Chronic kidney disease has restricted treatment options and leads to a lower quality of life, even before the end stage of renal disease is reached. The ability to generate new transplantable... Show moreChronic kidney disease has restricted treatment options and leads to a lower quality of life, even before the end stage of renal disease is reached. The ability to generate new transplantable kidney tissue could help millions of people worldwide and is therefore of great interest. This thesis explores options within regenerative medicine to develop new transplantable kidney tissue from a bio-engineering point of view. Show less
Despite being the object of intense study, embryonic development has been difficult to model due to a number of reasons. First, complex tissues can be comprised of many cell types, of which we... Show moreDespite being the object of intense study, embryonic development has been difficult to model due to a number of reasons. First, complex tissues can be comprised of many cell types, of which we probably only know a subset. Therefore, we first focused on the discovery of cell types by single-cell RNA-sequencing (scRNA-seq). Cell types are routinely identified by clustering scRNA-seq data, however, there was no principled way to determine the right number of clusters. To improve cell type classification, we developed phiclust, a clusterability measure for scRNA-seq. Another challenge in a developing tissue is that many signaling processes and morphogenic events occur simultaneously, which makes it hard to isolate the individual contributions. For this purpose, I looked at stem cell derived in vitro systems, in which a small number of specific cell types can be combined deliberately and studied in isolation. My analysis of different model systems shows that cellular communication causes structural and transcriptional changes in the developing cells. Finally, while tissue organization has been characterized extensively, we lack generative models that can relate specific patterns to the underlying gene regulatory mechanisms. Therefore, I later focused on deep learning-based approaches to infer gene regulatory networks from observed spatial patterns. Show less
Haan, M.J.A. de; Witjas, F.M.R.; Engelse, M.A.; Rabelink, T.J. 2021
The purpose of organ decellularization is to remove all cellular components whilst preserving the extracellular matrix (ECM). It has been hypothesized that this decellularized ECM can be used as a... Show moreThe purpose of organ decellularization is to remove all cellular components whilst preserving the extracellular matrix (ECM). It has been hypothesized that this decellularized ECM can be used as a scaffold for the development of personalized bioengineered kidneys by repopulating it with patient-derived cells. The renal artery, vein, and ureter are most frequently used for whole kidney repopulation. Cell perfusion through the artery and vein enables revascularization of decellularized kidneys. However, adequate repopulation of the epithelial compartment remains unattainable. Although it has become unlikely that recellularized whole kidneys will be the solution to reduce donor organ shortages within the foreseeable future, advances made within the field of whole organ decellularization and recellularization have paved the way for alternatives that actually may help to solve these shortages. This includes ex vivo refurbishment and personalization of discarded donor organs during machine perfusion. Show less
Ouweneel, A.B.; Reiche, M.E.; Snip, O.S.C.; Wever, R.; Wel, E.J. van der; Schaftenaar, F.H.; Kauerova, S.: Lutgens, E.: Eck, M. van, Hoekstra, M. 2021
The bone marrow has emerged as a potentially important target in cardiovascular disease as it generates all leukocytes involved in atherogenesis. In the current study, we evaluated whether a change... Show moreThe bone marrow has emerged as a potentially important target in cardiovascular disease as it generates all leukocytes involved in atherogenesis. In the current study, we evaluated whether a change in bone marrow functionality underlies the increased atherosclerosis susceptibility associated with high-density lipoprotein (HDL) deficiency. We found that HDL deficiency in mice due to the genetic lack of hepatocyte-derived apolipoprotein A1 (APOA1) was associated with an increase in the Lin-Sca-1+Kit+ (LSK) bone marrow stem cell population and lymphoid-primed multipotent progenitor numbers, which translated into a higher production and systemic flux of T cell subsets. In accordance with APOA1 deficiency-associated priming of stem cells to increase T lymphocyte production, atherogenic diet-fed low-density lipoprotein receptor knockout mice transplanted with bone marrow from APOA1-knockout mice displayed marked lymphocytosis as compared to wild-type bone marrow recipients. However, atherosclerotic lesion sizes and collagen contents were similar in the two groups of bone marrow recipients. In conclusion, systemic lack of APOA1 primes bone marrow stem cells for T cell lymphopoiesis. Our data provide novel evidence for a regulatory role of HDL in bone marrow functioning in normolipidemic mice. Show less
Hassani, R.T.J.; Sandali, O.; Ouadfel, A.; Packer, M.; Romano, F.; Thuret, G.; ... ; Baudouin, C. 2020
Phacoemulsification is the most frequently performed surgery in the world. Over the past few years, this surgery seems to have reached a plateau with no further innovative breakthroughs. In this... Show morePhacoemulsification is the most frequently performed surgery in the world. Over the past few years, this surgery seems to have reached a plateau with no further innovative breakthroughs. In this paper, we focus on alternatives techniques, the latest innovations, and the research and development pipeline in this field. (C) 2020 Elsevier Masson SAS. All rights reserved. Show less
Nawroth, J.C.; Barrile, R.; Conegliano, D.; Riet, S. van; Hiemstra, P.S.; Villenave, R. 2019
Pathologies of the respiratory system such as lung infections, chronic inflammatory lung diseases, and lung cancer are among the leading causes of morbidity and mortality, killing one in six people... Show morePathologies of the respiratory system such as lung infections, chronic inflammatory lung diseases, and lung cancer are among the leading causes of morbidity and mortality, killing one in six people worldwide. Development of more effective treatments is hindered by the lack of preclinical models of the human lung that can capture the disease complexity, highly heterogeneous disease phenotypes, and pharmacokinetics and pharmacodynamics observed in patients. The merger of two novel technologies, Organs-on-Chips and human stem cell engineering, has the potential to deliver such urgently needed models. Organs-on-Chips, which are microengineered bioinspired tissue systems, recapitulate the mechanochemical environment and physiological functions of human organs while concurrent advances in generating and differentiating human stem cells promise a renewable supply of patient-specific cells for personalized and precision medicine. Here, we discuss the challenges of modeling human lung pathophysiology in vitro, evaluate past and current models including Organs-on-Chips, review the current status of lung tissue modeling using human pluripotent stem cells, explore in depth how stem cell based Lung-on-Chips may advance disease modeling and drug testing, and summarize practical consideration for the design of Lung-on-Chips for academic and industry applications. (C) 2018 Elsevier B.V. All rights reserved. Show less
The studies presented in this thesis were aimed at developing and using in vitro models that could benefit research towards understanding asthma and COPD. We used an in vitro model... Show moreThe studies presented in this thesis were aimed at developing and using in vitro models that could benefit research towards understanding asthma and COPD. We used an in vitro model representing a Th2-high gene signature and studied how this gene signature may be affected by external factors such as cigarette smoke or drugs. Using these in vitro models may help to predict clinical outcomes, although they will require extensive validation. We also investigated the possibility of using primary human airway epithelial cells to model bacterial and viral exacerbations. Whereas this model is currently still under investigation, it could be particularly useful to study possible biomarkers of exacerbations and how these may be affected by external factors. Additionally, we also developed a new method to expand and differentiate mouse tracheal epithelial cells in vitro. Overall, studying airway epithelial cells may provide important clues for understanding disease pathogenesis, lead to identification of new treatment targets, and may provide important biomarkers. Using airway epithelial cells and their derived biomarkers could significantly improve our understanding in disease phenotypes of asthma and COPD. Additionally, with increasing knowledge of the disease phenotypes, we could better address the unmet need in treatment of asthma and COPD. Show less
Diabetes mellitus is amongst the leading causes of morbidity and mortality worldwide. Insulin-producing pancreatic β-cells are central in establishing adequate glucose regulation and loss of... Show moreDiabetes mellitus is amongst the leading causes of morbidity and mortality worldwide. Insulin-producing pancreatic β-cells are central in establishing adequate glucose regulation and loss of functional β-cells results in the development of diabetes. Although it was previously thought that fully differentiated cells cannot change phenotype, murine studies recently indicated that mature β-cells can change identity into other islet cells under conditions of (metabolic) stress.We present a novel agarose based microwell culture system that can be used for aggregate formation of human or rodent islet cells. We show that this platform provides reproducible results to study aggregation of primary human islet cells. Using this culture system together with β-cell specific lineage tracing, we find that mature human β-cells can spontaneously lose their identity and convert into glucagon-containing α-cells. We then used human pancreatic tissue from donors with T2DM and matched controls to explore loss of β-cell identity in T2DM. We report that cells indicative of loss of β-cell identity are found more frequently in tissue samples from donors with a history of T2DM. Finally, we show that Pax4 and GLP-1 receptor agonists can partially prevent loss of identity β-cell in our ex vivo model. Show less
The focus of this thesis is about cardiomyocytes derived from human pluripotent stem cells (hPSC-CMs). hPSC-CMs are an established model used to study cardiac diseases as well as a good tool for... Show moreThe focus of this thesis is about cardiomyocytes derived from human pluripotent stem cells (hPSC-CMs). hPSC-CMs are an established model used to study cardiac diseases as well as a good tool for drug efficacy and cardiotoxicity studies. The core aspect of the thesis is about hPSC-CMs derived from patients carrying genetic mutations that result in a cardiac arrhythmia known as Brugada syndrome. With these cells we manage to model the disease in vitro at the cellular level and assess the impact of specific drugs (readthrough-promoting) in an attempt to provide a valuable clinical perspective. The use of novel genetic engineering techniques (CRISPR-Cas9) helped us to further understand the link between the genotype of the patients and the phenotype of the disease. Furthermore the thesis contains our research attempts to improve hPSC-CMs so that they resemble more to adult human cardiomyocytes, since this would increase the validity of this model system and help us understand the nature of even more cardiac diseases. Show less
Knopp, P.; Krom, Y.D.; Banerji, C.R.S.; Panamarova, M.; Moyle, L.A.; Hamer, B. den; ... ; Zammit, P.S. 2016
This thesis describes research about the differentiation of human stem cells into cardiomyocytes (heart cells). During the differentiation process the stem cells become contractile myocytes... Show more This thesis describes research about the differentiation of human stem cells into cardiomyocytes (heart cells). During the differentiation process the stem cells become contractile myocytes that resemble the native heart cells. Nevertheless, the phenotype of these cardiomyocytes is comparable to a second trimester fetal heart cells. These thesis describes different approaches to induce maturity into the stem cell derived cardiomyocytes, such as changing the substrate stiffness, cell patterning and small molecule based medium. The maturation level achieved unveiled the contractile phenotype on cardiomyocytes derived from patients with hypertrophic cardiomyopathy. The end of this thesis describes a novel method to culture and expand multipotent cardiac progenitor cells. Show less
Cardiovascular disease is responsible for 17 million deaths globally each year. Research aimed at understanding the form and function of this vital organ will be key to improving patient care.... Show moreCardiovascular disease is responsible for 17 million deaths globally each year. Research aimed at understanding the form and function of this vital organ will be key to improving patient care. Although animal models such as rat, rabbit and dog have proven to be valuable to study heart physiology, there are a number of important species-specific differences, for e.g. heart rate, when compared with the human heart. In the recent years, research on cardiomyocytes(CMs) derived from human pluripotent stem cells has demonstrated that they resemble native human CMs and hence, make excellent models to study heart development and disease in vitro.In this dissertation,we present studies that describe the use of hPSC-CMs for pharamacological testing and for modeling inherited arrhythmogenic disorders.Combined with other novel technologies in the fields of genetic medicine, tissue engineering,and genome editing, hPSC-CM models will be valuable for 1) understanding lineage decisions determining CM specification, 2) unraveling molecular basis of disease, 3) translational applications such as target/drug discovery, diagnostic medicine and developing effective treatment strategies. Show less
Bomer, N.; Hollander, W. den; Suchiman, H.; Houtman, E.; Slieker, R.C.; Heijmans, B.T.; ... ; Meulenbelt, I. 2016
The discovery of human pluripotent stem cells has enabled the development of assays to model human disease in vitro. The research described in this thesis has focused on modeling Amyotrophic... Show moreThe discovery of human pluripotent stem cells has enabled the development of assays to model human disease in vitro. The research described in this thesis has focused on modeling Amyotrophic Lateral Sclerosis and Lesch Nyhan Syndrome using pluripotent stem cells. Chapter 1 contains the aim and outline of this thesis, Chapter 2 is introduction to the field and provides an overview of recent advances in stem cell modeling of Amyotrophic Lateral Sclerosis (ALS). Chapter 3 contains an introduction to the field of X-chromosome inactivation. In Chapter 4 we identify the Prostaglandin D2 DP1 receptor (DP1) as a therapeutic target for ALS and more generally validate that insights found in stem cell models of disease can be validated in vivo. In Chapter 5, we address whether non-steroidal anti-inflammatory drugs (NSAIDs) affect survival of motor neurons in ALS. In Chapter 6, we develop a stem cell assay to model Lesch Nyhan Syndrome (LNS). Finally, Chapter 7 is the general discussion of the work and contains a short perspective of the future. Show less
