| 1. |
- Allesøe, Rosa Lundbye, et al.
(författare)
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Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models
- 2023
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 41:3, s. 399-408
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Tidskriftsartikel (refereegranskat)abstract
- The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug–omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug–drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities.
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| 2. |
- Vendelbo Lind, Mads, 1988, et al.
(författare)
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Higher intake of fish and fat is associated with lower plasma s-adenosylhomocysteine: a cross-sectional study
- 2017
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Ingår i: Nutrition Research. - : Elsevier BV. - 0271-5317 .- 1879-0739. ; 46, s. 78-87
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Tidskriftsartikel (refereegranskat)abstract
- Several B-vitamins act as co-factors in one-carbon metabolism, a pathway that plays a central role in several chronic diseases. However, there is a lack of knowledge of how diet affects markers in one-carbon metabolism. The aim of this study was to explore dietary patterns and components associated with one-carbon metabolites. We hypothesized that intake of whole-grains and fish would be associated with lower Hcy, and higher SAM:SAH ratio due to their nutrient content. We assessed dietary information using a four-day dietary record in 118 men and women with features of the metabolic syndrome. In addition we assessed whole-blood fatty acid composition and plasma alkylresorcinols. Plasma s-adenosylmethionine (SAM), s-adenosylhomocysteine (SAH), homocysteine (Hcy) and vitamin B12 was included as one-carbon metabolism markers. We used principal component analysis (PCA) to explore dietary patterns and multiple linear regression models to examine associations between dietary factors and one-carbon metabolites. PCA separated subjects based on prudent and unhealthy dietary patterns, but the dietary pattern score was not related to the one-carbon metabolites. Whole grain intake was found to be inversely associated to plasma Hcy (?4.7% (?9.3; 0.0), P =.05) and total grain intake tended to be positively associated with SAM and SAH (2.4% (?0.5; 5.5), P =.08; 5.8% (?0.2; 12.1), P =.06, respectively, per SD increase in cereal intake). Fish intake was inversely associated with plasma Hcy and SAH concentrations (?5.4% (?9.7; ?0.8), P =.02 and ?7.0% (?12.1; ?1.5), P =.01, respectively) and positively associated with the SAM:SAH ratio (6.2% (1.6; 11.0), P =.008). In conclusion, intake and fish and whole-grain appear to be associated with a beneficial one-carbon metabolism profile. This indicates that dietary components could play a role in regulation of one-carbon metabolism with a potential impact on disease prevention.
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| 3. |
- Frederiksen, Lise, et al.
(författare)
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A multivariate approach to plant community distribution in the coastal dune zonation of NW Denmark
- 2006
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Ingår i: Phytocoenologia. - 0340-269X. ; 36:3, s. 321-342
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Tidskriftsartikel (refereegranskat)abstract
- A near-natural coastal dune system in NW Jutland, Denmark was investigated. The area contains a gradient in natural soil mobility with the highest values in dynamic white dunes dominated by Ammophila arenaria, and low mobility in fixed decalcified dune heath with Empetrum nigrum and Calluna vulgaris. A total of 267 plots was investigated and presence of mosses and rooted vascular plants recorded. Cluster analysis identified five communities: white dune, grey dune, outer dune heath, inner dune heath and humid dune heath. These communities were ordered along two main axes in a Detrended Correspondence Analysis (DCA). The relationship between DCA axes and several environmental variables, including soil characteristics and Ellenberg indicator values, were investigated by correlation. Two major complex gradients underlying compositional variation were identified; one short coenocline with an underlying steep gradient in habitat maturity, soil stability and nutrient-limited productivity, and one longer gradient in water-limited productivity and peat accumulation only applying to the older successional stages. Distance from the coast was an important correlate of several of the measured variables. Microclimatic indices, i.e. heat index and wind index, had limited value as descriptors of community patterns as they were not correlated with the DCA axes or with other environmental variables. However, within communities the microclimatic indices correlated with several explanatory variables.
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| 4. |
- Kilpeläinen, Tuomas O, et al.
(författare)
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Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10(-6) in 19,979 additional individuals. We identify five loci robustly associated (P<5 × 10(-8)) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health.
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| 5. |
- Kollman, Johannes, et al.
(författare)
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Limiting factors for seedling emergence and establishment of the invasive non-native Rosa rugosa in a coastal dune system
- 2007
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Ingår i: Biological Invasions. - : Springer Science and Business Media LLC. - 1387-3547 .- 1573-1464. ; 9:1, s. 31-42
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Tidskriftsartikel (refereegranskat)abstract
- The relative importance of seed, habitat and microhabitat limitation has rarely been investigated for invasive non-native species, although this is critical for their effective management and for predicting future range expansion. Rosa rugosa is an abundant non-native shrub in coastal habitats of NW Europe; it is common along the Baltic coast but more scarce in exposed dunes of the North Sea. To investigate whether invasion of exposed dunes is limited by seed, habitat and microhabitat limitation, seedling emergence and establishment were examined in a factorial sowing, transplant and disturbance experiment. Twenty plots were randomly placed in each of five dune habitats (white dune, Empetrum dune, grey dune, outer dune heath, inner dune heath), and studied over 2 years. Seedling emergence in control subplots was zero in all habitats, whereas 96% and 98% of the undisturbed and disturbed seeded subplots produced seedlings. Disturbance had a positive effect on emergence and subsequent survival in white dune, outer and inner dune heath. Seedling survival and growth, and growth of transplanted seedlings, were markedly lower in grey dune. These findings indicate that establishment of R. rugosa is seed-limited in coastal dune habitats, and that the species is able to establish in both active and fixed dunes once seeds have arrived. Although differential seedling emergence and growth indicate that habitats differ in their degree of invasion susceptibility by R. rugosa, the positive influence of small-scale disturbance suggests microhabitat limitation in some dune habitats as well. Dune management should aim to reduce seed production and dispersal of R. rugosa in near-natural sites, and anthropogenic changes of habitat dynamics should be prevented.
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| 6. |
- Marouli, Eirini, et al.
(författare)
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Rare and low-frequency coding variants alter human adult height
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 542:7640, s. 186-190
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Tidskriftsartikel (refereegranskat)abstract
- Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.
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| 7. |
- Turcot, Valerie, et al.
(författare)
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Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity
- 2018
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:1, s. 26-41
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are similar to 10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed similar to 7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
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