| 1. |
- Eriksson, Olivia, et al.
(författare)
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Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models
- 2019
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 35:2, s. 284-292
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Dynamical models describing intracellular phenomena are increasing in size and complexity as more information is obtained from experiments. These models are often over-parameterized with respect to the quantitative data used for parameter estimation, resulting in uncertainty in the individual parameter estimates as well as in the predictions made from the model. Here we combine Bayesian analysis with global sensitivity analysis (GSA) in order to give better informed predictions; to point out weaker parts of the model that are important targets for further experiments, as well as to give guidance on parameters that are essential in distinguishing different qualitative output behaviours.Results: We used approximate Bayesian computation (ABC) to estimate the model parameters from experimental data, as well as to quantify the uncertainty in this estimation (inverse uncertainty quantification), resulting in a posterior distribution for the parameters. This parameter uncertainty was next propagated to a corresponding uncertainty in the predictions (forward uncertainty propagation), and a GSA was performed on the predictions using the posterior distribution as the possible values for the parameters. This methodology was applied on a relatively large model relevant for synaptic plasticity, using experimental data from several sources. We could hereby point out those parameters that by themselves have the largest contribution to the uncertainty of the prediction as well as identify parameters important to separate between qualitatively different predictions. This approach is useful both for experimental design as well as model building.
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| 2. |
- Fuhlbrigge, Anne L., et al.
(författare)
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A novel endpoint for exacerbations in asthma to accelerate clinical development : A post-hoc analysis of randomised controlled trials
- 2017
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Ingår i: The Lancet Respiratory Medicine. - 2213-2600. ; 5:7, s. 577-590
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Tidskriftsartikel (refereegranskat)abstract
- Background: Occurrence of severe asthma exacerbations are the cornerstone of the evaluation of asthma management, but severe asthma exacerbations are rare events. Therefore, trials that assess drug efficacy on exacerbations are done late in clinical development programmes. We aimed to establish an endpoint capturing clinically relevant deteriorations (diary events) that, when combined with severe exacerbations, create a composite outcome (CompEx). CompEx needs to strongly mirror results seen with the severe exacerbation-validated outcome, to allow the design of clinical trials of shorter duration and that include fewer patients than trials assessing severe exacerbations. Methods: Data from 12 asthma trials of 6 months or 12 months duration and, with standardised collection of exacerbations and diary card variables, were used to construct and test CompEx. The study populations had a mean age of 35-53 years, 59-69% were female, and had a mean FEV1 percentage of predicted normal of 63-84%. With data from five trials, we established a series of diary events based on peak expiratory flow (P), reliever use (R), symptoms (S), awakenings (A), and threshold values for change from baseline and slopes to assess trends. For the development phase, we evaluated different variable combinations and deterioration criteria to select the most robust algorithm to define a diary event for the composite outcome. We defined a composite outcome, CompEx, as first occurrence of a diary event or a severe exacerbation. We assessed the performance of CompEx in seven trials by comparing the event frequency, treatment effect (hazard ratio; HR), and the sample size needed for future trials for the CompEx versus episodes of severe exacerbations. Findings: CompEx (based on PRS) was the algorithm that best fulfilled our two-set criteria. When censored at 3 months, CompEx resulted in 2·8 times more events than severe exacerbations, and while preserving the treatment effect observed on severe exacerbations (CompEx over severe exacerbation average HR 1·01). The increased number of events, together with the sustained treatment effect, resulted in a large net gain in power, with a 67% mean reduction in the number of patients required in a drug trial for severe exacerbations. In six of seven comparisons tested, CompEx reduced the sample size needed by at least 50%. Validation of independent test populations confirmed the ability of CompEx to increase event frequencies, preserve treatment effect, and reduce the number of patients needed. Interpretation: CompEx is a composite outcome for evaluation of new asthma therapies. CompEx allows design of shorter trials that require fewer patients than studies of severe exacerbations, while preserving the ability to show a treatment effect compared with severe exacerbations. Funding: AstraZeneca.
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| 3. |
- Gunnarsson, Lina-Maria, 1977, et al.
(författare)
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Evolutionary conservation of human drug targets in organisms used for environmental risk assessments.
- 2008
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Ingår i: Environmental science & technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 42:15, s. 5807-13
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Tidskriftsartikel (refereegranskat)abstract
- Pharmaceuticals are typically found in very low concentrations in the aquatic environment. Accordingly, environmental effects clearly assigned to residual drugs are consistent with high affinity interactions with conserved targets in affected wildlife species rather than with a general toxic effect. Thus, evolutionarily well-conserved targets in a given species are associated with an increased risk. In this study orthologs for 1318 human drug targets were predicted in 16 species of which several are relevant for ecotoxicity testing. The conservation of different functional categories of targets was also analyzed. Zebrafish had orthologs to 86% of the drug targets while only 61% were conserved in Daphnia and 35% in green alga. The predicted presence and absence of orthologs agrees well with published experimental data on the potential for specific drug target interaction in various species. Based on the conservation of targets we propose that aquatic environmental risk assessments for human drugs should always include comprehensive studies on aquatic vertebrates. Furthermore, individual targets, especially enzymes, are well conserved suggesting that tests on evolutionarily distant organisms would be highly relevant for certain drugs. We propose that the results can guide environmental risk assessments by improving the possibilities to identify species sensitive to certain types of pharmaceuticals or to other contaminants that act through well defined mechanisms of action. Moreover, we suggest that the results can be used to interpret the relevance of existing ecotoxicity data.
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| 4. |
- Jauhiainen, Alexandra, 1981, et al.
(författare)
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Distinct cytoplasmic and nuclear functions of the stress induced protein DDIT3/CHOP/GADD153
- 2012
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:4
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Tidskriftsartikel (refereegranskat)abstract
- DDIT3, also known as GADD153 or CHOP, encodes a basic leucine zipper transcription factor of the dimer forming C/EBP family. DDIT3 is known as a key regulator of cellular stress response, but its target genes and functions are not well characterized. Here, we applied a genome wide microarray based expression analysis to identify DDIT3 target genes and functions. By analyzing cells carrying tamoxifen inducible DDIT3 expression constructs we show distinct gene expression profiles for cells with cytoplasmic and nuclear localized DDIT3. Of 175 target genes identified only 3 were regulated by DDIT3 in both cellular localizations. More than two thirds of the genes were downregulated, supporting a role for DDIT3 as a dominant negative factor that could act by either cytoplasmic or nuclear sequestration of dimer forming transcription factor partners. Functional annotation of target genes showed cell migration, proliferation and apoptosis/survival as the most affected categories. Cytoplasmic DDIT3 affected more migration associated genes, while nuclear DDIT3 regulated more cell cycle controlling genes. Cell culture experiments confirmed that cytoplasmic DDIT3 inhibited migration, while nuclear DDIT3 caused a G1 cell cycle arrest. Promoters of target genes showed no common sequence motifs, reflecting that DDIT3 forms heterodimers with several alternative transcription factors that bind to different motifs. We conclude that expression of cytoplasmic DDIT3 regulated 94 genes. Nuclear translocation of DDIT3 regulated 81 additional genes linked to functions already affected by cytoplasmic DDIT3. Characterization of DDIT3 regulated functions helps understanding its role in stress response and involvement in cancer and degenerative disorders.
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| 5. |
- Jauhiainen, Alexandra, 1981
(författare)
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Microarray Analysis of mRNA Decay Assays and Prediction of Drug Target Conservation
- 2008
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis contains two papers concerning (I) the evolutionary conservation of drug targets and its potential use in environmental risk assessments and (II) mRNA degradation as a control mechanism during osmotic stress in the yeast S. cerevisiae. Environmental risk assessments are needed for the approval of new pharmaceutical compounds. To date, the risk assessments are mainly focused on organisms like algae and Daphnia. The conservation of drug targets in species relevant for ecotoxicity testing is a key aspect in developing more targeted test strategies on higher organisms like fish or amphibians. With information on predicted proteomes for a wide range of species it is possible to extract and compile data on evolutionary conservation for drug targets. In paper I, orthology data is compiled and analyzed for a set of drug targets in several species, and the result evaluated based on an extensive literature search. mRNA degradation can be investigated on a genome-wide scale with the use of a transcriptional inhibitor and subsequent hybridization of RNA pools, isolated at a set of timepoints, to microarrays. Due to the complexity of the microarray methodology in this context, the data are in need of processing and transformation to deduce relevant information on changes in degradation rates. In paper II, mRNA degradation is investigated as a posttranscriptional control effect in connection to hyperosmotic stress. We conclude that mRNA degradation mechanisms are important regulatory keys in the stress response.
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| 6. |
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| 7. |
- Jauhiainen, Alexandra, 1981
(författare)
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Statistics in Gene Expression, Metabolomics, and Comparative Genomics in Evolution
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis contains four papers concerning (I) the evolutionary conservation of drug targets and its potential use in environmental risk assessments, (II) RNA degradation as a control mechanism during osmotic stress in the yeast S. cerevisiae, (III) the localization and effects of the gene DDIT3 encoding a key regulator of stress response, and (IV) the integration and analysis of transcriptional and metabolic data to identify active metabolic pathways. Environmental risk assessments are needed for the approval of new pharmaceutical compounds. To date, the risk assessments have mainly been focused on organisms like algae and Daphnia. The conservation of drug targets in species relevant for ecotoxicity testing is a key aspect in developing more targeted test strategies on higher organisms like fish or amphibians. With information on predicted proteomes for a wide range of species it is possible to extract data on evolutionary conservation for drug targets. In paper I, orthology data is compiled and analyzed for a set of human drug targets in several species, and the result evaluated based on an extensive literature search. mRNA degradation can be investigated on a genome-wide scale with the use of a transcriptional inhibitor and subsequent hybridization of RNA pools, isolated at a set of time-points, to microarrays. Due to the complexity of the microarray methodology in this context, the data are in need of processing and transformation to deduce relevant information on changes in degradation rates. In paper II, mRNA degradation is investigated as a post-transcriptional control effect in connection to hyperosmotic stress. We conclude that mRNA degradation mechanisms are important regulatory keys in the stress response. The gene DDIT3 encodes a protein acting as a regulator of the stress response within human cells. For example DNA damage, hypoxia, and starvation are stress types inducing DDIT3 transcription. DDIT3 is a transcription factor and has mainly been reported as a nuclear protein. In paper III, the effects and target genes of DDIT3 are investigated using techniques like microarrays, RT-qPCR, and various bioinformatical and statistical methods. We report that DDIT3 also can be localized to the cytoplasm, and induces or represses different genes compared to the nuclear form. The cytoplasmic form of DDIT3 is involved in migration, and inhibits the migratory effects of fibrosarcoma cells. The development of different 'omics' technologies in molecular biology has resulted in several methods to characterize cells and tissues, for example microarrays to characterize the transcriptome (collection of gene transcripts) and spectrometry techniques like NMR to describe the metabolome (collection of small molecules). Interpretation of different 'omics' data is usually done separately, and often with respect to pathways, which are sets of reactions involving genes, metabolites, and proteins. A common research question is to deduce which pathways are active (regulated) when comparing two or several conditions. In paper IV, we propose a model to make such pathway level decisions by integrating transcriptomic and metabolomic data.
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| 8. |
- Jauhiainen, Alexandra, 1981, et al.
(författare)
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Transcriptional and metabolic data integration and modeling for identification of active pathways
- 2012
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Ingår i: Biostatistics. - : Oxford University Press (OUP). - 1465-4644 .- 1468-4357. ; 13:4, s. 748-761
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Tidskriftsartikel (refereegranskat)abstract
- With the growing availability of omics data generated to describe different cells and tissues, the modeling and interpretation of such data has become increasingly important. Pathways are sets of reactions involving genes, metabolites, and proteins highlighting functional modules in the cell. Therefore, to discover activated or perturbed pathways when comparing two conditions, for example two different tissues, it is beneficial to use several types of omics data. We present a model that integrates transcriptomic and metabolomic data in order to make an informed pathway-level decision. Since metabolites can be seen as end-points of perturbations happening at the gene level, the gene expression data constitute the explanatory variables in a sparse regression model for the metabolite data. Sophisticated model selection procedures are developed to determine an appropriate model. We demonstrate that the transcript profiles can be used to informatively explain the metabolite data from cancer cell lines. Simulation studies further show that the proposed model offers a better performance in identifying active pathways than, for example, enrichment methods performed separately on the transcript and metabolite data.
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| 9. |
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| 10. |
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| 11. |
- Marín-Navarro, Julia, et al.
(författare)
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Global estimation of mRNA stability in yeast
- 2011
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Ingår i: Methods in Molecular Biology. - Totowa, NJ : Humana Press. - 1064-3745 .- 1940-6029. ; 734, s. 3-23
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Tidskriftsartikel (refereegranskat)abstract
- Turnover of mRNA is an important level of gene regulation. Individual mRNAs have different intrinsic stabilities. Moreover, mRNA stability changes dynamically with conditions such as hormonal stimulation or cellular stress. While accurate methods exist to measure the half-life of an individual transcript, global methods to estimate mRNA turnover have limitations in terms of resolution in time and precision. We describe and compare two complementary approaches to estimating global transcript stability: (1) direct measurement of decay rates; (2) indirect estimation of turnover from determination of mRNA synthesis rates and steady-state levels. Since the two approaches have distinct strengths yet confer different cellular perturbations, it is valuable to consider results obtained with both methods. The practical aspects of the chapter are written from a yeast perspective; the general considerations hold true for all eukaryotes, however.
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| 12. |
- Molin, Claes, 1977, et al.
(författare)
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mRNA stability changes precede changes in steady-state mRNA amounts during hyperosmotic stress
- 2009
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Ingår i: RNA. - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 15:4, s. 600-614
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Tidskriftsartikel (refereegranskat)abstract
- Under stress, cells need to optimize the activity of a wide range of gene products during the response phases: shock, adaptation, and recovery. This requires coordination of several levels of regulation, including turnover and translation efficiencies ofmRNAs. Mitogen-activated protein (MAP) kinase pathways are implicated in many aspects of the environmental stress response,including initiation of transcription, translation efficiency, and mRNA turnover. In this study, we analyze mRNA turnover ratesand mRNA steady-state levels at different time points following mild hyperosmotic shock in Saccharomyces cerevisiae cells. Theregulation of mRNA stability is transient and affects most genes for which there is a change in transcript level. These changesprecede and prepare for the changes in steady-state levels, both regarding the initial increase and the later decline of stressinducedmRNAs. The inverse is true for stress-repressed genes, which become stabilized during hyperosmotic stress inpreparation of an increase as the cells recover. The MAP kinase Hog1 affects both steady-state levels and stability of stressresponsivetranscripts, whereas Rck2 influences steady-state levels without a major effect on stability. Regulation of mRNAstability is a wide-spread, but not universal, effect on stress-responsive transcripts during transient hyperosmotic stress. Bydestabilizing stress-induced mRNAs when their steady-state levels have reached a maximum, the cell prepares for thesubsequent recovery phase when these transcripts are to return to normal levels. Conversely, stabilization of stress-repressedmRNAs permits their rapid accumulation in the recovery phase. Our results show that mRNA turnover is coordinated withtranscriptional induction.
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| 13. |
- Nair, Anu G., et al.
(författare)
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Modeling Intracellular Signaling Underlying Striatal Function in Health and Disease
- 2014
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Ingår i: Computational Neuroscience. - Amsterdam : Elsevier. - 9780123978974 ; 123, s. 277-304
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Bokkapitel (refereegranskat)abstract
- Striatum, which is the input nucleus of the basal ganglia, integrates cortical and thalamic glutamatergic inputs with dopaminergic afferents from the substantia nigra pars cornpacta. The combination of dopamine and glutamate strongly modulates molecular and cellular properties of striatal neurons and the strength of corticostriatal synapses. These actions are performed via intracellular signaling networks, containing several intertwined feedback loops. Understanding the role of dopamine and other neuromodulators requires the development of quantitative dynamical models for describing the intracellular signaling, in order to provide precise unambiguous descriptions and quantitative predictions. Building such models requires integration of data from multiple data sources containing information regarding the molecular interactions, the strength of these interactions, and the subcellular localization of the molecules. Due to the uncertainty, variability, and sparseness of these data, parameter estimation techniques are critical for inferring or constraining the unknown parameters, and sensitivity analysis evaluates which parameters are most critical for a given observed macroscopic behavior. Here, we briefly review the modeling approaches and tools that have been used to investigate biochemical signaling in the striatum, along with some of the models built around striatum. We also suggest a future direction for the development of such models from the, now becoming abundant, high-throughput data.
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| 14. |
- Palmér, Robert, et al.
(författare)
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Dipeptidyl Peptidase 1 Inhibitor AZD7986 Induces a Sustained, Exposure-Dependent Reduction in Neutrophil Elastase Activity in Healthy Subjects
- 2018
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Ingår i: Clinical Pharmacology and Therapeutics. - : Wiley-Blackwell. - 0009-9236 .- 1532-6535. ; 104:6, s. 1155-1164
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Tidskriftsartikel (refereegranskat)abstract
- Neutrophil serine proteases (NSPs), such as neutrophil elastase (NE), are activated by dipeptidyl peptidase 1 (DPP1) during neutrophil maturation. High NSP levels can be detrimental, particularly in lung tissue, and inhibition of NSPs is therefore an interesting therapeutic opportunity in multiple lung diseases, including chronic obstructive pulmonary disease (COPD) and bronchiectasis. We conducted a randomized, placebo-controlled, first-in-human study to assess the safety, tolerability, pharmacokinetics, and pharmacodynamics of single and multiple oral doses of the DPP1 inhibitor AZD7986 in healthy subjects. Pharmacokinetic and pharmacodynamic data were analyzed using nonlinear mixed effects modeling and showed that AZD7986 inhibits whole blood NE activity in an exposure-dependent, indirect manner-consistent with in vitro and preclinical predictions. Several dose-dependent, possibly DPP1-related, nonserious skin findings were observed, but these were not considered to prevent further clinical development. Overall, the study results provided confidence to progress AZD7986 to phase II and supported selection of a clinically relevant dose.
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| 15. |
- Safavi, Setareh, et al.
(författare)
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HSP90 inhibition blocks ERBB3 and RET phosphorylation in myxoid/round cell liposarcoma and causes massive cell death in vitro and in vivo
- 2016
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Ingår i: OncoTarget. - : Impact Journals, LLC. - 1949-2553. ; 7:1, s. 433-445
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Tidskriftsartikel (refereegranskat)abstract
- Myxoid sarcoma (MLS) is one of the most common types of malignant soft tissue tumors. MLS is characterized by the FUS-DDIT3 or EWSR1-DDIT3 fusion oncogenes that encode abnormal transcription factors. The receptor tyrosine kinase (RTK) encoding RET was previously identified as a putative downstream target gene to FUS-DDIT3 and here we show that cultured MLS cells expressed phosphorylated RET together with its ligand Persephin. Treatment with RET specific kinase inhibitor Vandetanib failed to reduce RET phosphorylation and inhibit cell growth, suggesting that other RTKs may phosphorylate RET. A screening pointed out EGFR and ERBB3 as the strongest expressed phosphorylated RTKs in MLS cells. We show that ERBB3 formed nuclear and cytoplasmic complexes with RET and both RTKs were previously reported to form complexes with EGFR. The formation of RTK hetero complexes could explain the observed Vandetanib resistence in MLS. EGFR and ERBB3 are clients of HSP90 that help complex formation and RTK activation. Treatment of cultured MLS cells with HSP90 inhibitor 17-DMAG, caused loss of RET and ERBB3 phosphorylation and lead to rapid cell death. Treatment of MLS xenograft carrying Nude mice resulted in massive necrosis, rupture of capillaries and hemorrhages in tumor tissues. We conclude that complex formation between RET and other RTKs may cause RTK inhibitor resistance. HSP90 inhibitors can overcome this resistance and are thus promising drugs for treatment of MLS/RCLS.
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| 16. |
- Spjuth, Ola, 1977-, et al.
(författare)
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E-Science technologies in a workflow for personalized medicine using cancer screening as a case study
- 2017
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Ingår i: JAMIA Journal of the American Medical Informatics Association. - : Oxford University Press. - 1067-5027 .- 1527-974X. ; 24:5, s. 950-957
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Tidskriftsartikel (refereegranskat)abstract
- Objective: We provide an e-Science perspective on the workflow from risk factor discovery and classification of disease to evaluation of personalized intervention programs. As case studies, we use personalized prostate and breast cancer screenings.Materials and Methods: We describe an e-Science initiative in Sweden, e-Science for Cancer Prevention and Control (eCPC), which supports biomarker discovery and offers decision support for personalized intervention strategies. The generic eCPC contribution is a workflow with 4 nodes applied iteratively, and the concept of e-Science signifies systematic use of tools from the mathematical, statistical, data, and computer sciences.Results: The eCPC workflow is illustrated through 2 case studies. For prostate cancer, an in-house personalized screening tool, the Stockholm-3 model (S3M), is presented as an alternative to prostate-specific antigen testing alone. S3M is evaluated in a trial setting and plans for rollout in the population are discussed. For breast cancer, new biomarkers based on breast density and molecular profiles are developed and the US multicenter Women Informed to Screen Depending on Measures (WISDOM) trial is referred to for evaluation. While current eCPC data management uses a traditional data warehouse model, we discuss eCPC-developed features of a coherent data integration platform.Discussion and Conclusion: E-Science tools are a key part of an evidence-based process for personalized medicine. This paper provides a structured workflow from data and models to evaluation of new personalized intervention strategies. The importance of multidisciplinary collaboration is emphasized. Importantly, the generic concepts of the suggested eCPC workflow are transferrable to other disease domains, although each disease will require tailored solutions.
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