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- McGinn, Steven, et al.
(författare)
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New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
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Forskningsöversikt (refereegranskat)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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- Rosén, Emil, et al.
(författare)
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Inference of glioblastoma migration and proliferation rates using single time-point images
- 2023
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Cancer cell migration is a driving mechanism of invasion in solid malignant tumors. Anti-migratory treatments provide an alternative approach for managing disease progression. However, we currently lack scalable screening methods for identifying novel anti-migratory drugs. To this end, we develop a method that can estimate cell motility from single end-point images in vitro by estimating differences in the spatial distribution of cells and inferring proliferation and diffusion parameters using agent-based modeling and approximate Bayesian computation. To test the power of our method, we use it to investigate drug responses in a collection of 41 patient-derived glioblastoma cell cultures, identifying migration-associated pathways and drugs with potent anti-migratory effects. We validate our method and result in both in silico and in vitro using time-lapse imaging. Our proposed method applies to standard drug screen experiments, with no change needed, and emerges as a scalable approach to screen for anti-migratory drugs. The spatial positioning of cultured glioblastoma cells is used to estimate cell motility and drug effects from single end-point images in vitro.
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- Palsdottir, Vilborg, 1979, et al.
(författare)
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Prenatal essential fatty acid deficiency in mice results in long-term gender-specific effects on body weight and glucose metabolism
- 2011
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Ingår i: Molecular Medicine Reports. - : Spandidos Publications. - 1791-2997 .- 1791-3004. ; 4:4, s. 731-737
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Tidskriftsartikel (refereegranskat)abstract
- Essential fatty acids are important for normal growth and development in early life. However, the long-term effects of prenatal essential fatty acid deficiency (EFAD) on the adult metabolism remain to be determined. The aim of this study was to investigate the effects of an EFAD diet given to mice during late gestation on body weight and body composition, and metabolism in the adult offspring. Pregnant dams were given an EFAD or a control diet during the last 10 days of gestation. After delivery, all mice were fed normal chow and the body weight of the offspring was measured weekly. Furthermore, food intake, energy expenditure and intraperitoneal glucose tolera-nce were analysed in the adult offspring in addition to body composition (analysed by dual-energy X-ray absorptiometry), plasma levels of leptin, triglycerides and cholesterol. The body weight was lower in the EFAD offspring as compared to the controls during the first 4 weeks of age, and remained lower in the females throughout the study. Lean body mass and plasma leptin levels were also lower in the female EFAD offspring as compared to the controls. Male EFAD offspring were found to have higher fasting glucose and insulin levels as well as higher insulin levels during the glucose tolerance test compared to the controls. However, no differences were found in blood lipids, food intake or energy expenditure between EFAD and control mice of either gender. These results demonstrate that an EFAD diet given during the last 10 days of gestation results in long-term gender-specific effects on body weight and insulin sensitivity in the adult offspring.
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- Andersson, Annika, et al.
(författare)
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Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease
- 2019
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Ingår i: Clinica Chimica Acta. - : Elsevier B.V.. - 0009-8981 .- 1873-3492. ; 494, s. 79-93
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Tidskriftsartikel (refereegranskat)abstract
- Detailed knowledge of protein changes in cerebrospinal fluid (CSF) across healthy and diseased individuals would provide a better understanding of the onset and progression of neurodegenerative disorders. In this study, we selected 20 brain-enriched proteins previously identified in CSF by antibody suspension bead arrays (SBA) to be potentially biomarkers for Alzheimer's disease (AD) and verified these using an orthogonal approach. We examined the same set of 94 CSF samples from patients affected by AD (including preclinical and prodromal), mild cognitive impairment (MCI), non-AD dementia and healthy individuals, which had previously been analyzed by SBA. Twenty-eight parallel reaction monitoring (PRM) assays were developed and 13 of them could be validated for protein quantification. Antibody profiles were verified by PRM. For seven proteins, the antibody profiles were highly correlated with the PRM results (r > 0.7) and GAP43, VCAM1 and PSAP were identified as potential markers of preclinical AD. In conclusion, we demonstrate the usefulness of targeted mass spectrometry as a tool for the orthogonal verification of antibody profiling data, suggesting that these complementary methods can be successfully applied for comprehensive exploration of CSF protein levels in neurodegenerative disorders.
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- Dodig-Crnkovic, Tea, et al.
(författare)
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Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling
- 2020
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Ingår i: Ebiomedicine. - : Elsevier BV. - 2352-3964. ; 57
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Tidskriftsartikel (refereegranskat)abstract
- Background: Precision medicine approaches aim to tackle diseases on an individual level through molecular profiling. Despite the growing knowledge about diseases and the reported diversity of molecular phenotypes, the descriptions of human health on an individual level have been far less elaborate. Methods: To provide insights into the longitudinal protein signatures of well-being, we profiled blood plasma collected over one year from 101 clinically healthy individuals using multiplexed antibody assays. After applying an antibody validation scheme, we utilized > 700 protein profiles for in-depth analyses of the individuals' short-term health trajectories. Findings: We found signatures of circulating proteomes to be highly individual-specific. Considering technical and longitudinal variability, we observed that 49% of the protein profiles were stable over one year. We also identified eight networks of proteins in which 11-242 proteins covaried over time. For each participant, there were unique protein profiles of which some could be explained by associations to genetic variants. Interpretation: This observational and non-interventional study identifyed noticeable diversity among clinically healthy subjects, and facets of individual-specific signatures emerged by monitoring the variability of the circulating proteomes over time. To enable more personal hence precise assessments of health states, longitudinal profiling of circulating proteomes can provide a valuable component for precision medicine approaches.
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- Topa, Alexandra, 1978
(författare)
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Genetic studies of craniosynostosis with focus on syndromic forms
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Craniosynostosis (CS) represents the premature closure of skull sutures and affects ~1 in 2500 children. Untreated CS can lead to significant complications in craniofacial and psychomotor development. The only treatment available is surgical and requires access to highly specialized healthcare. The development of alternative and/or complementary therapeutic methods relies on an understanding of the intricate molecular and cellular mechanisms underlying CS. Genetic studies are of clinical importance to establish an etiologic diagnosis of inheritable craniofacial syndromes and enable patient prognosis and follow-up, including assessment of the recurrence risk in the family (genetic counseling). The aim of this thesis was to study the prevalence and spectrum of genetic alterations associated with CS in a retrospective cohort of patients that underwent surgery at the largest reference center in Sweden. The patients were initially screened with a targeted next-generation sequencing (NGS) panel covering CS-related genes. Patients with negative outcome were subsequently analyzed using whole-genome or whole-exome sequencing (WGS and WES, respectively). The results showed that targeted NGS screening demonstrated a high diagnostic yield in patients with syndromic forms of CS (>80%) regardless of sutural pattern. The particular case of a patient with coronal synostosis and a Kabuki-like phenotype, as well as a simultaneous de novo occurrence of a lysine-specific methyltransferase 2D (KMT2D) mutation and 10q22.3q23.1 microdeletion, suggests that CS may be an underdiagnosed feature of these conditions. Additionally, interleukin-11 receptor subunit α (IL11RA) was highlighted as an emerging core gene for autosomal recessive pansynostosis. The use of WGS/WES detected causal variants in 38% of the patients with rare syndromic forms of CS and a negative outcome at targeted screening. Furthermore, potentially relevant variants were observed in 87% of the remaining patients with syndromic or nonsyndromic forms of CS. These findings showed that both targeted NGS screening and WGS/WES demonstrated a high diagnostic yield in patients with syndromic CS. Moreover, the results suggested that WES/WGS has the potential to become a unique diagnostic tool that can be adapted to the phenotypic presentation by initial use of in silico gene panels, followed by exome/genome-wide analysis of rare forms of CS.
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