Systematic Review and Quantitative Data Synthesis of Peripheral Blood Mononuclear Cell Transcriptomics Reveals Consensus Gene Expression Changes in Response to a High Fat Meal

SCOPE

Metabolic flexibility is essential for a healthy response to a high fat meal, and is assessed by measuring postprandial changes in blood markers including peripheral blood mononuclear cells (PBMCs; lymphocytes and monocytes). However, there is no clear consensus on postprandial gene expression and protein changes in these cells.

METHOD AND RESULTS

The study systematically reviews the literature reporting transcriptional and proteomic changes in PBMCs after consumption of a high fat meal. After re-analysis of the raw data to ensure equivalence between studies, ≈85 genes are significantly changed (defined as in the same direction in ≥3 studies) with about half involved in four processes: inflammation/oxidative stress, GTP metabolism, apoptosis, and lipid localization/transport. For meals consisting predominantly of unsaturated fatty acids (UFA), notable additional processes are phosphorylation and glucocorticoid response. For saturated fatty acids (SFA), genes related to migration/angiogenesis and platelet aggregation are also changed.

CONCLUSION

Despite differences in study design, common gene changes are identified in PBMCs following a high fat meal. These common genes and processes will facilitate definition of the postprandial transcriptome as part of the overall postcibalome, linking all molecules and processes that change in the blood after a meal.

Precision nutrition for targeting pathophysiology of cardiometabolic phenotypes

Obesity is a heterogenous disease accompanied by a broad spectrum of cardiometabolic risk profiles. Traditional paradigms for dietary weight management do not address biological heterogeneity between individuals and have catastrophically failed to combat the global pandemic of obesity-related diseases. Nutritional strategies that extend beyond basic weight management to instead target patient-specific pathophysiology are warranted. In this narrative review, we provide an overview of the tissue-level pathophysiological processes that drive patient heterogeneity to shape distinct cardiometabolic phenotypes in obesity. Specifically, we discuss how divergent physiology and postprandial phenotypes can reveal key metabolic defects within adipose, liver, or skeletal muscle, as well as the integrative involvement of the gut microbiome and the innate immune system. Finally, we highlight potential precision nutritional approaches to target these pathways and discuss recent translational evidence concerning the efficacy of such tailored dietary interventions for different obesity phenotypes, to optimise cardiometabolic benefits.

Unlocking the potential of microRNAs: machine learning identifies key biomarkers for myocardial infarction diagnosis

BACKGROUND

MicroRNAs (miRNAs) play a crucial role in regulating adaptive and maladaptive responses in cardiovascular diseases, making them attractive targets for potential biomarkers. However, their potential as novel biomarkers for diagnosing cardiovascular diseases requires systematic evaluation.

METHODS

In this study, we aimed to identify a key set of miRNA biomarkers using integrated bioinformatics and machine learning analysis. We combined and analyzed three gene expression datasets from the Gene Expression Omnibus (GEO) database, which contains peripheral blood mononuclear cell (PBMC) samples from individuals with myocardial infarction (MI), stable coronary artery disease (CAD), and healthy individuals. Additionally, we selected a set of miRNAs based on their area under the receiver operating characteristic curve (AUC-ROC) for separating the CAD and MI samples. We designed a two-layer architecture for sample classification, in which the first layer isolates healthy samples from unhealthy samples, and the second layer classifies stable CAD and MI samples. We trained different machine learning models using both biomarker sets and evaluated their performance on a test set.

RESULTS

We identified hsa-miR-21-3p, hsa-miR-186-5p, and hsa-miR-32-3p as the differentially expressed miRNAs, and a set including hsa-miR-186-5p, hsa-miR-21-3p, hsa-miR-197-5p, hsa-miR-29a-5p, and hsa-miR-296-5p as the optimum set of miRNAs selected by their AUC-ROC. Both biomarker sets could distinguish healthy from not-healthy samples with complete accuracy. The best performance for the classification of CAD and MI was achieved with an SVM model trained using the biomarker set selected by AUC-ROC, with an AUC-ROC of 0.96 and an accuracy of 0.94 on the test data.

CONCLUSIONS

Our study demonstrated that miRNA signatures derived from PBMCs could serve as valuable novel biomarkers for cardiovascular diseases.

Research gaps and opportunities in precision nutrition: an NIH workshop report

Precision nutrition is an emerging concept that aims to develop nutrition recommendations tailored to different people's circumstances and biological characteristics. Responses to dietary change and the resulting health outcomes from consuming different diets may vary significantly between people based on interactions between their genetic backgrounds, physiology, microbiome, underlying health status, behaviors, social influences, and environmental exposures. On 11-12 January 2021, the National Institutes of Health convened a workshop entitled "Precision Nutrition: Research Gaps and Opportunities" to bring together experts to discuss the issues involved in better understanding and addressing precision nutrition. The workshop proceeded in 3 parts: part I covered many aspects of genetics and physiology that mediate the links between nutrient intake and health conditions such as cardiovascular disease, Alzheimer disease, and cancer; part II reviewed potential contributors to interindividual variability in dietary exposures and responses such as baseline nutritional status, circadian rhythm/sleep, environmental exposures, sensory properties of food, stress, inflammation, and the social determinants of health; part III presented the need for systems approaches, with new methods and technologies that can facilitate the study and implementation of precision nutrition, and workforce development needed to create a new generation of researchers. The workshop concluded that much research will be needed before more precise nutrition recommendations can be achieved. This includes better understanding and accounting for variables such as age, sex, ethnicity, medical history, genetics, and social and environmental factors. The advent of new methods and technologies and the availability of considerably more data bring tremendous opportunity. However, the field must proceed with appropriate levels of caution and make sure the factors listed above are all considered, and systems approaches and methods are incorporated. It will be important to develop and train an expanded workforce with the goal of reducing health disparities and improving precision nutritional advice for all Americans.

Effects of Polyphenols on Glucose-Induced Metabolic Changes in Healthy Human Subjects and on Glucose Transporters

Dietary polyphenols interact with glucose transporters in the small intestine and modulate glucose uptake after food or beverage consumption. This review assesses the transporter interaction in vitro and how this translates to an effect in healthy volunteers consuming glucose. As examples, the apple polyphenol phlorizin inhibits sodium-glucose linked transporter-1; in the intestinal lumen, it is converted to phloretin, a strong inhibitor of glucose transporter-2 (GLUT2), by the brush border digestive enzyme lactase. Consequently, an apple extract rich in phlorizin attenuates blood glucose and insulin in healthy volunteers after a glucose challenge. On the other hand, the olive phenolic, oleuropein, inhibits GLUT2, but the strength of the inhibition is not enough to modulate blood glucose after a glucose challenge in healthy volunteers. Multiple metabolic effects and oxidative stresses after glucose consumption include insulin, incretin hormones, fatty acids, amino acids, and protein markers. However, apart from acute postprandial effects on glucose, insulin, and some incretin hormones, very little is known about the acute effects of polyphenols on these glucose-induced secondary effects. In summary, attenuation of the effect of a glucose challenge in vivo is only observed when polyphenols are strong inhibitors of glucose transporters.

Association between Habitual Diet and the Postprandial Glucose Response-An Enable Study

SCOPE

It is inconclusive which factors influence inter-individual variations of postprandial glucose response (PPGR). This study investigates whether the habitual diet is associated with PPGR.

METHODS AND RESULTS

Data from healthy adults (young adults with 18-25 years, middle-aged adults with 40-65 years, and older adults with 75-85 years) is collected at baseline and during an oral glucose tolerance test (OGTT) collected. Habitual diet is assessed by a food frequency questionnaire and two 24-h food lists. Associations between habitual diet and glucose incremental area under the curve (iAUC_min ) are examined by regression models. The intake of cereals and cereal products is negatively associated with glucose iAUC_min (p = 0.002) in the total cohort (N = 459, 50% women, 55 ± 21 years, BMI 26 ± 5 kg m^{- 2} ). Up to 9% of the variance in the glycemic response is explained by the respective dietary parameters identified in the models of the specific age groups.

CONCLUSION

There are age-specific diet-related effects on PPGR. The usual intake of cereals and cereal products seems to play a greater role in PPGR in more than one age group. Further research is needed, to establish how diet can be optimized based on age and PPGR.

Meal-induced inflammation: postprandial insights from the Personalised REsponses to DIetary Composition Trial (PREDICT) study in 1000 participants

BACKGROUND

Meal-induced metabolic changes trigger an acute inflammatory response, contributing to chronic inflammation and associated diseases.

OBJECTIVES

We aimed to characterize variability in postprandial inflammatory responses using traditional (IL-6) and novel [glycoprotein acetylation (GlycA)] biomarkers of inflammation and dissect their biological determinants with a focus on postprandial glycemia and lipemia.

METHODS

Postprandial (0-6 h) glucose, triglyceride (TG), IL-6, and GlycA responses were measured at multiple intervals after sequential mixed-nutrient meals (0 h and 4 h) in 1002 healthy adults aged 18-65 y from the PREDICT (Personalised REsponses to DIetary Composition Trial) 1 study, a single-arm dietary intervention study. Measures of habitual diet, blood biochemistry, gut microbiome composition, and visceral fat mass (VFM) were also collected.

RESULTS

The postprandial changes in GlycA and IL-6 concentrations were highly variable between individuals. Participants eliciting an increase in GlycA and IL-6 (60% and 94% of the total participants, respectively) had mean 6-h increases of 11% and 190%, respectively. Peak postprandial TG and glucose concentrations were significantly associated with 6-h GlycA (r = 0.83 and r = 0.24, respectively; both P < 0.001) but not with 6-h IL-6 (both P > 0.26). A random forest model revealed the maximum TG concentration was the strongest postprandial TG predictor of postprandial GlycA and structural equation modeling revealed that VFM and fasting TG were most strongly associated with fasting and postprandial GlycA. Network Mendelian randomization demonstrated a causal link between VFM and fasting GlycA, mediated (28%) by fasting TG. Individuals eliciting enhanced GlycA responses had higher predicted cardiovascular disease risk (using the atherosclerotic disease risk score) than the rest of the cohort.

CONCLUSIONS

The variable postprandial increases in GlycA and their associations with TG metabolism highlight the importance of modulating TG in concert with obesity to reduce GlycA and associated low-grade inflammation-related diseases.This trial was registered at clinicaltrials.gov as NCT03479866.

Discriminating Dietary Responses by Combining Transcriptomics and Metabolomics Data in Nutrition Intervention Studies

Scope

Combining different “omics” data types in a single, integrated analysis may better characterize the effects of diet on human health.

Methods and results

The performance of two data integration tools, similarity network fusion tool (SNFtool) and Data Integration Analysis for Biomarker discovery using Latent variable approaches for “Omics” (DIABLO; MixOmics), in discriminating responses to diet and metabolic phenotypes is investigated by combining transcriptomics and metabolomics datasets from three human intervention studies: a postprandial crossover study testing dairy foods (n = 7; study 1), a postprandial challenge study comparing obese and non‐obese subjects (n = 13; study 2); and an 8‐week parallel intervention study that assessed three diets with variable lipid content on fasting parameters (n = 39; study 3). In study 1, combining datasets using SNF or DIABLO significantly improve sample classification. For studies 2 and 3, the value of SNF integration depends on the dietary groups being compared, while DIABLO discriminates samples well but does not perform better than transcriptomic data alone.

Conclusion

The integration of associated “omics” datasets can help clarify the subtle signals observed in nutritional interventions. The performance of each integration tool is differently influenced by study design, size of the datasets, and sample size.

Integrated Analys of High-Fat Challenge-Induced Changes in Blood Cell Whole-Genome Gene Expression

SCOPE

Several studies have examined the whole-genome gene expression response in blood cells to high-fat challenges with differing results. The study aims to identify consistently up- or downregulated genes and pathways in response to a high-fat challenge using several integration methods.

METHODS AND RESULTS

Three studies measuring the gene expression response to a high-fat challenge in white blood cells are evaluated for common trends using several integration methods. Overlap in differentially expressed genes between separate studies is examined, p-values of each separate study are combined, and data are analyzed as one merged dataset. Differentially expressed genes and pathways are compared between these methods. Selecting genes differentially expressed in the three separate studies result in 67 differentially expressed genes, primarily involved in circadian pathways. Using the Fishers p-value method and a merged dataset analysis, changes in 1097 and 1182 genes, respectively, are observed. The upregulated genes upon a high-fat challenge are related to inflammation, whereas downregulated genes are related to unfolded protein response, protein processing, cholesterol biosynthesis, and translation.

CONCLUSION

A general gene expression response to a high-fat challenge is identified. Compared to separate analyses, integrated analysis provides added value for the discovery of a consistent gene expression response.

Replacing Saturated Fat With Walnuts or Vegetable Oils Improves Central Blood Pressure and Serum Lipids in Adults at Risk for Cardiovascular Disease: A Randomized Controlled-Feeding Trial

Background Walnuts have beneficial effects on cardiovascular risk factors, but it is unclear whether these effects are attributable to the fatty acid ( FA ) content, including α-linolenic acid ( ALA ), and/or bioactives. Methods and Results A randomized, controlled, 3-period, crossover, feeding trial was conducted in individuals at risk for cardiovascular disease (n=45). Following a 2-week standard Western diet run-in (12% saturated FAs [ SFA ], 7% polyunsaturated FAs, 12% monounsaturated FAs), participants consumed 3 isocaloric weight-maintenance diets for 6 weeks each: a walnut diet ( WD ; 7% SFA , 16% polyunsaturated FAs, 3% ALA , 9% monounsaturated FAs); a walnut FA -matched diet; and an oleic acid-replaced- ALA diet (7% SFA , 14% polyunsaturated FAs, 0.5% ALA , 12% monounsaturated FAs), which substituted the amount of ALA from walnuts in the WD with oleic acid. This design enabled evaluation of the effects of whole walnuts versus constituent components. The primary end point, central systolic blood pressure, was unchanged, and there were no significant changes in arterial stiffness. There was a treatment effect ( P=0.04) for central diastolic blood pressure; there was a greater change following the WD versus the oleic acid-replaced-ALA diet (-1.78±1.0 versus 0.15±0.7 mm Hg, P=0.04). There were no differences between the WD and the walnut fatty acid-matched diet (-0.22±0.8 mm Hg, P=0.20) or the walnut FA-matched and oleic acid-replaced-ALA diets ( P=0.74). The WD significantly lowered brachial and central mean arterial pressure. All diets lowered total cholesterol, LDL (low-density lipoprotein) cholesterol, HDL (high-density lipoprotein) cholesterol, and non- HDL cholesterol. Conclusions Cardiovascular benefits occurred with all moderate-fat, high-unsaturated-fat diets. As part of a low- SFA diet, the greater improvement in central diastolic blood pressure following the WD versus the oleic acid-replaced-ALA diet indicates benefits of walnuts as a whole-food replacement for SFA . Clinical Trial Registration URL : https://www.clinicaltrials.gov . Unique identifier: NCT02210767.

Acute effects of dietary plant nutrients on transcriptome profiles: evidence from human studies

The health benefits of long-term dietary plant ingestion are well-established. However, literature on acute nutritional challenges is very limited. This study aimed to identify available evidence on transcriptomics responses to acute ingestion of plants or plant extracts and identify signature gene profiles that may serve as biomarkers of health status. We systematically searched electronic databases and extracted information based-on inclusion criteria such as human clinical studies, single plant-based nutrients and outcomes reported on acute transcriptome responses. A total of 11 studies reported on acute intake of plant dietary interventions. Four studies investigating natural oil extracts with three reporting on whole plants and two studies on natural plant-derived extracts. Gene expression was found to be associated with immune response (7 studies), inflammation (9 studies), metabolism (8 studies), cellular processes and cancer. The finding of this systematic review suggests that acute ingestion may significantly impact diverse physiological and pathological pathways including inflammatory, immune, cancer and oxidative stress pathways. Transcriptomics approach is proven to be an effective strategy in discovery of these anticipated mechanisms. Further studies are now required to validate and continue exploring the short-term health impact of dietary plants and their bioactive phytochemicals on gene expression and function.

Timing of eating in adults across the weight spectrum: Metabolic factors and potential circadian mechanisms

Timing of eating is recognized as a significant contributor to body weight regulation. Disruption of sleep-wake cycles from a predominantly diurnal (daytime) to a delayed (evening) lifestyle leads to altered circadian rhythms and metabolic dysfunction. This article reviews current evidence for timed and delayed eating in individuals of normal weight and those with overweight or obesity: although some findings indicate a benefit of eating earlier in the daytime on weight and/or metabolic outcomes, results have not been uniformly consistent, and more rigorous and longer-duration studies are needed. We also review potential circadian mechanisms underlying the metabolic- and weight-related changes resulting from timed and delayed eating. Further identification of such mechanisms using deep phenotyping is required to determine targets for medical interventions for obesity and for prevention of metabolic syndrome and diabetes, and to inform clinical guidelines regarding eating schedules for management of weight and metabolic disease.

Weighted Gene Co-Expression Network Analysis Identifies Gender Specific Modules and Hub Genes Related to Metabolism and Inflammation in Response to an Acute Lipid Challenge

SCOPE

Inflammation is characteristic of diet-related diseases including obesity and type 2 diabetes (T2D). However, biomarkers of inflammation that reflect the early stage metabolic derangements are not optimally sensitive. Lipid challenges elicit postprandial inflammatory and metabolic responses. Gender-specific transcriptomic networks of the peripheral blood mononuclear cell (PBMC) were constructed in response to a lipid challenge.

METHODS AND RESULTS

Eighty-six adult males and females of comparable age, anthropometric, and biochemical profiles completed an oral lipid tolerance test (OLTT). PBMC transcriptome was profiled following OLTT. Weighted gene coexpression networks were constructed separately for males and females. Functional ontology analysis of network modules was performed and hub genes identified. Two modules of interest were identified in females-an "inflammatory" module and an "energy metabolism" module. NLRP3, which plays a central role in inflammation and STARD3 that is involved in cholesterol metabolism, were identified as hub genes for the respective modules.

CONCLUSION

The OLTT induced some gender-specific correlations of gene coexpression network modules. In females, biological processes relating to energy metabolism and inflammation pathways were evident. This suggests a gender specific link between inflammation and energy metabolism in response to lipids. In contrast, G-protein coupled receptor protein signaling pathway was common to both genders.

Impact of anti-inflammatory nutrients on obesity-associated metabolic-inflammation from childhood through to adulthood

Obesity-related metabolic conditions such as insulin resistance (IR), type 2 diabetes and CVD share a number of pathological features, one of which is metabolic-inflammation. Metabolic-inflammation results from the infiltration of immune cells into the adipose tissue, driving a pro-inflammatory environment, which can induce IR. Furthermore, resolution of inflammation, an active process wherein the immune system counteracts pro-inflammatory states, may be dysregulated in obesity. Anti-inflammatory nutritional interventions have focused on attenuating this pro-inflammatory environment. Furthermore, with inherent variability among individuals, establishing at-risk populations who respond favourably to nutritional intervention strategies is important. This review will focus on chronic low-grade metabolic-inflammation, resolution of inflammation and the putative role anti-inflammatory nutrients have as a potential therapy. Finally, in the context of personalised nutrition, the approaches used in defining individuals who respond favourably to nutritional interventions will be highlighted. With increasing prevalence of obesity in younger people, age-dependent biological processes, preventative strategies and therapeutic options are important to help protect against development of obesity-associated co-morbidities.