Coming dissertations at MedFak
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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.
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Effects of psychosocial stimulation on children’s development and growth using an unconditional cash transfer programme for lactating mothers of a deprived urban setting in Bangladesh
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-540088
An estimated 249 million children under the age of five in low-and-middle-income countries (LMICs) are at risk of not reaching their developmental potential, with the majority of them living in South Asia. Despite this, there is limited evidence of early childhood development (ECD) programs focused on parenting for 0-3 years children in urban areas of LMICs. This study aimed to deliver a parenting programme in combination with a social safety-net (unconditional cash transfer-UCT) initiative to enhance child development and mother’s well-being.
A cluster randomized controlled trial (cRCT) was implemented with 599 mother-child dyads (children aged 6-16 months) in the deprived urban settings of Rangpur City Corporation, Bangladesh, from 2018 to 2020. The parenting intervention was integrated into the Bangladesh Government’s UCT programme for a period of one year. The cRCT consisted of two arms: i) Parenting and nutrition education combined with UCT (n=299, clusters=10) and ii) UCT only (n=300, clusters=10). Intention-to-treat analysis was performed to assess the effects and the cost effectiveness of the intervention in the trial.
Baseline information from the cRCT in children (n=599) indicated that factors such as age, sex, stunting, and quality of home stimulation environment were common determinants of child development. Attrition rate was only 6.2% (n=37) after one year of intervention. Adjusted multiple linear regression analysis (n=562) controlling for clusters showed that the intervention improved children’s cognitive, language and motor development. However, there was no improvement in physical growth. The intervention also improved fathers’ engagement in child development activities and reduced household violence against mothers. Mothers’ knowledge of childcare and home stimulation environment were the positive mediators for child development. The study also found that the intervention reduced maternal depressive symptoms and improved quality of life (n=547). The incremental cost effectiveness analysis within trial arms confirmed that the intervention was cost-effective for children’s development. An additional US$100 expenditure for parenting intervention was estimated to improve 0.42 SD in cognition, 0.38 SD in language and 0.17 SD in motor development.
Parenting intervention using UCT platform can improve child development outcomes for disadvantaged children and enhance mother’s well-being. These interventions have the potential to be scaled up in similar urban settings within LMICs.