymorphism modulates cardiometabolic impacts of four consecutive weeks, dawn to sunset Ramadan intermittent fasting among subjects with overweight/obesity

AIMS

Haptoglobin (Hp) is a multifaceted marker of inflammation, and mediates the interplay between obesity, inflammation, and cardiometabolic dysfunction. However, the role of the Hp phenotype in modulating intermittent fasting (IF)-induced cardiometabolic changes remains to be elucidated.

METHODS

Hp phenotype was determined for the study subjects. Cardiometabolic markers were assessed before and at the end of four consecutive weeks, dawn to sunset IF.

RESULTS

A total of 114 subjects (75 males and 39 females, 38.7 ± 11.7 years, body mass index (BMI) of 30.41 ± 5.09 kg/m²) were recruited. Hp2-2 (n = 55, 48.2 %) and Hp2-1 (n = 53, 46.5 %) were the predominant phenotypes. Significant reductions were observed in serum Hp, IL-6, TNF-α, triglycerides (TG), total cholesterol (TC), LDL, BMI, and fat mass (FM), while a significant elevation was observed in serum CD163, HDL, and IL-10 at the end of the IF month for the whole population. Based on the Hp polymorphism, significant decreases in Hp, BMI, FM, TG, LDL, and TNF-α, with significant increases in HDL and CD163 levels were observed among subjects with Hp2-2 and Hp2-1 phenotypes. A more pronounced reduction in FM was reported in subjects with Hp2-2 in comparison with Hp2-1.

CONCLUSION

Hp gene polymorphism modulates IF-induced changes in cardiometabolic markers.

CLINICAL TRIAL REGISTRATION NUMBER

ISRCTN18205186; https://trialsearch.who.int/?TrialID=ISRCTN18205186.

Feedomics provides bidirectional omics strategies between genetics and nutrition for improved production in cattle

Increasing the efficiency and sustainability of cattle production is an effective way to produce valuable animal proteins for a growing human population. Genetics and nutrition are the 2 major research topics in selecting cattle with beneficial phenotypes and developing genetic potentials for improved performance. There is an inextricable link between genetics and nutrition, which urgently requires researchers to uncover the underlying molecular mechanisms to optimize cattle production. Feedomics integrates a range of omic techniques to reveal the mechanisms at different molecular levels related to animal production and health, which can provide novel insights into the relationships of genes and nutrition/nutrients. In this review, we summarized the applications of feedomics techniques to reveal the effect of genetic elements on the response to nutrition and investigate how nutrients affect the functional genome of cattle from the perspective of both nutrigenetics and nutrigenomics. We highlighted the roles of rumen microbiome in the interactions between host genes and nutrition. Herein, we discuss the importance of feedomics in cattle nutrition research, with a view to ensure that cattle exhibit the best production traits for human consumption from both genetic and nutritional aspects.

Expression of B. subtilis Phytase gene driven by fruit specific E8 promoter for enhanced minerals, metabolites and phytonutrient in cucumber fruit

The fruit nutrigenomics is an interesting and important research area towards nutrition enhancement. The phytic acid is one of the major antinutrient compound, present in seeded fruits and crops. It hinders the absorption of iron (Fe), zinc (Zn), magnesium (Mg), potassium (K) and calcium (Ca), causing mineral deficiencies. In the present study, the BsPhy gene was overexpressed in the cucumber fruits using the tomato fruit specific E8 and constitutive CaMV 35S promoter. The E8 promoter imparted heterologous expression of GUS gene in cucumber fruits, furthermore, the fruit specific expression of E8 promoter with BsPhy gene was confirmed in transgenics (E8::BsPhy) using anti rabbit-phytase antibody. The physio-biochemical analysis of transgenics revealed, maximum phytase activity in E8::BsPhy cucumber fruits at 10 days after anthesis (DAA) compared to 35S::BsPhy and wild-type (WT) fruits. Consequently, E8::BsPhy fruits also showed increased amount of inorganic phosphorus (Pi), total phosphorus (P), minerals (Zn, Fe, Mg, K, Ca), total carotenoid and other macronutrients at 10 DAA compared to 35S::BsPhy fruits. The metabolite profiling of fruits (10 DAA) showed increased sugars, amino acids, sugar acids and polyols, in both E8::BsPhy and 35S::BsPhy transgenics suggesting higher phytate metabolism, compared to WT fruits. Interestingly, both the transgenic fruits showed higher fruit biomass and yield along with improved nutritional quality, which can be attributed to increased P and Zn contents in transgenic fruits, compared to WT fruits. Our findings reveal that the BsPhy gene enhances minerals and macronutrients in transgenic cucumber fruits making it nutritious and healthy.

Effects of Nigella sativa supplementation on blood concentration and mRNA expression of TNF-α, PPAR-γ and adiponectin, as major adipogenesis-related markers, in obese and overweight women: a crossover, randomised-controlled trial

Adipocyte expansion through adipogenesis can offset the adverse metabolic effects of obesity. Nigella sativa (NS) (black seed) oil is shown to have therapeutic features in the management of obesity. NS oil might have beneficial changes in obese populations through mediating serum levels of adipogenesis-related parameters and relative transcriptional gene-diet interactions (nutrigenomics), though no previous studies assessed this mechanism in overweight/obese participants. This study assessed the effects of NS oil supplements on blood concentration and mRNA expression levels of TNF-α, PPAR-γ and serum adiponectin and expression of AdipoR1, as major adipogenesis and obesity-related parameters, in overweight/obese women using a cross-over design. Eligible women were randomised to receive either NS oil supplements (2000 mg/d) or placebo. Two periods of interventions (8 weeks in each) were cross-changed by a 4-week washout period. An individualised diet plan without calorie deficits was given to participants to match their energy/macronutrient intakes. The Pkcross procedure and intention-to-treat analysis were performed using Stata. Cohen's d(d) was estimated to measure the magnitude of the effects. Forty-six participants were included. NS oil capsules reduced transcription levels ((d = -2·31), P < 0·001) and blood concentrations of TNF-α ((d = -0·29), P < 0·001). AdipoR1 expression (d = 2·24, P < 0·001) and serum adiponectin (d = 0·88, P < 0·001) showed a significant augmentation with a medium-high effect size, as did gene expression (d = 0·69, P < 0·001) and serum levels of PPAR-γ (d = 0·97, P < 0·001). There was a moderate but significant decrease in body weight (d = 0·6, P < 0·001). The present beneficial findings would provide strong information for future nutrigenomics/clinical trial studies assessing the role of NS in the management of obesity and other comorbidities.

Zinc supplementation modifies brain tissue transcriptome of Apis mellifera honeybees

BACKGROUND

Bees are the most important group of pollinators worldwide and their populations are declining. In natural conditions, Apis mellifera depends exclusively on food from the field to meet its physiological demands. In the period of scarcity, available resources are insufficient and artificial supplementation becomes essential for maintaining the levels of vitamins, proteins, carbohydrates, and minerals of colonies. Among these minerals, zinc is essential in all living systems, particularly for the regulation of cell division and protein synthesis, and is a component of more than 200 metalloenzymes.

RESULTS

The total RNA extracted from the brain tissue of nurse bees exposed to different sources and concentrations of zinc was sequenced. A total of 1,172 genes in the treatment that received an inorganic source of zinc and 502 genes that received an organic source of zinc were found to be differentially expressed among the control group. Gene ontology enrichment showed that zinc can modulate important biological processes such as nutrient metabolism and the molting process.

CONCLUSIONS

Our results indicate that zinc supplementation modulates the expression of many differentially expressed genes and plays an important role in the development of Apis mellifera bees. All the information obtained in this study can contribute to future research in the field of bee nutrigenomics.

Therapeutic approaches to preserve the musculature in Duchenne Muscular Dystrophy: The importance of the secondary therapies

Muscular dystrophies (MDs) are heterogeneous diseases, characterized by primary wasting of skeletal muscle, which in severe cases, such as Duchenne Muscular Dystrophy (DMD), leads to wheelchair dependency, respiratory failure, and premature death. Research is ongoing to develop efficacious therapies, particularly for DMD. Most of the efforts, currently focusing on correcting or restoring the primary defect of MDs, are based on gene-addition, exon-skipping, stop codon read-through, and genome-editing. Although promising, most of them revealed several practical limitations. Shared knowledge in the field is that, in order to be really successful, any therapeutic approach has to rely on spared functional muscle tissue, restricting the number of patients eligible for clinical trials to the youngest and less compromised individuals. In line with this, many therapeutic strategies aim to preserve muscle tissue and function. This Review outlines the most interesting and recent studies addressing the secondary outcomes of DMD and how to better deliver the therapeutic agents. In the future, the effective treatment of DMD will likely require combinations of therapies addressing both the primary genetic defect and its consequences.

Utilizing the underutilized plant resources for development of life style foods: Putting nutrigenomics to use

Sufficient amount of minerals, vitamins, and proteins in human diet play indispensable role in maintaining the active metabolism for better human health. All the essential nutrients that are requisite for an individual's survival are acquired from plants as well as animals. Micronutrients and macronutrients directly influence the metabolic pathways and their deficiencies play a substantial role in development of manifold disorders. In addition to environmental factors, quality and quantity of foods are key factors in maintaining the human health. Transition from healthy to diseased state is concurrent with the pattern of gene expression that is largely influenced by nutrition and environment. A combined approach to study the influence of nutrition on expression of numerous genes can be well explored through nutrigenomic studies. Nutrigenomics includes studies wherein applied genomics is used to investigate nutritional science to understand the compartmentalization of genes that influence the cause of diet-related complications. This review describes the role of underutilized crops as frontline foods to circumvent the health complications through the nutrigenomic studies. Further dynamics of nutrigenomic tools to study the impact of nutrition on the changing pattern of genome stability and gene expression for developing precise safety measures against wide range of health ailments linked to metabolic networks. Additionally, this review provides detailed information on nutrigenomic studies undertaken to unravel the potential of underutilized crops to augment the human health and to carry the agronomic/genomic approaches to enhance nutritional profile of underutilized crops to overcome diet-related disorders.

Consequences of a low protein diet on the liver and longissimus dorsi transcriptome of Duroc × Iberian crossbred pigs

Low protein diets supplied during the growing period of pigs can diminish their growth rate and increase the intramuscular fat (IMF) content which affects the sensorial and technological characteristics of the products. In the present study, the effects of a low protein diet supplied during the growing period of Duroc × Iberian crossbred pigs on several phenotypic traits and on liver and longissimus dorsi transcriptome were analysed at the beginning (EARLY) and at the end (LATE) of the growing period. Two experimental groups of 10 crossbred pigs each were fed two isocaloric diets with different protein content: control diet (C) with 16.5% protein and 0.8% lysine and low protein diet (LP) with 11% CP and 0.6% lysine. Animals fed LP diet have a slower growth than those fed C diet, but no effect of LP diet was observed on the IMF content. The transcriptomes of liver and longissimus dorsi were characterised and quantified through RNA-sequencing (RNA-seq). In liver, 134 and 480 differentially expressed annotated genes and new isoforms (DEGs) were detected between C and LP diets for EARLY and LATE animals, respectively. In muscle, 128 and 68 DEGs were detected at EARLY and LATE time-points. Functional interpretation revealed that LP diet may inhibit immune system molecules and processes in both tissues at EARLY stage. In liver, the DEGs mainly affect lipid and cholesterol metabolic processes, while in muscle, the expression changes would be involved in growth, development and meat quality. In conclusion, a low protein diet supplied during the growing period seems to slow down the growth of Duroc × Iberian crossbred pigs, but it also seems to affect multiple biological processes that could compromise the immune system of Duroc × Iberian crossbred pigs. Therefore, these results question the adequacy of this type of regime in Duroc × Iberian pigs that must be studied in greater depth before being implemented.

High protein diet-induced metabolic changes are transcriptionally regulated via KLF15-dependent and independent pathways

High protein diet (HPD) is an affordable and positive approach in prevention and treatment of many diseases. It is believed that transcriptional regulation is responsible for adaptation after HPD feeding and Kruppel-like factor 15 (KLF15), a zinc finger transcription factor that has been proved to perform transcriptional regulation over amino acid, lipid and glucose metabolism, is known to be involved at least in part in this HPD response. To gain more insight into molecular mechanisms by which HPD controls expressions of genes involved in amino acid metabolism in the liver, we performed RNA-seq analysis of mice fed HPD for a short period (3 days). Compared to a low protein diet, HPD feeding significantly increased hepatic expressions of enzymes involved in the breakdown of all the 20 amino acids. Moreover, using KLF15 knockout mice and in vivo Ad-luc analytical system, we were able to identify Cth (cystathionine gamma-lyase) as a new target gene of KLF15 transcription as well as Ast (aspartate aminotransferase) as an example of KLF15-independent gene despite its remarkable responsiveness to HPD. These findings provide us with a clue to elucidate the entire transcriptional regulatory mechanisms of amino acid metabolic pathways.