Coming dissertations at MedFak
-
Imprints on the gut microbiome : A study of sleep apnea, physical activity, and antibiotic use
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-539738
Growing evidence has highlighted the importance of the gut microbiome for human health. However, detailed investigations on how specific host factors influence the gut microbiome are lacking. The research in this thesis examined the relationship of obstructive sleep apnea (OSA), physical activity, and antibiotic use with the gut microbiome. The studies in this thesis used gut microbiome data from deep fecal shotgun metagenomics in large population-based cohorts.
Study I used the baseline data of 3,570 individuals aged 50-65 from the Swedish CArdioPulmonary bioImage Study (SCAPIS). OSA was assessed with respiratory polygraphy. We identified 128 microbiome species associated with the number of oxygen desaturation events per hour of sleep or the percentage of sleep time in hypoxia. For instance, more severe hypoxia during sleep was associated with higher abundance of Collinsela aerofaciens and Blautia obeum. Additionally, C. aerofaciens was also associated with increased systolic blood pressure.
Study II used baseline data from 8,416 SCAPIS participants who had valid accelerometer-derived physical activity data. The distribution of awake time in sedentary behavior or physical activity of different intensities was associated with the abundance of 651 gut microbiome species. For example, longer time in moderate-intensity physical activity and shorter time in sedentary behavior were associated with higher abundance of Prevotella copri and Faecalibacterium prausnitzii and lower abundance of Escherichia coli and [Ruminococcus] torques.
Study III investigated the association between antibiotic use in the past eight years and the gut microbiome in 15,131 participants from SCAPIS, the Swedish Infrastructure for Medical Population-based Life-course and Environmental Research (SIMPLER), and the Malmö Offspring Study (MOS). Antibiotic use 4–8 years and 1–4 years earlier was associated with lower gut microbiome alpha diversity after adjustment for more recent use, sociodemographics, lifestyle, and comorbidities. Most of the species-level associations were found for the antibiotics clindamycin, fluoroquinolones, and flucloxacillin.
Study IV assessed the causal effect of physical activity on the gut microbiome using a two-sample Mendelian randomization (MR) analysis based on summary statistics from genome-wide association studies. We found evidence of a positive effect of moderate-to-vigorous intensity physical activity (MVPA) on gut microbiome alpha diversity. Using a multivariable MR analysis, we found that MVPA had a positive on alpha diversity independent of BMI, smoking, education, or liking of a low-calorie diet.
This thesis has applied diverse epidemiology and statistical methods to rigorously investigate host factor associations with the gut microbiome. Altogether, it underlines the tight host-microbiome connection through detailed analyses of OSA, physical activity, and antibiotic use with the gut microbiome.
-
Functional characterization of candidate genes for cardiometabolic diseases : A CRISPR/Cas9 and in vivo image-based approach
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-540195
Cardiometabolic diseases encompass a series of metabolic insults that are connected through an intricate network of shared and unique etiological pathways. Obesity and insulin resistance -leading to type-2 diabetes (T2D)- are major risk factors for developing metabolic dysfunction-associated steatotic liver disease (MASLD), which in turn, increases the risk of cardiovascular events. Genome-wide association studies (GWAS) have identified thousands of variants associated with risk of cardiometabolic diseases. However, the translation of those associations into causal mechanisms remains a challenge. In this thesis, we developed and validated model systems that use zebrafish larvae to functionally characterize the role of cardiometabolic candidate genes on disease development.
In Study I, I contributed to the validation of CRISPR/Cas9 and image-based approaches to study the role of genetic factors in adiposity. We concluded that 10-days post-fertilization is too early to detect meaningful genetic effects on adiposity in zebrafish larvae. However, we did observe genetic effects on cardiometabolic traits that are independent of body fat accumulation.
In Study II, we targeted 61 T2D candidate genes. I identified 21 genes that affect at least one of five examined T2D traits in zebrafish larvae upon gene perturbation, including 12 -out of 13- well established T2D genes. I performed follow-up experiments to identify genes that also affect basal glucose content in 7-day-old larvae and/or early developmental traits in 3-day-old larvae. With the three efforts combined, I highlighted sirt1 and poldip2 as T2D genes.
In Study III, I successfully validated an image-based model system in zebrafish larvae to characterize the role of candidate genes and drugs in MASLD. We then examined 100 cardiometabolic candidate and identified 13 genes that affect liver fat content upon perturbation. Amongst the 13 genes, I emphasised the role of glucose transporter 2 (GLUT2) as putatively causal genes for MASLD. Additionally, I provided evidence for 8 other genes not previously implicated in MASLD. Finally, in Study IV we went from a genome-wide interaction study (GEWIS) of Body Mass Index (BMI) for alanine aminotransferase (ALT), to pinpointing and functionally characterizing in zebrafish larvae the putative causal gene (cyp7a1) for a role in MASLD.
We hope these contributions help to improve our understanding of disease aetiology and fuel further efforts that could potentially result in new therapeutic targets for patients.
-
Effects of Endocrine Disrupting Chemicals on endometrial cells : Life in plastic is not fantastic
Link: http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-540289
Endocrine Disrupting Chemicals (EDCs) are compounds that interfere with normal hormone balances. Reproductive functions rely on precise endocrine regulation involving hormones produced in the brain and ovaries. Several epidemiological studies have shown associations with EDC exposure and adverse fertility outcomes. However, effects of EDCs on the endometrium are still not well investigated. Therefore, this PhD thesis aimed to unravel the effects of EDCs, especially phthalates, on endometrial cell function.
Study I showed the effects of several EDCs on decidualisation, a key process for a successful pregnancy. Protein kinases involved in the decidualisation process, as well as PRL and IGFBP1 excretion, were reduced by different EDCs. To continue our search for candidate genes and pathways affected by EDCs, we exposed different endometrial primary cells and cell lines to phthalate mixtures in study II. Phthalate mixtures were based on urine samples from the Midlife Women’s Health study cohort. All mixtures affected endometrial cells, with MEHHP being the main actor in the phthalate mixtures. Many genes and pathways found with RNA sequencing were involved with the cytoskeleton and mitochondria.
Therefore, we conducted study III, where we investigated the effect of MEHHP on mitochondrial metabolism and structure in the endometrial stromal cell line T-HESC. While mitochondrial metabolism was not significantly affected overall, a significant concentration-response effect was observed in spare respiratory capacity. Mitochondrial structure was significantly altered by MEHHP exposure, resulting in decreased branching and volume, but increased sphericity.
In conclusion, EDCs affected endometrial cells by disrupting decidualisation; phthalates specifically affected genes related to mitochondria and the cytoskeleton. MEHHP had the most substantial effect on gene expression, significantly affecting spare respiratory capacity and mitochondrial structure. Future studies should investigate the effects of phthalates on the cytoskeleton and other mitochondrial parameters, with implications for embryo implantation.