| 1. |
- Björn, Niclas, 1990-
(författare)
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Pharmacogenetic biomarkers for chemotherapy-induced adverse drug reactions
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cancer is a serious disease expected to be the world-leading cause of death in the 21st century. The use of harsh chemotherapies is motivated and accepted but, unfortunately, is often accompanied by severe toxicity and adverse drug reactions (ADRs). These occur because the classical chemotherapies’ common modes of action effectively kill and/or reduce the growth rate not only of tumour cells, but also of many other rapidly dividing healthy cells in the body. There are also considerable interindividual differences in ADRs, even between patients with similar cancers and disease stage treated with equal doses; some experience severe to life-threatening ADRs after one dose, leading to treatment delays, adjustments, or even discontinuation resulting in suboptimal treatment, while others remain unaffected through all treatment cycles. Being able to predict which patients are at high or low risk of ADRs, and to adjust doses accordingly before treatment, would probably decrease toxicity and patient suffering while also increasing treatment tolerability and effects. In this thesis, we have used next-generation sequencing (NGS) and bioinformatics for the prediction of myelosuppressive ADRs in lung and ovarian cancer patients treated with gemcitabine/carboplatin and paclitaxel/carboplatin.Paper I shows that ABCB1 and CYP2C8 genotypes have small effects inadequate for stratification of paclitaxel/carboplatin toxicity. This supports the transition to whole-exome sequencing (WES) and whole-genome sequencing (WGS). Papers II and IV, respectively, use WES and WGS, and demonstrate that genetic variation in or around genes involved in blood cell regulation and proliferation, or genes differentially expressed at chemotherapy exposure, can be used in polygenic prediction models for stratification of gemcitabine/carboplatininduced myelosuppression. Paper III reassuringly shows that WES and WGS are concordant and mostly yield comparable genotypes across the exome. Paper V proves that single-cell RNA sequencing of hematopoietic stem cells is a feasible method for elucidating differential transcriptional effects induced as a response to in vitro chemotherapy treatment.In conclusion, our results supports the transition to genome-wide approaches using WES, WGS, and RNA sequencing to establish polygenic models that combine effects of multiple pharmacogenetic biomarkers for predicting chemotherapy-induced ADRs. This approach could be applied to improve risk stratification and our understanding of toxicity and ADRs related to other drugs and diseases. We hope that our myelosuppression prediction models can be refined and validated to facilitate personalized treatments, leading to increased patient wellbeing and quality of life.
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| 2. |
- Björn, Niclas, 1990-, et al.
(författare)
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Single-Cell RNA Sequencing of Hematopoietic Stem and Progenitor Cells Treated with Gemcitabine and Carboplatin.
- 2020
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- Treatments that include gemcitabine and carboplatin induce dose-limiting myelosuppression. The understanding of how human bone marrow is affected on a transcriptional level leading to the development of myelosuppression is required for the implementation of personalized treatments in the future. In this study, we treated human hematopoietic stem and progenitor cells (HSPCs) harvested from a patient with chronic myelogenous leukemia (CML) with gemcitabine/carboplatin. Thereafter, scRNA-seq was performed to distinguish transcriptional effects induced by gemcitabine/carboplatin. Gene expression was calculated and evaluated among cells within and between samples compared to untreated cells. Cell cycle analysis showed that the treatments effectively decrease cell proliferation, indicated by the proportion of cells in the G2M-phase dropping from 35% in untreated cells to 14.3% in treated cells. Clustering and t-SNE showed that cells within samples and between treated and untreated samples were affected differently. Enrichment analysis of differentially expressed genes showed that the treatments influence KEGG pathways and Gene Ontologies related to myeloid cell proliferation/differentiation, immune response, cancer, and the cell cycle. The present study shows the feasibility of using scRNA-seq and chemotherapy-treated HSPCs to find genes, pathways, and biological processes affected among and between treated and untreated cells. This indicates the possible gains of using single-cell toxicity studies for personalized medicine.
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| 3. |
- Björn, Niclas, 1990-, et al.
(författare)
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Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients
- 2020
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Ingår i: npj Systems Biology and Applications. - : Nature Publishing Group. - 2056-7189. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Gemcitabine/carboplatin chemotherapy commonly induces myelosuppression, including neutropenia, leukopenia, and thrombocytopenia. Predicting patients at risk of these adverse drug reactions (ADRs) and adjusting treatments accordingly is a long-term goal of personalized medicine. This study used whole-genome sequencing (WGS) of blood samples from 96 gemcitabine/carboplatin-treated non-small cell lung cancer (NSCLC) patients and gene network modules for predicting myelosuppression. Association of genetic variants in PLINK found 4594, 5019, and 5066 autosomal SNVs/INDELs with p ≤ 1 × 10−3 for neutropenia, leukopenia, and thrombocytopenia, respectively. Based on the SNVs/INDELs we identified the toxicity module, consisting of 215 unique overlapping genes inferred from MCODE-generated gene network modules of 350, 345, and 313 genes, respectively. These module genes showed enrichment for differentially expressed genes in rat bone marrow, human bone marrow, and human cell lines exposed to carboplatin and gemcitabine (p < 0.05). Then using 80% of the patients as training data, random LASSO reduced the number of SNVs/INDELs in the toxicity module into a feasible prediction model consisting of 62 SNVs/INDELs that accurately predict both the training and the test (remaining 20%) data with high (CTCAE 3–4) and low (CTCAE 0–1) maximal myelosuppressive toxicity completely, with the receiver-operating characteristic (ROC) area under the curve (AUC) of 100%. The present study shows how WGS, gene network modules, and random LASSO can be used to develop a feasible and tested model for predicting myelosuppressive toxicity. Although the proposed model predicts myelosuppression in this study, further evaluation in other studies is required to determine its reproducibility, usability, and clinical effect.
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| 4. |
- Fong, Stephanie, 1990-
(författare)
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Brain morphology and behaviour in the guppy (Poecilia reticulata) : Effects of plasticity and mosaic brain evolution
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Understanding how brains have evolved and subsequently culminated in the huge variation in brain morphology among contemporary vertebrate species has fascinated researchers for many decades. It has been recognized that brain morphology is both genetically and environmentally determined. Adaptations to ecological challenges, for one, has been proposed to be a major force in brain diversification processes. Considering the large energetic costs of neural tissue, it is believed that brain evolution is a highly complex process, involving a delicate balance between the corresponding costs and benefits. Using the guppy (Poecilia reticulata) as the model organism, I first examined the conditions under which diversity in brain morphology is generated. This was done by investigating factors known to exert an influence on brain plasticity, namely environmental and cognitive effects (Paper I). Existing studies generally indicate that the provision of environmental enrichment lead to the enlargement of specific brain structures. While plastic alterations in brain morphology was found to respond to environmental complexity in my study, successful performance in two cognitive tasks did not produce any significant changes. I next assessed the feasibility of the mosaic brain evolution hypothesis by artificially selecting for an increase and decrease in the relative size of the telencephalon (Paper II). Telencephalon size was shown to respond rapidly to divergent selection pressures, with no substantial changes in any of the other brain regions. A comparison with wild fish revealed that fish from the unselected control treatment had telencephalon sizes most similar to that of wild populations, whereas both up-selected and down-selected fish had considerably larger and smaller telencephalon, respectively. I tested fish from the artificial selection lines in a test battery to determine if known differences in telencephalon size affects boldness (Paper III). Individuals were subjected to an emergence test, an open field test and a novel object test. I found no differences in boldness levels across selection treatments, but distinct sex differences were noted whereby males were more active and bolder. The cognitive benefits associated with a larger telencephalon were examined in males in a test of self-control (Paper IV). Guppies from the up-selected lines attained a steeper learning curve and made more correct detours compared to their down-selected conspecifics. In conclusion, I provide experimental evidence for the mosaic brain evolution hypothesis by showing that a specific brain region (telencephalon) can evolve rapidly and independently under directed selection. Future tests on other cognitive benefits as well as implicated costs, together with underlying neuronal changes would help to further unravel the factors governing brain evolution.
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| 5. |
- Fong, Stephanie, 1990-, et al.
(författare)
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Rapid mosaic brain evolution under artificial selection for relative telencephalon size in the guppy (Poecilia reticulata)
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The vertebrate brain displays enormous morphological variation and the quest to understand the evolutionary causes and consequences of this variation has spurred over a century of research. The mosaic brain evolution hypothesis, stating that brain regions can evolve relatively independently, is a highly influential idea in this research field. Here we provide the first experimental support for this hypothesis through an artificial selection experiment in the guppy (Poecilia reticulata). After three generations of selection on relative telencephalon volume in replicated up-selected, down-selected and control selection lines, we found substantial overall changes in relative telencephalon size (i.e. relative to brain size), but no changes in other brain regions. The differences were not evident at birth but present at the time of sexual maturation. There was a non-significant trend towards asymmetry in the response to selection in both sexes, with larger changes occurring during upwards selection as opposed to downwards selection. Our results demonstrate that independent evolutionary changes in specific brain regions can be an important mechanism during cognitive evolution.
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| 6. |
- Svedberg, Anna, 1988-, et al.
(författare)
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Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.
- 2020
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Ingår i: Lung Cancer. - : Elsevier. - 0169-5002 .- 1872-8332. ; 147, s. 106-114
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Gemcitabine/carboplatin treatment is known to cause severe adverse drug reactions which can lead to the need for reduction or cessation of chemotherapy. It would be beneficial to identify patients at risk of severe hematological toxicity in advance before treatment start. This study aims to identify genetic markers for gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients.MATERIAL AND METHODS: Whole-exome sequencing was performed on 215 patients. Association analysis was performed on single-nucleotide variants (SNVs) and genes, and the validation was based on an independent genome-wide association study (GWAS). Based on the association and validation analyses the genetic variants were then selected for and used in weighted genetic risk score (wGRS) prediction models for leukopenia and neutropenia.RESULTS: Association analysis identified 50 and 111 SNVs, and 12 and 20 genes, for leukopenia and neutropenia, respectively. Of these SNVS 20 and 19 were partially validated for leukopenia and neutropenia, respectively. The genes SVIL (p = 2.48E-06) and EFCAB2 (p = 4.63E-06) were significantly associated with leukopenia contain the partially validated SNVs rs3740003, rs10160013, rs1547169, rs10927386 and rs10927387. The wGRS prediction models showed significantly different risk scores for high and low toxicity patients.CONCLUSION: We have identified and partially validated genetic biomarkers in SNVs and genes correlated to gemcitabine/carboplatin-induced leukopenia and neutropenia and created wGRS models for predicting the risk of chemotherapy-induced hematological toxicity. These results provide a strong foundation for further studies of chemotherapy-induced toxicity.
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| 7. |
- Åstrand, Anna, et al.
(författare)
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Activation of the μ-opioid receptor by alicyclic fentanyls : Changes from high potency full agonists to low potency partial agonists with increasing alicyclic substructure
- 2021
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Ingår i: Drug Testing and Analysis. - : John Wiley & Sons. - 1942-7603 .- 1942-7611. ; 13:1, s. 169-174
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Tidskriftsartikel (refereegranskat)abstract
- Fentanyl analogs represent an important group of new psychoactive substances and knowing their efficacy and potency might assist in interpreting observed concentrations. The potency of fentanyl analogs can be estimated from in vitro studies and can be used to establish structure-activity relationships. In this study, recombinant CHO-K1 cells (AequoScreen) expressing the human μ-opioid receptor were used to establish dose-response curves via luminescent analysis for cyclopropyl-, cyclobutyl-, cyclopentyl-, cyclohexyl-, and 2,2,3,3-tetramethylcyclopropylfentanyl (TMCPF), on three separate occasions, using eight different concentrations in an eight-fold serial dilution in triplicates starting at ~60 μM. Fentanyl was used as a full agonist reference while morphine and buprenorphine were included for comparison. Cyclopropylfentanyl (EC50 = 4.3 nM), cyclobutylfentanyl (EC50 = 6.2 nM), and cyclopentylfentanyl (EC50 = 13 nM) were full agonists slightly less potent than fentanyl (EC50 = 1.7 nM). Cyclohexylfentanyl (EC50 = 3.1 μM, efficacy 48%) and TMCPF (EC50 = 1.5 μM, efficacy 65%) were partial agonists less potent than morphine (EC50 = 430 nM). Based on the results, cyclopropyl-, cyclobutyl-, and cyclopentylfentanyl would be expected to induce intoxication or cause fatal poisonings at similar concentrations to fentanyl, while the toxic or fatal concentrations of cyclohexylfentanyl and TMCPF would be expected to be much higher.
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