| 1. |
- Atabaki Pasdar, Naeimeh, et al.
(författare)
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Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts
- 2020
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Ingår i: PLoS Medicine. - San Francisco : Public Library of Science (PLoS). - 1549-1676 .- 1549-1277. ; 17:6, s. 1003149-1003149
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is highly prevalent and causes serious health complications in individuals with and without type 2 diabetes (T2D). Early diagnosis of NAFLD is important, as this can help prevent irreversible damage to the liver and, ultimately, hepatocellular carcinomas. We sought to expand etiological understanding and develop a diagnostic tool for NAFLD using machine learning. METHODS AND FINDINGS: We utilized the baseline data from IMI DIRECT, a multicenter prospective cohort study of 3,029 European-ancestry adults recently diagnosed with T2D (n = 795) or at high risk of developing the disease (n = 2,234). Multi-omics (genetic, transcriptomic, proteomic, and metabolomic) and clinical (liver enzymes and other serological biomarkers, anthropometry, measures of beta-cell function, insulin sensitivity, and lifestyle) data comprised the key input variables. The models were trained on MRI-image-derived liver fat content (
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| 2. |
- Coral, Daniel
(författare)
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Characterisation of the genetic discordance between body mass index and type 2 diabetes: a phenome-wide analysis : No 111
- 2020
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Ingår i: Diabetologia. - : Springer Science and Business Media LLC. - 1432-0428 .- 0012-186X. ; 63
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Konferensbidrag (refereegranskat)abstract
- Background and aims: Obesity is on the rise globally, and is a leading risk factor for T2D. However, it is very heterogeneous, with varying degrees of T2D risk within the same levels of BMI. Better classification may lead to improve outcomes of current preventive and therapeutic strategies. Moreover, by elucidating the mechanisms uncoupling obesity from T2D risk, new possible therapeutic targets may emerge. Leveraging the vast amount of genetic data produced to date may contribute to reach these goals while overcoming the obstacles imposed by common assumptions, biases and confounders present in observational studies. Our aim is to compare the phenome-wide association patterns of BMI-increasing genetic profiles that either concordantly increase or discordantly decrease T2D risk. Materials and methods: Highly concordant and highly discordant SNPs between BMI and T2D were obtained from the latest GWAS for both conditions. Their standardized effect sizes (SES) across multiple traits in the phenome, metabolome, proteinome and transcriptome were retrieved from the online genomic repositories. After alignment to the BMI-increasing allele, these effects were organized into a SNP x Trait matrix. A hierarchical clustering technique, combining PCA and Random Forest algorithms was applied, retrieving the optimal number of clusters of traits, organized in order of importance, useful to distinguish a discordant from a concordant SNP. Posterior probabilities of colocalization with T2D were calculated for each gene using transcriptome results. Tissue, biological process, molecular mechanism and cellular component enrichments were evaluated. The predictive potential of GRSs informed by these findings were assessed in the UK Biobank dataset. Results: 121 SNPs were found to be significantly associated with BMI and T2D. 18 were discordant and 104 concordant. A total of 1372 variables were included in the analyses (Phenome = 546, Metabolome = 233, Proteinome = 593). The most important difference between discordant and concordant SNPs in the phenome matrix was found in a cluster of traits led by hypertension (Mean discordant SES = -1.59, Mean concordant SES = 2.56), highly correlated with two clusters led by coronary heart disease and overall health status, respectively. The second most important cluster was led by physical activity-adjusted WHR (Mean discordant SES = -2.69, Mean concordant SES = 0.24). The model obtained from the phenome matrix had the highest classification performance (Matthews Correlation Coefficient, MCC = 0.79). Metabolome results showed differences in polyunsaturated fatty acids and lipid contents in VLDL, but with lower performance (MCC = 0.67). The model from the proteinome matrix was unable to correctly classify SNPs (MCC = -0.03). Two genes (CCDC92 and DNAH10) showed the strongest association within the discordant set in adipose tissue, both involved in cilia formation. A GRS of these 121 SNPs with weights derived from the clusters with high classification performance was highly associated with T2D in both the general and obese populations in UK Biobank (p < 1x1016). Conclusion: The main difference between BMI-increasing genetic profiles that either discordantly decrease or concordantly increase T2D risk is found in hypertension risk and physical activity-adjusted WHR. These traits can be used to inform GRSs to better classify T2D risk in obesity. Molecular mechanisms behind the discordant profile appear to involve cilia formation in the adipose tissue.
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| 3. |
- Gudmundsdottir, Valborg, et al.
(författare)
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Whole blood co-expression modules associate with metabolic traits and type 2 diabetes : an IMI-DIRECT study
- 2020
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Ingår i: Genome Medicine. - : BioMed Central. - 1756-994X .- 1756-994X. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The rising prevalence of type 2 diabetes (T2D) poses a major global challenge. It remains unresolved to what extent transcriptomic signatures of metabolic dysregulation and T2D can be observed in easily accessible tissues such as blood. Additionally, large-scale human studies are required to further our understanding of the putative inflammatory component of insulin resistance and T2D. Here we used transcriptomics data from individuals with (n = 789) and without (n = 2127) T2D from the IMI-DIRECT cohorts to describe the co-expression structure of whole blood that mainly reflects processes and cell types of the immune system, and how it relates to metabolically relevant clinical traits and T2D.Methods: Clusters of co-expressed genes were identified in the non-diabetic IMI-DIRECT cohort and evaluated with regard to stability, as well as preservation and rewiring in the cohort of individuals with T2D. We performed functional and immune cell signature enrichment analyses, and a genome-wide association study to describe the genetic regulation of the modules. Phenotypic and trans-omics associations of the transcriptomic modules were investigated across both IMI-DIRECT cohorts.Results: We identified 55 whole blood co-expression modules, some of which clustered in larger super-modules. We identified a large number of associations between these transcriptomic modules and measures of insulin action and glucose tolerance. Some of the metabolically linked modules reflect neutrophil-lymphocyte ratio in blood while others are independent of white blood cell estimates, including a module of genes encoding neutrophil granule proteins with antibacterial properties for which the strongest associations with clinical traits and T2D status were observed. Through the integration of genetic and multi-omics data, we provide a holistic view of the regulation and molecular context of whole blood transcriptomic modules. We furthermore identified an overlap between genetic signals for T2D and co-expression modules involved in type II interferon signaling.Conclusions: Our results offer a large-scale map of whole blood transcriptomic modules in the context of metabolic disease and point to novel biological candidates for future studies related to T2D.
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| 4. |
- Marcos-Pérez, Diego, et al.
(författare)
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Association of inflammatory mediators with frailty status in older adults : results from a systematic review and meta-analysis
- 2020
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Ingår i: GeroScience. - : Springer Science and Business Media LLC. - 2509-2715 .- 2509-2723. ; 42:6, s. 1451-1473
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Forskningsöversikt (refereegranskat)abstract
- Frailty is a geriatric syndrome defined as a status of extreme vulnerability to stressors, leading to a higher risk of negative health-related outcomes. “Inflammaging”, an age-related state of low-grade chronic inflammation, is characterized by an increased concentration of pro-inflammatory cytokines and acute phase proteins. Inflammaging has been postulated as an underlying mechanism of frailty, and several studies tested the relationship between frailty and concentration of inflammatory mediators. The aim of this systematic review and meta-analysis was to test whether inflammatory mediators are overproduced in frail older adults. Among the 758 articles identified in the literature search, 50 were included in the systematic review, and 39 in the three meta-analyses, i.e., C-reactive protein (CRP), interleukin 6 (IL6), and tumor necrosis factor α. To reduce heterogeneity, meta-analyses were restricted to studies identifying frailty by the Fried et al. [1] [J. Gerontol. A. Biol. Sci. Med. Sci. 56, M146–56] phenotypic criteria. Quantitative analyses measuring the association between frailty and biomarker concentrations showed significant differences when frail subjects were compared to non-frail and pre-frail subjects for CRP and IL6. This work established strong association between inflammatory biomarkers and frailty, confirming the role of age-related chronic inflammation in frailty development.
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| 5. |
- Marcos-Pérez, Diego, et al.
(författare)
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Low vitamin d levels and frailty status in older adults : A systematic review and meta-analysis
- 2020
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Ingår i: Nutrients. - : MDPI AG. - 2072-6643. ; 12:8
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Forskningsöversikt (refereegranskat)abstract
- Serum vitamin D deficiency is widespread among older adults and is a potential modifiable risk factor for frailty. Moreover, frailty has been suggested as an intermediate step in the association between low levels of vitamin D and mortality. Hence, we conducted a systematic review of the literature and meta-analysis to test the possible association of low concentrations of serum 25-hydroxyvitamin D (25(OH)D), a marker of vitamin D status, with frailty in later life. We reviewed cross-sectional or longitudinal studies evaluating populations of older adults and identifying frailty by a currently validated scale. Meta-analyses were restricted to cross-sectional data from studies using Fried’s phenotype to identify frailty. Twenty-six studies were considered in the qualitative synthesis, and thirteen studies were included in the meta-analyses. Quantitative analyses showed significant differences in the comparisons of frail (standardized mean difference (SMD)—1.31, 95% confidence interval (CI) (−2.47, −0.15), p = 0.0271) and pre-frail (SMD—0.79, 95% CI (−1.58, −0.003), p = 0.0491) subjects vs. non-frail subjects. Sensitivity analyses reduced heterogeneity, resulting in a smaller but still highly significant between-groups difference. Results obtained indicate that lower 25(OH)D levels are significantly associated with increasing frailty severity. Future challenges include interventional studies testing the possible benefits of vitamin D supplementation in older adults to prevent/palliate frailty and its associated outcomes.
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| 6. |
- van Zuydam, Natalie R., et al.
(författare)
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Genetic Predisposition to Coronary Artery Disease in Type 2 Diabetes Mellitus
- 2020
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Ingår i: Circulation. - : Lippincott Williams & Wilkins. - 2574-8300. ; 13:6, s. 640-648
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Coronary artery disease (CAD) is accelerated in subjects with type 2 diabetes mellitus (T2D).METHODS: To test whether this reflects differential genetic influences on CAD risk in subjects with T2D, we performed a systematic assessment of genetic overlap between CAD and T2D in 66 643 subjects (27 708 with CAD and 24 259 with T2D). Variants showing apparent association with CAD in stratified analyses or evidence of interaction were evaluated in a further 117 787 subjects (16 694 with CAD and 11 537 with T2D).RESULTS: None of the previously characterized CAD loci was found to have specific effects on CAD in T2D individuals, and a genome-wide interaction analysis found no new variants for CAD that could be considered T2D specific. When we considered the overall genetic correlations between CAD and its risk factors, we found no substantial differences in these relationships by T2D background.CONCLUSIONS: This study found no evidence that the genetic architecture of CAD differs in those with T2D compared with those without T2D.
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