| 1. |
- Fresard, Laure, et al.
(författare)
-
Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
-
Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
-
Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
|
|
| 2. |
|
|
| 3. |
- Forsgård, Richard A., 1987-, et al.
(författare)
-
Chemotherapy-induced gastrointestinal toxicity is associated with changes in serum and urine metabolome and fecal microbiota in male Sprague-Dawley rats
- 2017
-
Ingår i: Cancer Chemotherapy and Pharmacology. - : Springer. - 0344-5704 .- 1432-0843. ; 80:2, s. 317-332
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose: Chemotherapy-induced gastrointestinal toxicity (CIGT) is a complex process that involves multiple pathophysiological mechanisms. We have previously shown that commonly used chemotherapeutics 5-fluorouracil, oxaliplatin, and irinotecan damage the intestinal mucosa and increase intestinal permeability to iohexol. We hypothesized that CIGT is associated with alterations in fecal microbiota and metabolome. Our aim was to characterize these changes and examine how they relate to the severity of CIGT.Methods: A total of 48 male Sprague-Dawley rats were injected intraperitoneally either with 5-fluorouracil (150 mg/kg), oxaliplatin (15 mg/kg), or irinotecan (200 mg/kg). Body weight change was measured daily after drug administration and the animals were euthanized after 72 h. Blood, urine, and fecal samples were collected at baseline and at the end of the experiment. The changes in the composition of fecal microbiota were analyzed with 16S rRNA gene sequencing. Metabolic changes in serum and urine metabolome were measured with 1 mm proton nuclear magnetic resonance (1H-NMR).Results: Irinotecan increased the relative abundance of Fusobacteria and Proteobacteria, while 5-FU and oxaliplatin caused only minor changes in the composition of fecal microbiota. All chemotherapeutics increased the levels of serum fatty acids and N(CH3)(3) moieties and decreased the levels of Krebs cycle metabolites and free amino acids.Conclusions: Chemotherapeutic drugs, 5-fluorouracil, oxaliplatin, and irinotecan, induce several microbial and metabolic changes which may play a role in the pathophysiology of CIGT. The observed changes in intestinal permeability, fecal microbiota, and metabolome suggest the activation of inflammatory processes.
|
|
| 4. |
- Forsgård, Richard A., 1987-, et al.
(författare)
-
Intestinal permeability to iohexol as an in vivo marker of chemotherapy-induced gastrointestinal toxicity in Sprague-Dawley rats
- 2016
-
Ingår i: Cancer Chemotherapy and Pharmacology. - : Springer. - 0344-5704 .- 1432-0843. ; 78:4, s. 863-874
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose: Gastrointestinal toxicity is the most common adverse effect of chemotherapy. Chemotherapeutic drugs damage the intestinal mucosa and increase intestinal permeability. Intestinal permeability is one of the key markers of gastrointestinal function and measuring intestinal permeability could serve as a useful tool for assessing the severity of chemotherapy-induced gastrointestinal toxicity.Methods: Male Sprague-Dawley rats were injected intraperitoneally either with 5-fluorouracil (150 mg/kg), oxaliplatin (15 mg/kg) or irinotecan (200 mg/kg). Clinical signs of gastrointestinal toxicity were assessed daily by weighing the animals and by checking for diarrhea. After 48 h, intestinal permeability to iohexol was measured in vivo by giving the animals 1 ml of 647 mg/ml iohexol solution by oral gavage and collecting all the excreted urine for 24 h. All of the animals were euthanized 72 h after drug administration and tissue samples were harvested from the jejunum and colon.Results: All chemotherapeutics caused significant body weight loss and diarrhea. Intestinal permeability to iohexol was also increased in all treatment groups and histological analysis revealed significant intestinal damage in both jejunum and colon. Iohexol permeability correlated with the severity of clinical signs of gastrointestinal toxicity and with acute colonic injury.Conclusions: Chemotherapeutic drugs, such as 5-fluorouracil, oxaliplatin, and irinotecan, increase intestinal permeability to iohexol. Measuring intestinal permeability to iohexol could provide a simple marker for assessing chemotherapy-induced gastrointestinal toxicity.
|
|
| 5. |
- Forsgård, Richard A., 1987-, et al.
(författare)
-
Two-Week Aflibercept or Erlotinib Administration Does Not Induce Changes in Intestinal Morphology in Male Sprague-Dawley Rats But Aflibercept Affects Serum and Urine Metabolic Profiles
- 2019
-
Ingår i: Translational Oncology. - : Elsevier. - 1944-7124 .- 1936-5233. ; 12:8, s. 1122-1130
-
Tidskriftsartikel (refereegranskat)abstract
- Gastrointestinal toxicity is a frequently observed adverse event during cancer treatment with traditional chemotherapeutics. Currently, traditional chemotherapeutics are often combined with targeted biologic agents. These biologics, however, possess a distinct toxicity profile, and they may also exacerbate the adverse effects of traditional chemotherapeutics. In this study, we aimed to characterize the gastrointestinal and metabolic changes after a 2-week treatment period with aflibercept, an antiangiogenic VEGFR decoy, and with erlotinib, a tyrosine-kinase inhibitor. Male rats were treated either with aflibercept or erlotinib for 2 weeks. During the 2-week treatment period, the animals in the aflibercept group received twosubcutaneous doses of 25 mg/kg aflibercept. The erlotinib group got 10 mg/kg of erlotinib by oral gavage every other day. The control groups were treated similarly but received either saline injections or oral gavage of water. Intestinal toxicity was assessed by measuring intestinal permeability and by histological analyses of intestinal tissues. Metabolic changes were measured with H-1 nuclear magnetic resonance in serum and urine. Neither aflibercept nor erlotinib induced changes in intestinal permeability or intestinal tissue morphology. However, aflibercept treatment resulted in stunted body weight gain and altered choline, amino acid, and lipid metabolism. Two-week treatment with aflibercept or erlotinib alone does not induce observable changes in gastrointestinal morphology and function. However, observed aflibercept-treatment related metabolic changes suggest alterations in intestinal microbiota, nutrient intake, and adipose tissue function. The metabolic changes are also interesting in respect to the systemic effects of aflibercept and their possible associations with adverse events caused by aflibercept administration.
|
|
| 6. |
- Gumberidze, Alexandre, et al.
(författare)
-
Angular Distribution of Characteristic Radiation Following the Excitation of He-Like Uranium in Relativistic Collisions
- 2021
-
Ingår i: Atoms. - : MDPI AG. - 2218-2004. ; 9:2
-
Tidskriftsartikel (refereegranskat)abstract
- In this paper, we present an experimental and theoretical study of excitation processes for the heaviest stable helium-like ion, that is, He-like uranium occurring in relativistic collisions with hydrogen and argon targets. In particular, we concentrate on angular distributions of the characteristic K alpha radiation following the K -> L excitation of He-like uranium. We pay special attention to the magnetic sub-level population of the excited 1s2l(j) states, which is directly related to the angular distribution of the characteristic K alpha radiation. We show that the experimental data can be well described by calculations taking into account the excitation by the target nucleus as well as by the target electrons. Moreover, we demonstrate for the first time an important influence of the electron-impact excitation process on the angular distributions of the K alpha radiation produced by excitation of He-like uranium in collisions with different targets.
|
|
| 7. |
- Lestinsky, Michael, et al.
(författare)
-
First Experiments with CRYRING@ESR
- 2022
-
Ingår i: Atoms. - : MDPI AG. - 2218-2004. ; 10:4
-
Tidskriftsartikel (refereegranskat)abstract
- The low-energy heavy ion storage ring CRYRING was transported from Stockholm to Darmstadt, modernized and reconfigured, and recommissioned as CRYRING@ESR. The machine is now in operation with all installations in service and is available as a user facility for experiments proposed through the SPARC collaboration. During the 2020–2022 period, we brought a number of experimental installations into service and used them to measure first data: the ultra-cold electron cooler for merged-beam electron–ion collisions, the gas jet target for atomic collisions, a next-generation microcalorimeter-based X-ray spectroscopy setup, and others. Ions can be injected either in low charge states from a local ion source through a 300 keV/u RFQ linac, or in high charge states from the GSI accelerator chain through ESR. This allows for very broad access to ions across the entire periodic table. CRYRING@ESR is able to de- or accelerate ions and cool and store beams of isotopically pure species in a desired charge state. While the analysis is still largely ongoing, the first experimental data already show that the machine reached its expected performance level, and our high expectations regarding achievable resolution in spectroscopy experiments have been fulfilled. With access to new classes of ions available through ESR injection and a new generation of experimental instrumentation, CRYRING@ESR is a unique facility for experiments with heavy, highly charged ions. Here, we will review our present setup and machine performance, discuss the data from our first commissioning experiments and briefly preview the upcoming new installations for the coming years.
|
|
| 8. |
- Lestinsky, M., et al.
(författare)
-
Physics book: CRYRING@ESR
- 2016
-
Ingår i: European Physical Journal: Special Topics. - : Springer Science and Business Media LLC. - 1951-6401 .- 1951-6355. ; 225:5, s. 797-882
-
Forskningsöversikt (refereegranskat)abstract
- The exploration of the unique properties of stored and cooled beams of highly-charged ions as provided by heavy-ion storage rings has opened novel and fascinating research opportunities in the realm of atomic and nuclear physics research. Since the late 1980s, pioneering work has been performed at the CRYRING at Stockholm (Abrahamsson et al. 1993) and at the Test Storage Ring (TSR) at Heidelberg (Baumann et al. 1988). For the heaviest ions in the highest charge-states, a real quantum jump was achieved in the early 1990s by the commissioning of the Experimental Storage Ring (ESR) at GSI Helmholtzzentrum für Schwerionenforschung (GSI) in Darmstadt (Franzke 1987) where challenging experiments on the electron dynamics in the strong field regime as well as nuclear physics studies on exotic nuclei and at the borderline to atomic physics were performed. Meanwhile also at Lanzhou a heavy-ion storage ring has been taken in operation, exploiting the unique research opportunities in particular for medium-heavy ions and exotic nuclei (Xia et al. 2002).
|
|
| 9. |
- Sguazzin, M., et al.
(författare)
-
Determining neutron-induced reaction cross sections through surrogate reactions at storage rings
- 2023
-
Ingår i: Journal of Physics: Conference Series. - 1742-6588 .- 1742-6596. ; 2586:1
-
Konferensbidrag (refereegranskat)abstract
- Determining the cross sections of neutron-induced reactions on short-lived nuclei is imperative to rate calculations in stellar nucleosynthesis and applications of nuclear physics. It is also an immense experimental challenge due to the radioactivity of the targets involved. Our goal is to circumvent this obstacle by using surrogate reactions in inverse kinematics at the heavy-ion storage rings of GSI/FAIR. We present here preliminary results from the first proof of principle experiment, where a beam of 208Pb impinged on a H2 gas jet target in the Experimental Storage Ring (ESR).
|
|
| 10. |
- Sguazzin, M., et al.
(författare)
-
Indirect measurements of neutron -induced reaction cross sections at heavy -ion storage rings
- 2023
-
Ingår i: 15TH INTERNATIONAL CONFERENCE ON NUCLEAR DATA FOR SCIENCE AND TECHNOLOGY, ND2022. - 2100-014X. ; 284
-
Konferensbidrag (refereegranskat)abstract
- Neutron-induced reaction cross sections of unstable nuclei are essential for understanding the synthesis of heavy elements in stars and for applications in nuclear technology. However, their measurement is very complicated due to the radioactivity of the targets involved. We propose to circumvent this problem by using the surrogate reaction method in inverse kinematics, where the nucleus formed in the neutroninduced reaction of interest is produced by a reaction involving a radioactive heavy -ion beam and a stable, light target nucleus. The probabilities as a function of the compound -nucleus excitation energy for y -ray emission, neutron emission and fission, which can be measured with the surrogate reaction, are particularly useful to constrain model parameters and to obtain more accurate predictions of the neutron-induced reaction cross sections of interest. Yet, the full development of the surrogate method is hampered by numerous longstanding target issues, which can be solved by combining surrogate reactions with the unique and largely unexplored possibilities at heavy -ion storage rings. In this contribution, we describe the developments we are carrying out to measure for the first time simultaneously y-ray emission, neutron emission and fission probabilities at the storage rings of the GSI/FAIR facility. In particular, we will present the first results of the proof of principle experiment, which we performed in June 2022 at the Experimental Storage Ring (ESR)
|
|
