Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices.

BACKGROUND: The aim of a recent research project was the investigation of the mechanisms involved in the onset of type 2 diabetes in the absence of familiarity. This has led to the development of a computational model that recapitulates the aetiology of the disease and simulates the immunological and metabolic alterations linked to type-2 diabetes subjected to clinical, physiological, and behavioural features of prototypical human individuals. RESULTS: We analysed the time course of 46,170 virtual subjects, experiencing different lifestyle conditions. We then set up a statistical model able to recapitulate the simulated outcomes. CONCLUSIONS: The resulting machine learning model adequately predicts the synthetic dataset and can, therefore, be used as a computationally-cheaper version of the detailed mathematical model, ready to be implemented on mobile devices to allow self-assessment by informed and aware individuals. The computational model used to generate the dataset of this work is available as a web-service at the following address: http://kraken.iac.rm.cnr.it/T2DM .

Personalizing physical exercise in a computational model of fuel homeostasis.

The beneficial effects of physical activity for the prevention and management of several chronic diseases are widely recognized. Mathematical modeling of the effects of physical exercise in body metabolism and in particular its influence on the control of glucose homeostasis is of primary importance in the development of eHealth monitoring devices for a personalized medicine. Nonetheless, to date only a few mathematical models have been aiming at this specific purpose. We have developed a whole-body computational model of the effects on metabolic homeostasis of a bout of physical exercise. Built upon an existing model, it allows to detail better both subjects' characteristics and physical exercise, thus determining to a greater extent the dynamics of the hormones and the metabolites considered.

Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development.

We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named "fight-club hubs" characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named "switch genes" was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.

Glucagon-like peptide-1 and interleukin-6 interaction in response to physical exercise: An in-silico model in the framework of immunometabolism.

BACKGROUND AND OBJECTIVE: Glucagon-like peptide 1 (GLP-1) is classically identified as an incretin hormone, secreted in response to nutrient ingestion and able to enhance glucose-stimulated insulin secretion. However, other stimuli, such as physical exercise, may enhance GLP-1 plasma levels, and this exercise-induced GLP-1 secretion is mediated by interleukin-6 (IL-6), a cytokine secreted by contracting skeletal muscle. The aim of the study is to propose a mathematical model of IL-6-induced GLP-1 secretion and kinetics in response to physical exercise of moderate intensity. METHODS: The model includes the GLP-1 subsystem (with two pools: gut and plasma) and the IL-6 subsystem (again with two pools: skeletal muscle and plasma); it provides a parameter of possible clinical relevance representing the sensitivity of GLP-1 to IL-6 (k0). The model was validated on mean IL-6 and GLP-1 data derived from the scientific literature and on a total of 100 virtual subjects. RESULTS: Model validation provided mean residuals between 0.0051 and 0.5493 pg⋅mL-1 for IL-6 (in view of concentration values ranging from 0.8405 to 3.9718 pg⋅mL-1) and between 0.0133 and 4.1540 pmol⋅L-1 for GLP-1 (in view of concentration values ranging from 0.9387 to 17.9714 pmol⋅L-1); a positive significant linear correlation (r = 0.85, p<0.001) was found between k0 and the ratio between areas under GLP-1 and IL-6 curve, over the virtual subjects. CONCLUSIONS: The model accurately captures IL-6-induced GLP-1 kinetics in response to physical exercise.

A computational model of the effects of macronutrients absorption and physical exercise on hormonal regulation and metabolic homeostasis.

Regular physical exercise and appropriate nutrition affect metabolic and hormonal responses and may reduce the risk of developing chronic non-communicable diseases such as high blood pressure, ischemic stroke, coronary heart disease, some types of cancer, and type 2 diabetes mellitus. Computational models describing the metabolic and hormonal changes due to the synergistic action of exercise and meal intake are, to date, scarce and mostly focussed on glucose absorption, ignoring the contribution of the other macronutrients. We here describe a model of nutrient intake, stomach emptying, and absorption of macronutrients in the gastrointestinal tract during and after the ingestion of a mixed meal, including the contribution of proteins and fats. We integrated this effort to our previous work in which we modeled the effects of a bout of physical exercise on metabolic homeostasis. We validated the computational model with reliable data from the literature. The simulations are overall physiologically consistent and helpful in describing the metabolic changes due to everyday life stimuli such as multiple mixed meals and variable periods of physical exercise over prolonged periods of time. This computational model may be used to design virtual cohorts of subjects differing in sex, age, height, weight, and fitness status, for specialized in silico challenge studies aimed at designing exercise and nutrition schemes to support health.

Mathematical model of insulin kinetics accounting for the amino acids effect during a mixed meal tolerance test.

Amino acids (AAs) are well known to be involved in the regulation of glucose metabolism and, in particular, of insulin secretion. However, the effects of different AAs on insulin release and kinetics have not been completely elucidated. The aim of this study was to propose a mathematical model that includes the effect of AAs on insulin kinetics during a mixed meal tolerance test. To this aim, five different models were proposed and compared. Validation was performed using average data, derived from the scientific literature, regarding subjects with normal glucose tolerance (CNT) and with type 2 diabetes (T2D). From the average data of the CNT and T2D people, data for two virtual populations (100 for each group) were generated for further model validation. Among the five proposed models, a simple model including one first-order differential equation showed the best results in terms of model performance (best compromise between model structure parsimony, estimated parameters plausibility, and data fit accuracy). With regard to the contribution of AAs to insulin appearance/disappearance (kAA model parameter), model analysis of the average data from the literature yielded 0.0247 (confidence interval, CI: 0.0168 - 0.0325) and -0.0048 (CI: -0.0281 - 0.0185) µU·ml-1/(µmol·l-1·min), for CNT and T2D, respectively. This suggests a positive effect of AAs on insulin secretion in CNT, and negligible effect in T2D. In conclusion, a simple model, including single first-order differential equation, may help to describe the possible AAs effects on insulin kinetics during a physiological metabolic test, and provide parameters that can be assessed in the single individuals.

Essentiality is an emergent property of metabolic network wiring.

The topological bases of essentiality in the yeast metabolic network from the perspective of double mutations are the subject of this study. A strong relationship between essentiality and the 'missing alternative' topological property is shown in terms of the presence of multiple genes synthesizing the same enzyme, supplementary enzymes participating in the same metabolic reaction, and availability of other pathways in the graph connecting the separated nodes after the knockouts. We demonstrate that the 'missing alternative' paradigm is sufficient to explain the generation of essentiality for double mutations in which each single deleted element is non-essential.

A system model of the effects of exercise on plasma Interleukin-6 dynamics in healthy individuals: Role of skeletal muscle and adipose tissue.

Interleukin-6 (IL-6) has been recently shown to play a central role in glucose homeostasis, since it stimulates the production and secretion of Glucagon-like Peptide-1 (GLP-1) from intestinal L-cells and pancreas, leading to an enhanced insulin response. In resting conditions, IL-6 is mainly produced by the adipose tissue whereas, during exercise, skeletal muscle contractions stimulate a marked IL-6 secretion as well. Available mathematical models describing the effects of exercise on glucose homeostasis, however, do not account for this IL-6 contribution. This study aimed at developing and validating a system model of exercise's effects on plasma IL-6 dynamics in healthy humans, combining the contributions of both adipose tissue and skeletal muscle. A two-compartment description was adopted to model plasma IL-6 changes in response to oxygen uptake's variation during an exercise bout. The free parameters of the model were estimated by means of a cross-validation procedure performed on four different datasets. A low coefficient of variation (<10%) was found for each parameter and the physiologically meaningful parameters were all consistent with literature data. Moreover, plasma IL-6 dynamics during exercise and post-exercise were consistent with literature data from exercise protocols differing in intensity, duration and modality. The model successfully emulated the physiological effects of exercise on plasma IL-6 levels and provided a reliable description of the role of skeletal muscle and adipose tissue on the dynamics of plasma IL-6. The system model here proposed is suitable to simulate IL-6 response to different exercise modalities. Its future integration with existing models of GLP-1-induced insulin secretion might provide a more reliable description of exercise's effects on glucose homeostasis and hence support the definition of more tailored interventions for the treatment of type 2 diabetes.

Human monocyte-derived dendritic cells exposed to hyperthermia show a distinct gene expression profile and selective upregulation of IGFBP6.

Fever plays a role in activating innate immunity while its relevance in activating adaptive immunity is less clear. Even brief exposure to elevated temperatures significantly impacts on the immunostimulatory capacity of dendritic cells (DCs), but the consequences on immune response remain unclear. To address this issue, we analyzed the gene expression profiles of normal human monocyte-derived DCs from nine healthy adults subjected either to fever-like thermal conditions (39°C) or to normal temperature (37°C) for 180 minutes. Exposure of DCs to 39°C caused upregulation of 43 genes and downregulation of 24 genes. Functionally, the up/downregulated genes are involved in post-translational modification, protein folding, cell death and survival, and cellular movement. Notably, when compared to monocytes, DCs differentially upregulated transcription of the secreted protein IGFBP-6, not previously known to be specifically linked to hyperthermia. Exposure of DCs to 39°C induced apoptosis/necrosis and resulted in accumulation of IGFBP-6 in the conditioned medium at 48 h. IGFBP-6 may have a functional role in the hyperthermic response as it induced chemotaxis of monocytes and T lymphocytes, but not of B lymphocytes. Thus, temperature regulates complex biological DC functions that most likely contribute to their ability to induce an efficient adaptive immune response.

Metabolic pathways variability and sequence/networks comparisons.

BACKGROUND: In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. RESULTS: We demonstrate both the ability of the proposed method to build reliable biological classification of a set of microorganisms and the strong correlation between the metabolic network wiring and involved enzymes sequence space. CONCLUSION: The method represents a valuable tool for the investigation of genotype/phenotype correlations allowing for a direct comparison of different species as for their metabolic machinery. In addition the detection of enzymes whose sequence space is maximally correlated with the metabolic network space gives an indication of the most crucial (on an evolutionary viewpoint) steps of the metabolic process.

Functional essentiality from topology features in metabolic networks: a case study in yeast.

The relation between the position of mutations in Saccharomyces cerevisiae metabolic network and their lethality is the subject of this work. We represent the topology of the network by a directed graph: nodes are metabolites and arcs represent the reactions; a mutation corresponds to the removal of all the arcs referring to the deleted enzyme. Using publicly available knock-out data, we show that lethality corresponds to the lack of alternative paths in the perturbed network linking the nodes affected by the enzyme deletion. Such feature is at the basis of the recently recognized importance of 'marginal' arcs of metabolic networks.

Kinetics effects and modeling of mRNA turnover.

Broader comprehension of gene expression regulatory mechanisms can be gained from a global analysis of how transcription and degradation are coordinated to orchestrate complex cell responses. The role of messenger RNA (mRNA) turnover modulation in gene expression levels has become increasingly recognized. From such perspective, in this review we briefly illustrate how a simple but effective mathematical model of mRNA turnover and some experimental findings, may together shed light on the molecular mechanisms underpinning the major role of mRNA decay rates in shaping the kinetics of gene activation and repression.