4,228 research outputs found

    Undergraduate Catalog of Studies, 2023-2024

    Get PDF

    Exploring missing heritability in neurodevelopmental disorders:Learning from regulatory elements

    Get PDF
    In this thesis, I aimed to solve part of the missing heritability in neurodevelopmental disorders, using computational approaches. Next to the investigations of a novel epilepsy syndrome and investigations aiming to elucidate the regulation of the gene involved, I investigated and prioritized genomic sequences that have implications in gene regulation during the developmental stages of human brain, with the goal to create an atlas of high confidence non-coding regulatory elements that future studies can assess for genetic variants in genetically unexplained individuals suffering from neurodevelopmental disorders that are of suspected genetic origin

    Graduate Catalog of Studies, 2023-2024

    Get PDF

    Investigating the impact of lung cancer cell-of-origin on tumour metabolic phenotype and heterogeneity

    Get PDF
    Non-small-cell lung cancer has been described as highly heterogenous which results in different metabolic phenotypes. There are multiple factors which contribute to this heterogeneity, one of which is the tumour cell-of-origin. In the lung, there are five cell types reported to be cells-of-origin: alveolar epithelial type 2, club, basal, neuroendocrine and bronchioalveolar stem cells. This project focuses on the interaction between the cell-of-origin and the metabolic phenotype of lung cancer, and we aim to assess the contribution of the cell-of-origin to lung cancer metabolic resultant phenotype and heterogeneity. To accomplish this, we have established two complementary model systems, one in vitro and one in vivo. In our in vitro model, we isolated specific lung cell types, including AT2 cells, basal cells, and club cells, utilising their unique cell surface markers. By introducing oncogenic KRAS mutations and deleting the P53 gene, we are creating lineage-restricted organoids. These organoids will serve as valuable tools for characterizing the metabolic aspects of tumours arising from different cell-of-origin backgrounds within an in vitro setting. In our in vivo model, we induced NSCLC tumours in mice with genetic modifications using viral vectors, namely Ad5-mSPC-Cre, Ad5-CC10-Cre, and Ad5- bk5-Cre. These vectors are selectively expressed in AT2, club, and basal cells, respectively. To ensure the validity of our comparisons, we have carefully monitored tumour growth dynamics and burden in these mouse models. Our comprehensive analysis has revealed three distinct transcriptomic subtypes (S1, S2, and Acetate) within these NSCLC tumours. Notably, S1 and Acetate subtypes are enriched in tumours originating from specific cell types. Positron emission tomography (PET) imaging has unveiled metabolic variations, with S1 tumours displaying heightened [18F]FDG uptake and the Acetate subtype exhibiting increased [11C]acetate uptake. Furthermore, our multi-omics approach, encompassing transcriptomics, proteomics, and metabolomics, has exposed disparities in critical metabolic pathways, such as glycolysis, hypoxia response, and apoptosis. In summary, our research provides a comprehensive examination of the metabolic heterogeneity of NSCLC based on the cell-of-origin independently of genomic alterations

    Undergraduate Catalog of Studies, 2023-2024

    Get PDF

    Dynamic PET-Tau Quantification for Progressive Supranuclear Palsy Diagnosis

    Full text link
    Treballs Finals de Grau d'Enginyeria Biomèdica. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona. Curs: 2023-2024. Tutor: Raúl Tudela ; Director: Aida Niñerola, Raúl TudelaTauopathies are neurodegenerative diseases caused by the abnormal accumulation of tau proteins in the brain. One uncommon tauopathy is progressive supranuclear palsy (PSP), whose symptoms often overlap with other brain disorders, and its detection is only possible postmortem since there is not an available ideal biomarker. PET-tau imaging has the potential to revolutionize the early detection of this disease. PET is a nuclear imaging test which allows seeing the functionality of organs and tissues in vivo using a radiotracer that emits radiation from inside the body. A new PET tracer called 18F-PI-2620 has shown promising results concerning the detection of PSP, with high affinity to tau aggregates and low off-target binding. This project consists of designing and testing a software for the quantification of PET images of the brain with a dynamic acquisition, which show the radiotracer distribution through time. The software performs a coregistration of the images to the standard space, where the different regions of the brain can be segmented using an atlas, and provides two physiologically meaningful parameters which are the Distribution Volume Ratio (DVR) and Standardized Uptake Value Ratio (SUVR). It gives out the DVR and SUVR values for any region of interest, as well as parametric images which help visualizing the radiotracer distribution in the brain. A set of brain PET images from 13 subjects acquired using 18F-PI-2620 has been used for the development and testing of the software, divided into healthy controls, subjects with Down syndrome, some of whom have developed Alzheimer’s disease (AD), which also implies a higher amount of abnormal deposited tau proteins. The results have shown higher DVR and SUVR values for several brain regions in those subjects who have developed AD, confirming that they have a higher radiotracer uptake and a greater amount of deposited tau proteins. This proves the correct functionality of the software and its potential as a future tool for detecting tauopathies such as PSP in combination with the radiotracer

    Converging organoids and extracellular matrix::New insights into liver cancer biology

    Get PDF

    Converging organoids and extracellular matrix::New insights into liver cancer biology

    Get PDF
    Primary liver cancer, consisting primarily of hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), is a heterogeneous malignancy with a dismal prognosis, resulting in the third leading cause of cancer mortality worldwide [1, 2]. It is characterized by unique histological features, late-stage diagnosis, a highly variable mutational landscape, and high levels of heterogeneity in biology and etiology [3-5]. Treatment options are limited, with surgical intervention the main curative option, although not available for the majority of patients which are diagnosed in an advanced stage. Major contributing factors to the complexity and limited treatment options are the interactions between primary tumor cells, non-neoplastic stromal and immune cells, and the extracellular matrix (ECM). ECM dysregulation plays a prominent role in multiple facets of liver cancer, including initiation and progression [6, 7]. HCC often develops in already damaged environments containing large areas of inflammation and fibrosis, while CCA is commonly characterized by significant desmoplasia, extensive formation of connective tissue surrounding the tumor [8, 9]. Thus, to gain a better understanding of liver cancer biology, sophisticated in vitro tumor models need to incorporate comprehensively the various aspects that together dictate liver cancer progression. Therefore, the aim of this thesis is to create in vitro liver cancer models through organoid technology approaches, allowing for novel insights into liver cancer biology and, in turn, providing potential avenues for therapeutic testing. To model primary epithelial liver cancer cells, organoid technology is employed in part I. To study and characterize the role of ECM in liver cancer, decellularization of tumor tissue, adjacent liver tissue, and distant metastatic organs (i.e. lung and lymph node) is described, characterized, and combined with organoid technology to create improved tissue engineered models for liver cancer in part II of this thesis. Chapter 1 provides a brief introduction into the concepts of liver cancer, cellular heterogeneity, decellularization and organoid technology. It also explains the rationale behind the work presented in this thesis. In-depth analysis of organoid technology and contrasting it to different in vitro cell culture systems employed for liver cancer modeling is done in chapter 2. Reliable establishment of liver cancer organoids is crucial for advancing translational applications of organoids, such as personalized medicine. Therefore, as described in chapter 3, a multi-center analysis was performed on establishment of liver cancer organoids. This revealed a global establishment efficiency rate of 28.2% (19.3% for hepatocellular carcinoma organoids (HCCO) and 36% for cholangiocarcinoma organoids (CCAO)). Additionally, potential solutions and future perspectives for increasing establishment are provided. Liver cancer organoids consist of solely primary epithelial tumor cells. To engineer an in vitro tumor model with the possibility of immunotherapy testing, CCAO were combined with immune cells in chapter 4. Co-culture of CCAO with peripheral blood mononuclear cells and/or allogenic T cells revealed an effective anti-tumor immune response, with distinct interpatient heterogeneity. These cytotoxic effects were mediated by cell-cell contact and release of soluble factors, albeit indirect killing through soluble factors was only observed in one organoid line. Thus, this model provided a first step towards developing immunotherapy for CCA on an individual patient level. Personalized medicine success is dependent on an organoids ability to recapitulate patient tissue faithfully. Therefore, in chapter 5 a novel organoid system was created in which branching morphogenesis was induced in cholangiocyte and CCA organoids. Branching cholangiocyte organoids self-organized into tubular structures, with high similarity to primary cholangiocytes, based on single-cell sequencing and functionality. Similarly, branching CCAO obtain a different morphology in vitro more similar to primary tumors. Moreover, these branching CCAO have a higher correlation to the transcriptomic profile of patient-paired tumor tissue and an increased drug resistance to gemcitabine and cisplatin, the standard chemotherapy regimen for CCA patients in the clinic. As discussed, CCAO represent the epithelial compartment of CCA. Proliferation, invasion, and metastasis of epithelial tumor cells is highly influenced by the interaction with their cellular and extracellular environment. The remodeling of various properties of the extracellular matrix (ECM), including stiffness, composition, alignment, and integrity, influences tumor progression. In chapter 6 the alterations of the ECM in solid tumors and the translational impact of our increased understanding of these alterations is discussed. The success of ECM-related cancer therapy development requires an intimate understanding of the malignancy-induced changes to the ECM. This principle was applied to liver cancer in chapter 7, whereby through a integrative molecular and mechanical approach the dysregulation of liver cancer ECM was characterized. An optimized agitation-based decellularization protocol was established for primary liver cancer (HCC and CCA) and paired adjacent tissue (HCC-ADJ and CCA-ADJ). Novel malignancy-related ECM protein signatures were found, which were previously overlooked in liver cancer transcriptomic data. Additionally, the mechanical characteristics were probed, which revealed divergent macro- and micro-scale mechanical properties and a higher alignment of collagen in CCA. This study provided a better understanding of ECM alterations during liver cancer as well as a potential scaffold for culture of organoids. This was applied to CCA in chapter 8 by combining decellularized CCA tumor ECM and tumor-free liver ECM with CCAO to study cell-matrix interactions. Culture of CCAO in tumor ECM resulted in a transcriptome closely resembling in vivo patient tumor tissue, and was accompanied by an increase in chemo resistance. In tumor-free liver ECM, devoid of desmoplasia, CCAO initiated a desmoplastic reaction through increased collagen production. If desmoplasia was already present, distinct ECM proteins were produced by the organoids. These were tumor-related proteins associated with poor patient survival. To extend this method of studying cell-matrix interactions to a metastatic setting, lung and lymph node tissue was decellularized and recellularized with CCAO in chapter 9, as these are common locations of metastasis in CCA. Decellularization resulted in removal of cells while preserving ECM structure and protein composition, linked to tissue-specific functioning hallmarks. Recellularization revealed that lung and lymph node ECM induced different gene expression profiles in the organoids, related to cancer stem cell phenotype, cell-ECM integrin binding, and epithelial-to-mesenchymal transition. Furthermore, the metabolic activity of CCAO in lung and lymph node was significantly influenced by the metastatic location, the original characteristics of the patient tumor, and the donor of the target organ. The previously described in vitro tumor models utilized decellularized scaffolds with native structure. Decellularized ECM can also be used for creation of tissue-specific hydrogels through digestion and gelation procedures. These hydrogels were created from both porcine and human livers in chapter 10. The liver ECM-based hydrogels were used to initiate and culture healthy cholangiocyte organoids, which maintained cholangiocyte marker expression, thus providing an alternative for initiation of organoids in BME. Building upon this, in chapter 11 human liver ECM-based extracts were used in combination with a one-step microfluidic encapsulation method to produce size standardized CCAO. The established system can facilitate the reduction of size variability conventionally seen in organoid culture by providing uniform scaffolding. Encapsulated CCAO retained their stem cell phenotype and were amendable to drug screening, showing the feasibility of scalable production of CCAO for throughput drug screening approaches. Lastly, Chapter 12 provides a global discussion and future outlook on tumor tissue engineering strategies for liver cancer, using organoid technology and decellularization. Combining multiple aspects of liver cancer, both cellular and extracellular, with tissue engineering strategies provides advanced tumor models that can delineate fundamental mechanistic insights as well as provide a platform for drug screening approaches.<br/

    The medical applications of hyperpolarized Xe and nonproton magnetic resonance imaging

    Get PDF
    Hyperpolarized 129Xe (HP 129Xe) magnetic resonance imaging (MRI) is a relatively young field which is experiencing significant advancements each year. Conventional proton MRI is widely used in clinical practice as an anatomical medical imaging due to its superb soft tissue contrast. HP 129Xe MRI, on the other hand, may provide valuable information about internal organs functions and structure. HP 129Xe MRI has been recently clinically approved for lung imaging in the United Kingdom and the United States. It allows quantitative assessment of the lung function in addition to structural imaging. HP 129Xe has unique properties of anaesthetic, and may transfer to the blood stream and be further carried to the highly perfused organs. This gives the opportunity to assess brain perfusion with HP 129Xe and perform molecular imaging. However, the further progression of the HP 129Xe utilization for brain perfusion quantification and molecular imaging implementation is limited by the absence of certain crucial milestones. This thesis focused on providing important stepping stones for the further development of HP 129Xe molecular imaging and brain imaging. The effect of glycation on the spectroscopic characteristics of HP 129Xe was studied in whole sheep blood with magnetic resonance spectroscopy. An additional peak of HP 129Xe bound to glycated hemoglobin was observed. This finding should be implemented in the spectroscopic HP 129Xe studies in patients with diabetes. [...

    Fit for surgery? The impact of muscular and cardiopulmonary function on surgical outcomes after major abdominal surgery

    Get PDF
    Background: Poor physical function predicts outcomes after major abdominal surgery. The aim of this thesis is to assess the ability of perioperative patients’ function to prognose adverse surgical outcome and the efficacy of supervised pre-operative exercise programs to reduce adverse surgical outcomes. Methods: Reliability of ultrasound to measure Vastus Lateralis (VL) size, architecture and quality was assessed. Differences in VL size and quality between hepatobiliary surgery patients, old healthy adults and master athletes (MAs) were assessed. Ability of preoperative cardiopulmonary exercise testing, VL size, architecture and quality assessment, body composition using abdominal computed tomography scans, maximum isometric knee extension, rate of force development during maximum voluntary contraction (MVC) and changes in VL size and architecture during in-hospital recovery to prognose surgical outcome were assessed. Effectiveness of supervised pre-operative exercise programs to improve patient fitness and surgical outcome was assessed with a systematic review and meta-analysis. Results: Ultrasound images showed varying degrees of intra-rater (Intraclass correlation coefficient [ICC]≥0.824), inter-rater (ICC≥0.520) and inter machine (against magnetic resonance imaging) (ICC≥0.892) reliability. Pre-operative VL quality was lower in hepatobiliary surgery patients compared to healthy older adults and MAs (18.9±6.0, 26.7±4.9 and 28.3±7.0, respectively, p<0.001). Pre-operative low Psoas muscle index and high equivalents of carbon dioxide increased the risk of 3-years mortality (Hazard ratio [95% confidence interval]: 2.372 [1.246-4.515], p=0.009). Patients who performed two supervised exercise sessions per week before surgery showed higher six-minute walk distance (mean difference between groups [95%CI]: +47 [20-75] m., p<0.001) and lower relative risk (RR) of post-operative complications (RR [95%CI]: 0.59 [0.46-0.75], p<0.001) compared to patients following usual care (UC). Patients undergoing abdominal aortic aneurysms repair that performed a prehabilitation program showed similar peak oxygen uptake compared to UC group (mean difference between groups [95%CI]: 1.42 [0.51-2.34] ml·kg-1·min-1, p<0.001). Conclusion: Cardiopulmonary fitness and psoas muscle mass can predict long-term mortality. Two or more weekly supervised sessions are needed to improve fitness and surgical outcome
    • …
    corecore