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| 2. |
- Nakayasu, Ernesto S, et al.
(författare)
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Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity
- 2023
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Ingår i: Cell Reports Medicine. - 2666-3791. ; 4:7
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Tidskriftsartikel (refereegranskat)abstract
- Type 1 diabetes (T1D) results from autoimmune destruction of β cells. Insufficient availability of biomarkers represents a significant gap in understanding the disease cause and progression. We conduct blinded, two-phase case-control plasma proteomics on the TEDDY study to identify biomarkers predictive of T1D development. Untargeted proteomics of 2,252 samples from 184 individuals identify 376 regulated proteins, showing alteration of complement, inflammatory signaling, and metabolic proteins even prior to autoimmunity onset. Extracellular matrix and antigen presentation proteins are differentially regulated in individuals who progress to T1D vs. those that remain in autoimmunity. Targeted proteomics measurements of 167 proteins in 6,426 samples from 990 individuals validate 83 biomarkers. A machine learning analysis predicts if individuals would remain in autoimmunity or develop T1D 6 months before autoantibody appearance, with areas under receiver operating characteristic curves of 0.871 and 0.918, respectively. Our study identifies and validates biomarkers, highlighting pathways affected during T1D development.
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| 3. |
- Plubell, Deanna L., et al.
(författare)
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Putting Humpty Dumpty Back Together Again : What Does Protein Quantification Mean in Bottom-Up Proteomics? br
- 2022
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 21:4, s. 891-898
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Tidskriftsartikel (refereegranskat)abstract
- Bottom-up proteomics provides peptide measurements and has beeninvaluable for moving proteomics into large-scale analyses. Commonly, a singlequantitative value is reported for each protein-coding gene by aggregating peptidequantities into protein groups following protein inference or parsimony. However, giventhe complexity of both RNA splicing and post-translational protein modification, it isoverly simplistic to assume that all peptides that map to a singular protein-coding genewill demonstrate the same quantitative response. By assuming that all peptides from aprotein-coding sequence are representative of the same protein, we may miss thediscovery of important biological differences. To capture the contributions of existingproteoforms, we need to reconsider the practice of aggregating protein values to a singlequantity per protein-coding gene.
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| 4. |
- van Hylckama Vlieg, Marte A.M., et al.
(författare)
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The risk of recurrent venous thromboembolism after discontinuation of anticoagulant therapy in patients with cancer-associated thrombosis: a systematic review and meta-analysis
- 2023
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Ingår i: eClinicalMedicine. - 2589-5370. ; 64
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Forskningsöversikt (refereegranskat)abstract
- Background: The optimal duration of anticoagulation in patients with active cancer and venous thromboembolism (VTE) is unknown. Current clinical guidelines advocate anticoagulant therapy for 3–6 months and to continue anticoagulant therapy for as long as the cancer is active. However, an adequate systematic review on the rate of recurrent VTE after discontinuation of anticoagulant therapy has not been performed. Methods: For this systemic review and meta-analysis, we searched Embase.com, Medline (Ovid), Web of Science, Cochrane Library, and Google Scholar, from database inception to February 16, 2023, for studies on anticoagulant therapy in patients with cancer and the recurrence of venous thromboembolism after discontinuation of this therapy. We included randomised controlled trials and cohort studies published in English that reported on patients who met the following: cancer and a first VTE, completed at least 3 months of anticoagulant therapy, were followed after discontinuation of anticoagulant therapy, and with symptomatic recurrent VTE as an outcome during follow-up. Study-level data were requested from study authors. The primary outcome was the rate of recurrent VTE after discontinuation of anticoagulant therapy. A Bayesian random-effects meta-analysis was used to estimate the rate of recurrent VTE per 100 person-years for the pooled studies at different time intervals after discontinuation of anticoagulation therapy. We also calculated the cumulative VTE recurrence rate at different time intervals. Forest plots were mapped and the results were summarized by the median and 95% credible interval (CIs). This study was registered with PROSPERO, CRD42021249060. Findings: Of 3856 studies identified in our search, 33 studies were identified for inclusion. After requesting study-level data, 14 studies involving 1922 patients with cancer-associated thrombosis were included. The pooled rate of recurrent VTE per 100 person-years after discontinuation of anticoagulant therapy was 14.6 events (95% credible interval 6.5–22.8) in the first three months, decreasing to 1.1 events (95% CI 0.3–2.1) in year 2–3, and 2.2 events (95% CI 0.0–4.4) in year 3–5 after discontinuation of anticoagulant therapy. The cumulative VTE recurrence rate was 28.3% (95% CI 15.6–39.6%) at 1 year; 31.1% (95% CI 16.5–43.8%) at 2 years; 31.9% (95% CI 16.8–45.0%) at 3 years; and 35.0% (95% CI 16.8–47.4%) at 5 years after discontinuation of anticoagulant therapy. Interpretation: This meta-analysis demonstrates a high rate of recurrent VTE over time after discontinuation of anticoagulant therapy in patients with cancer-associated thrombosis. Our results support the current clinical guidelines to continue anticoagulant therapy in patients with active cancer. Funding: Erasmus MC.
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| 5. |
- Halfvarson, Jonas, 1970-, et al.
(författare)
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Dynamics of the human gut microbiome in inflammatory bowel disease
- 2017
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Ingår i: Nature Microbiology. - London, United Kingdom : Nature Publishing Group. - 2058-5276. ; 2:5
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Tidskriftsartikel (refereegranskat)abstract
- Inflammatory bowel disease (IBD) is characterized by flares of inflammation with a periodic need for increased medication and sometimes even surgery. The aetiology of IBD is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD subtypes, including ulcerative colitis, colonic Crohn's disease and ileal Crohn's disease. Although IBD is dynamic, microbiome studies have primarily focused on single time points or a few individuals. Here, we dissect the long-term dynamic behaviour of the gut microbiome in IBD and differentiate this from normal variation. Microbiomes of IBD subjects fluctuate more than those of healthy individuals, based on deviation from a newly defined healthy plane (HP). Ileal Crohn's disease subjects deviated most from the HP, especially subjects with surgical resection. Intriguingly, the microbiomes of some IBD subjects periodically visited the HP then deviated away from it. Inflammation was not directly correlated with distance to the healthy plane, but there was some correlation between observed dramatic fluctuations in the gut microbiome and intensified medication due to a flare of the disease. These results will help guide therapies that will redirect the gut microbiome towards a healthy state and maintain remission in IBD.
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