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Coming dissertations at MedFak

  • Induced pluripotent stem cell (iPSC) modelling for the identification of mechanisms behind neurodevelopmental disorders Author: Loora Laan Link: Publication date: 2020-01-17 12:55

    Human induced pluripotent stem cells (iPSCs) have opened new possibilities to recapitulate disease mechanisms and to model disorders in vitro. In the studies presented here, iPSCs were established to model neural differentiation in Down syndrome (DS), caused by trisomy for chromosome 21 (T21); Dravet syndrome (DRS), caused by variants in the SCN1A gene; and an ataxia syndrome, caused by a variant in the NFASC gene. The major aim has been to uncover molecular and cellular mechanisms behind perturbed neurogenesis in the three disorders.

    In Paper I, the analysis of transcriptomes and proteomes of the DS iPSC derived neural model revealed several perturbed gene clusters with strong temporal dynamics along neural differentiation, markedly down-regulated mitochondrial genes and a dysregulation of hub proteins. These results predict complex and genome-wide changes in T21 neural cells associated with prolonged cell cycle, reduced cell growth and a perturbed energy metabolism.

    In Paper II, it was demonstrated that the transcriptional profile of iPSC based neural model system for DS was enriched for differentially methylated genes and gene families when compared to a corresponding euploid model. The differentially methylated genes were enriched for transcriptional regulation and chromatin structure, suggesting novel mechanistic links between the genomic imbalance caused by T21 and the global transcriptional dysregulation in DS.

     In Paper III, it was shown that DRS patient iPSCs differentiated into GABAergic interneurons exhibit a dysregulated epilepsy gene network as well as an altered expression of genes involved in chromatin remodelling, accompanied by abnormal electrophysiological properties and increased stress sensitivity.

    In Paper IV, it was shown that neural iPSCs, established from a patient with an ataxia syndrome and a novel homozygous variant in the NFASC gene, lack a full-length neurofascin-186 important for cell adhesion. The patient derived neural iPSCs showed delayed neuronal differentiation, reduced sprouting, shorter neurites and altered electrophysiology.

    The Papers I-IV show that patient derived neural iPSCs enable to identify molecular and cellular mechanisms associated with neuropathogenesis. Besides specific dysregulated pathways and cellular defects in models of three developmental disorders, with shortlists of novel candidate disease biomarkers, the results are consistent with prior data and clinical presentation of patients. The knowledge gained is of paramount importance for translation into clinical settings and a step towards development of novel therapies with the ultimate goal to alleviate symptoms of affected individuals.

  • Cardiopulmonary Function in Healthy Individuals and in Patients After Hematopoietic Cell Transplantation Author: Margareta Genberg Link: Publication date: 2020-01-17 09:53

    Background: The cardiopulmonary exercise test (CPET) is the gold standard of clinical exercise tests, combining conventional stress testing with measurement of oxygen uptake and carbon dioxide production. In order to interpret CPET findings, adequate reference values are needed. Currently, no Swedish reference values exist.

    Hematopoietic cell transplantation (HCT) is an established treatment for childhood leukemia, with a growing number of long-term survivors. This increases the importance of identifying and treating this therapy’s late cardiac and pulmonary consequences.

    Aims: The main aim of Study I was to compare the peak oxygen uptake (VO2peak) of healthy, 50-year-old Swedes with four commonly used international reference values. Secondary aims were to analyze peak workload and VO2peak in regard to achieved respiratory exchange ratio (RER), and the significance of breathing reserve (BR) at peak exercise in healthy individuals.

    The main aim of Studies II–IV was to investigate long-term cardiopulmonary effects in a group of patients, in median 18 years after HCT including preparative chemotherapy and total body irradiation.

    Methods: A group of healthy, 50-year-old Swedes (n = 181; 91 females) were investigated in Study I, using CPET. The investigated subjects in Studies II–IV were aged 17–37 years and were compared with an age- and sex-matched control group. Cardiac function and pulmonary function were studied through echocardiography, spirometry and CPET at a single occasion.

    Results: All reference values analyzed in Study I underestimated VO2peak in women. VO2peak was best predicted, for both men and women, using reference values by Jones et al. No evidence was found that RER > 1.1 would be better than RER > 1.0 as an indicator of good exercise performance in healthy individuals. In healthy individuals, lower BR is likely a response to higher workloads.

    In Studies II–IV, all echocardiographic parameters were within normal range in patients after HCT. However, systolic and diastolic left ventricular function, and right ventricular function, were reduced in comparison with healthy controls. Exercise tests and CPET showed that long-term survivors after HCT, when compared with healthy individuals, had significantly decreased exercise capacity and reduced VO2peak and other CPET parameters, reflecting effects on both the cardiac and the pulmonary functions.

    Conclusions: All investigated reference values underestimated VO2peak in 50-year-old Swedes, suggesting a need for Swedish reference values. HCT-treated leukemia patients displayed reduced exercise capacity and VO2peak. Regular follow-up of these patients with CPET could contribute to early detection of functional impairment.

  • Genetic Adaptation and Speciation in Darwin’s Finches and Atlantic Herring Author: Fan Han Link: Publication date: 2020-01-13 13:30

    Natural selection acts on existing genetic variation to drive genetic adaptation of organisms to various ecological niches. Interaction between closely related populations, through processes such as competition and hybridization, may either lead to their divergence or population fusion, which has consequences for adaptation and the formation of species. This thesis aims to use two natural populations, Darwin’s finches and Atlantic herring, as models to explore the genetic mechanisms underlying ecological adaptation and speciation.

    The ecological adaptation of Darwin’s finches across the Galápagos Islands is primarily reflected by variation in beak morphology. Using whole-genome re-sequencing of all Darwin’s finch species, we discover that a locus, HMGA2, is highly associated with variation in beak size. Data collected before and after a severe drought show that this locus plays a critical role for ecological character displacement in large ground finches Geospiza magnirostris and medium ground finches G. fortis.

    Genomic islands of divergence refer to genomic regions of elevated divergence when comparing the genomes of closely related taxa. Establishment of these genomic islands can reflect a role in reproductive isolation or be related to ecological adaptation or background selection. Investigating their properties can shed light on how new species evolve. We study the landscape of genomic islands in Darwin’s finches, and find that the most pronounced genomic islands are likely ancient balanced polymorphisms, which govern adaptive variation in beak morphology.

    Hybridization is increasingly recognized as an important evolutionary process which may lead to speciation. We study two cases of hybridization in Darwin’s finches. In the first case, a new lineage of Darwin’s finches was founded through hybridization between a resident medium ground finch G. fortis and an immigrant Española cactus finch G. conirostris. In the second case, female-biased introgression occurred predominantly from medium ground finches G. fortis to common cactus finches G. scandens. Our genetic analysis on the mosaic genomes of hybrid finches show that non-random mating and natural selection primarily determine the outcome of hybridization.

    We generate a chromosome-level assembly of the Atlantic herring with a total size of 726 Mb, which coincides with a high-resolution linkage map and an LD-based recombination map. This facilitates the identification of an ~8Mb inversion, which is likely to be associated with ecological adaptation in herring to differences in water temperature. The contiguity of the assembly sorts placement of loci under selection that were identified based on a previous, highly fragmented draft assembly of the herring genome.