A type 2 diabetes mellitus (T2DM) subtyping method that determines the T2DM phenotype based on an extended oral glucose tolerance test is proposed. It assigns participants to one of seven subtypes... Show moreA type 2 diabetes mellitus (T2DM) subtyping method that determines the T2DM phenotype based on an extended oral glucose tolerance test is proposed. It assigns participants to one of seven subtypes according to their β-cell function and the presence of hepatic and/or muscle insulin resistance. The effectiveness of this subtyping approach and subsequent personalized lifestyle treatment in ameliorating T2DM was assessed in a primary care setting. Sixty participants, newly diagnosed with (pre)diabetes type 2 and not taking diabetes medication, completed the intervention. Retrospectively collected data of 60 people with T2DM from usual care were used as controls. Bodyweight (p < 0.01) and HbA1c (p < 0.01) were significantly reduced after 13 weeks in the intervention group, but not in the usual care group. The intervention group achieved 75.0% diabetes remission after 13 weeks (fasting glucose ≤ 6.9 mmol/L and HbA1c < 6.5% (48 mmol/mol)); for the usual care group, this was 22.0%. Lasting (two years) remission was especially achieved in subgroups with isolated hepatic insulin resistance. Our study shows that a personalized diagnosis and lifestyle intervention for T2DM in a primary care setting may be more effective in improving T2DM-related parameters than usual care, with long-term effects seen especially in subgroups with hepatic insulin resistance. Show less
Hettne, K.M.; Boorsma, A.; Dartel, D.A.M. van; Goeman, J.J.; Jong, E. de; Piersma, A.H.; ... ; Kors, J.A. 2013
Background: Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can... Show moreBackground: Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can be created by next-generation text mining (next-gen TM), and that these can be used with gene set analysis (GSA) methods for chemical treatment identification, for pharmacological mechanism elucidation, and for comparing compound toxicity profiles.Methods: We created 30,211 chemical response-specific gene sets for human and mouse by next-gen TM, and derived 1,189 (human) and 588 (mouse) gene sets from the Comparative Toxicogenomics Database (CTD). We tested for significant differential expression (SDE) (false discovery rate -corrected p-values < 0.05) of the next-gen TM-derived gene sets and the CTD-derived gene sets in gene expression (GE) data sets of five chemicals (from experimental models). We tested for SDE of gene sets for six fibrates in a peroxisome proliferator-activated receptor alpha (PPARA) knock-out GE dataset and compared to results from the Connectivity Map. We tested for SDE of 319 next-gen TM-derived gene sets for environmental toxicants in three GE data sets of triazoles, and tested for SDE of 442 gene sets associated with embryonic structures. We compared the gene sets to triazole effects seen in the Whole Embryo Culture (WEC), and used principal component analysis (PCA) to discriminate triazoles from other chemicals.Results: Next-gen TM-derived gene sets matching the chemical treatment were significantly altered in three GE data sets, and the corresponding CTD-derived gene sets were significantly altered in five GE data sets. Six next-gen TM-derived and four CTD-derived fibrate gene sets were significantly altered in the PPARA knock-out GE dataset. None of the fibrate signatures in cMap scored significant against the PPARA GE signature. 33 environmental toxicant gene sets were significantly altered in the triazole GE data sets. 21 of these toxicants had a similar toxicity pattern as the triazoles. We confirmed embryotoxic effects, and discriminated triazoles from other chemicals.Conclusions: Gene set analysis with next-gen TM-derived chemical response-specific gene sets is a scalable method for identifying similarities in gene responses to other chemicals, from which one may infer potential mode of action and/or toxic effect. Show less
Hettne, K.M.; Boorsma, A.; Dartel, D.A.M. van; Goeman, J.J.; Jong, E. de; Piersma, A.H.; ... ; Kors, J.A. 2013
