Coming dissertations at Uppsala university
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Thermal mismatch in high latitude host-parasite interactions
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-540783
Emerging infectious diseases and climate change are urgent wildlife threats responsible for many population reductions and extinctions, but their synergistic effects can be hard to predict, as temperature shifts influence host-parasite dynamics in complex ways. The thermal mismatch hypothesis predicts that cold-adapted hosts will become increasingly susceptible to parasites as temperatures rise. However, temperature effects on host-parasite interactions in high latitudes remain understudied. My thesis investigates the role of temperature and thermal adaptations in shaping host-parasite interactions in high latitudes. For this, I use amphibians and their fungal parasite Batrachochytrium dendrobatidis (Bd), and perform experimental infections in different temperatures, followed by analysis of the survival, growth and gene expression of each host. The fungus Bd causes the disease chytridiomycosis, which has decimated amphibian populations worldwide and is a global conservation concern, with its severity varying between hosts, populations, Bd strains and environmental conditions.
In paper I, I analyse the transcriptomic responses of two populations of common toads to infection with two Bd strains of different origin and uncover tissue differences in gene expression. In paper II, I look at the effects of temperature on the survival and growth of four amphibian species from southern Sweden. I discover that the two more cold-adapted species have higher survival and growth when infected with Bd at low temperatures compared to one of the warm-adapted ones, that the second warm adapted species is not at all affected by Bd infection and that the Bd strain I used appears to tolerate high temperature less well than expected. In paper III, I make comparisons between the cold-adapted southern species and individuals of the same species from northern Sweden, and find that northern populations may be less susceptible to Bd infection despite their overall lower survival. In paper IV, I look at the transcriptomic responses of the two cold-adapted species from both populations and find that immune system activity is increased in infected hosts, especially in lower temperatures, but is not always associated with higher survival.
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Towards 3D bio-printed spinal cord organoids
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-540590
The development of 3D bioprinting technology has provided a new direction for the replacement of organs or tissues and the development of drug testing models. Testing cell adhesion, proliferation, and differentiation in different printed scaffolds for creating functional 3D bio-printed structures provides the possibility of establishing a patient-specific in vitro model for neurodegenerative diseases. This thesis aims to establish a 3D bio-printed spinal cord model for drug research of ALS by exploring the factors affecting cell adhesion, growth, and differentiation in different hydrogels, and the suitable printing conditions.
In Paper I, we compared the adhesion and cell survival rates of BCs on the surfaces of the scaffolds with different stiffness and different chemical covering substracts and found the effects of physical and chemical factors for cell adhesion, proliferation, and differentiation through comparison, which can be used as a reference for exploring the conditions for further 3D printing mixing with cells inside.
In Paper II, gelatin-based hydrogel was selected as the main material for printing the scaffold. By testing the survival rate of BCs in the different concentrations of gelatin with different concentrations of crosslinker, we selected a protocol that is suitable for cell viability, cell differentiation, and bioprintability. Unfortunately, when this protocol is applied to hiPSCs, it can obtain the viability of cells after printing, but cell differentiation was only observed on the surface of the scaffolds since cells in the middle of the printed structure lack contact with the surrounding culture medium.
Paper III showed that BCs attracted endothelial cells sprouting from aortic rings in their co-cultured 3D-printed scaffolds and guided the migration direction of endothelial cells. Also, after implantation at the injury DRTZ, they helped with vascularization by increasing the blood vessel volume and vessel diameters.
In Paper IV, we improved the protocol from Paper II for hiPSCs-derived MNs by reducing the concentration of gelatin and adding MSP loaded with cintrofin and gliafin. Two printable methods that could keep the printed structures during culturing were tested, and one was chosen for further printing based on cell viability during bio-ink preparation. A lower concentration of gelatin helped with getting better access to the surrounding culture medium and achieving motor neuron differentiation inside the scaffolds.
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Genomic and Epigenomic Profiling of Cancer
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-540331
Cancer is a genetic disease that arises from cells undergoing genomic alterations. Understanding the role of genomic instability in tumorigenesis, progression, and metastasis is crucial for advancing cancer diagnosis, treatment, and drug development. The development of cancer is driven by a combination of genetic variations, epigenetic dysregulation, and environmental influences. Among the most aggressive malignancies worldwide, gastroesophageal cancer and glioblastoma are characterized by extremely poor prognoses and limited therapeutic options. We explored GCA from a genomic perspective, integrating whole exome sequencing, RNAseq, proteomics, and metabolomics to identify key genetic alterations and signaling pathways that drive tumorigenesis. Additionally, we investigated the epigenetic landscape of glioblastoma to reveal the role of epigenetic dysregulation in tumor heterogeneity and progression.
In Paper I, we performed whole genome sequencing on 36 pairs of tumor and tumor-matched normal samples from a GCA cohort and conducted immunohistochemistry of HER2 in 1668 GCA patients. We found that focal amplifications were detected in 77.8% of all cases, while ecDNAs were identified in 52.8% of total cases. Surprisingly, we found patients with ERBB2 focal amplification or IHC HER2 positive staining are associated with better prognosis, which is inconsistent with many of the previous studies that the oncogene ERBB2 typically correlates with poorer prognosis in patients.
In Paper II, we conducted multi-omics profiling of 128 GCA patients, categorizing them into HER2-high, HER2-low, and HER2-negative groups. HER2 was identified as a favorable prognostic marker, with DNA repair features enriched in the HER2-high group and inflammation predominant in the HER2-low and HER2-negative groups. ARID1A mutations were particularly prognostic in the HER2-negative group. Our findings suggest antiinflammatory therapies and CD47/SIRPA immune checkpoint inhibition as potential strategies for HER2-negative GCA, offering new avenues for personalized treatment.
In Paper III, we integrated analyses of chromatin accessibility, histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3), and chromatin loops in human and mouse GSCs. We found the enhancer marker H3K4me1 and the repressive marker H3K27me3 in human GSCs could separate patients into two groups with significant survival differences and enhancer signatures that define glioblastoma stem cell subtypes. Transcription factor (TF) enrichment analysis suggested that neural progenitor lineage-specific TFs, such as OLIG2, SOX4, POU family TFs are acting TFs in different types of enhancers and determine the lineage specificity of human GSCs. Cross-species analysis between human and mouse GSCs identified key TFs that define lineage-specific subtypes and observed both conserved and species-specific TFs.