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I completed my MSc training in Molecular Genetics at the University of Brussels, Belgium. I have been fortunate to work with an enthusiastic group of graduate students and researchers in this lab for over a decade. My responsibilities include overseeing the daily activities of the lab, organizing and controlling all aspects of the lab environment, ordering and keeping track of all equipment and supplies, and maintaining and stocking all hESC lines. I also provide training and technical support for new lab members.
Currently I'm involved in an endoderm differentiation project. My main focus is on optimizing differentiation conditions to generate large amounts of pancreatic progenitors.
My goal is to try my best to assist others in the lab.
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My research interests focus on theoretical and computational aspects of stem cell biology and engineering. Specifically, I am interested in how the behaviour of pluripotent stem cells (proliferation vs. differentiation, for example) is controlled at a molecular and cellular level both in vitro and in vivo. How do the myriad of signals impinging on a stem cell determine how it will behave, and can the rules of stem cell behaviour be described in simple yet mathematically robust ways? Can knowledge of these rules be used to quantitatively control cell behaviour in a way that is efficient and beneficial to regenerative medicine and tissue engineering? Although the majority of modeling work on this problem has so far focused on intracellular regulation (i.e. genetic and signaling cascades), the interactions between cells in a population are no doubt equally decisive factors in controlling fate choice in complex cell populations, both in vitro and in vivo. Currently, my research focuses on this second class of problem, in which I use methods and concepts from biology, physics, computer science, and mathematics to develop simulations and abstract models of interacting populations of stem cells to analyze and predict cell fate choices within these heterogeneous populations.
Human umbilical cord blood (UCB) is a source for haematopoietic stem cell transplantation. It is also considered an accessible and less immunogenic source for mesenchymal, unrestricted somatic and other stem cells with pluri/multipotent properties. One of the hopes for UCB enhancement strategies is to generate a sufficient number of haematopoetic progenitor cells (HPCs) to successfully perform "single umbilical cord transplant" (sUCBT). However, despite two decades of studies, no technology has been approved or adopted into clinical practice.
"Future development of successful UCB enhancement approaches should solve a number of existing controversies. First, does one need to select a subset of cells to expand, and if so, which cell subpopulation to expand must be defined. Second, the most optimal conditions for UCB ex vivo expansion need to be determined: whether or not liquid cultures, static or continuous perfusion cultures with or without stromal cells must be defined. Third, manipulation of the molecular pathways that regulate stem cell maintenance and self-renewal appears most promising, but this is still in its infancy of development. Fourth, better ways to increase cell yield at the time of collection, and reducing cell loss during processing and at time of thaw are important lines of inquiry. Fifth, methods to enhance homing are also promising but still need testing in clinical trials. Sixth, the long-term fate of expanded UCB progenitors also remains unclear and it is not known if certain manipulations may be associated with earlier senescence or apoptosis". (Norkin et al., 2012)
My project is associated with ex vivo manipulations to characterize and enhance UCB potency (hematopietic and non-hematopoietic) for preclinical and clinical approaches.
Development of clinically relevant, spatially ordered tissues and organs requires a quantitative understanding of the principles that regulate human development, and strategies that enable us to harness those principles reproducibly and with precision at the clinical scale. Computational modeling, which offers tightly controlled parameters that can be manipulated economically and speedily, has been touted to play a key role in quantifying these principles. Yet, despite the availability of a wide array of computational techniques our progress has been modest. A key factor behind this is absence of computational paradigms that offer realistic representations to cells and their environment. My research is centered on developing computational strategies (models and frameworks) that address this issue, and offer the means to quantify how information exchange between environmental, cellular, and sub-cellular levels leads to the spatiotemporal evolution of spatially ordered cell populations and tissues. Such computational tools can also be utilized to quantify biological systems to gain insights into mechanisms responsible for normal and pathological behaviors. As such, these tools can be employed for drug & medical device design and optimization. More specifically, my research focuses on the formation of germ layers during gastrulation, transition of osteoblasts into osteocytes, engineering the thymic environment, and pathogenesis of asthma as well as pharmacodynamics of potential asthma therapies.
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The immune system has the life-long formidable task of protecting the organism against pathogens and the insurgence of tumors. T cells constitute one of the major players in the establishment of immunological defense and tolerance, and are constantly generated in a primary lymphoid organ, the thymus. Here, specialized thymic epithelial cells (TEC) provide a specialized microenvironment that supports the differentiation of lymphoid progenitors into mature T cells. When thymic functionality declines – e.g., due to aging or radio-chemotherapy ablative treatments- the organism experiences weakened immunity and increased susceptibility to infections. Although maintenance and prompt restoration of an efficient immune system is considered crucial, our ability to influence T-lymphopoiesis is still very limited, mainly due to the lack of available in vitro models of the thymic microenvironment. Therefore, my project aims at developing a bioengineered thymic organoid by modulating composition, architecture, and physical properties of an in vitro microenvironment that will be able to maintain TEC functionality ex vivo. As a result, we will generate a functional stromal substrate that mimics the thymic functionality, thus allowing for the generation of mature and competent T cells in vitro. After the validation of the system, we will investigate the mechanisms underlying the cross talk between thymic stromal cells and T cells, and the possible avenues for the exploitation of regenerative medicine approaches.
Applying synthetic biology principles- such as rational design and implementation of synthetic networks- to human pluripotent stem cells (hPSC) can complement and expand the tremendous potential of manufacturing clinical relevant stem-cell derived tissues. Yet, mammalian synthetic biology is in its infancy and engineering of synthetic networks in the complex environment of human cells remains challenging and is even largely unexplored in hPSC. My work involves the development of a synthetic biology platform for genetic engineering of human induced PSC (iPSC). This includes the generation of an efficient integration strategy for stable long-term integration of synthetic gene networks into the iPSC genome, characterization of synthetic genetic parts and optimiziation of those for tailored operation in iPSC. With this platform, I envision to build gene networks that can be programmed to perform specific and predictive functions inside human iPSC without disturbing the cells pluripotency characteristics. On the application side, I am particularly interested to develop synthetic reporting- and control systems for dissecting and promoting the in-vitro generation of hPSC-derived progenitor T cells thereby complementing the Labs ongoing efforts in scalable manufacturing technologies for immunotherapy.
Myocardial infarction (MI) is a leading cause of congestive heart failure, which is the number one cause of mortality worldwide. MI induced inflammatory responses play a critical role in the formation of fibrotic scar in the myocardium, however, very little is known about the key cellular and molecular mechanisms in this process. Utilizing microfluidics, an in vitro inter-tissue MI model will be developed to study immune cell – cardiac tissue interactions . In particular, the activation of signaling pathways involved in the maturation process of dendritic cells and the transition between pro-inflammatory and anti-inflammatory stages with respect to inflammatory cytokine production will be analyzed in hypoxic conditions mimicking ischemia. The findings from this study will enhance our understanding of the role of immune system activation in MI, and could lead to the development of early stage pharmaceutical interventions capable of modulating heart disease progression.
The development of T cells from stem cells is coordinated by dense gene regulatory networks (GRNs) that respond to environmental signals like Notch. However, existing static models of these GRNs provide limited insight into the multi-stage dynamics of T cell specification. We are applying Boolean networks to computationally model the dynamic response of T cell progenitors to different biological situations and predict new ways to control their cell fate. Our computational simulations map the transcriptional space that progenitors can access given different signals or genetic perturbations. Using methods from graph theory, we can identify sources of heterogeneity and trace the full repertoire of differentiation trajectories that are available to T cell progenitors. Overall, these models will be harnessed to answer fundamental questions about T cell biology, develop improved in vitro differentiation protocols, and explore the potential role of developmental GRNs during reprogramming of T cell progenitors into induced pluripotent stem (iPS) cells.
The development of human induced pluripotent stem cell (iPSC) technology has been hindered by a lack of robust and well characterized bioprocesses for their scalable generation. Our lab has recently developed a method to generate high density cultures of murine iPSCs by reprogramming somatic cells to pluripotency in suspension. High density industrial scale bioprocesses rely heavily on control and modulation of cellular metabolism for optimal operation, yet the metabolic properties of iPSCs have not been elucidated. My project aims to translate our lab's suspension reprogramming process to human iPSCs, and to investigate the metabolic pathways and requirements during reprogramming of iPSCs in this high density system.
Petra's current project focuses on developing a cure for myocardial infarction, which is the leading cause of death worldwide. A promising new approach is the use of targeted protein therapeutics for in situ regeneration of lost myocardial tissue, which would circumvent the need for cell or tissue transplantation. The drugs would contain growth factors or cytokines that prevent further cell death and that stimulate surviving cardiac cells to regenerate the heart. On a cellular level, two essential steps are necessary for regeneration: initiation of cell cycle re-entry of the remaining mature cardiomyocytes to restore original cell numbers, as well as maturation of newly formed cells to ensure full functional recovery. Using human embryonic stem cell-derived cardiomyocytes as an in vitro model for adult cardiac tissue in combination with sophisticated high-throughput screening tools, the goal of this project is to determine growth factor candidates for protein therapeutics.
Hematopoietic stem cells (HSCs) are the only cell type capable of reconstituting long-term blood cell production. Outcomes of clinical marrow transplants depend critically on the number of HSCs in the donor sample, and research strategies aimed at deriving or expanding HSC populations are similarly constrained by the need to monitor their numbers. However, there is currently no direct way of enumerating HSCs. My project is focused on the development of a high-throughput, microdroplet-based PCR platform to quantify rare populations of hematopoietic stem cells (HSCs) based on the expression of HSC-specific transcripts. We aim to identify a transcript expression profile that is unique to long-term reconstituting HSCs and perform single-cell RT-PCR by encapsulating single cells in picolitre droplets using a microfluidics system. Ultimately, this automatable platform will be transformed into a system usable in any diagnostic laboratory for the robust enumeration of rare cell types such as HSC.
It is proposed that the leukemic stem cell (LSC) is the source of initiation, progression, and persistence in leukemias. By using in silico techniques to gain insight into how a healthy signalling network can be perturbed to result in deregulated hematopoiesis, I hope to uncover novel and potent control points that can serve as potential therapeutic targets to disrupt leukemogenesis.
To date, technologies capable of guiding embryonic stem cells (ESC) into specific lineages, such as blood cells, are inefficient. Cells residing in the embryo are exposed to a microenvironment comprised of numerous signaling factors and cell-cell interactions. My research will investigate a scalable bioengineering approach to control the spatial and temporal aspects of ESC differentiation into blood progenitor cells.
Since their discovery in 2006, research into the potential for Induced Pluripotent Stem (iPS) cells to provide a source of patient-specific cells for regenerative medicine applications has shown great promise. However, harnessing iPS technology has proven difficult due to our lack of understanding of the reprogramming process. Insights into the mechanism of reprogramming may not only aid in improving protocols for developing iPS cells, but will likely pave the way for developing a standardized criteria for selecting clinically usable iPS cells. My work aims to take a biomedical engineering approach, by combining mathematical modelling and experimental biology, to understand the state transitions involved in driving cells from a differentiated to iPS cell state. In doing so, I aim to shed light on how this process can be better controlled to improve current iPS production strategies, thus moving these cells one step closer to clinical use.
The goal of my project is to develop novel ways to drive embryonic and induced pluripotent stem cells (ESCs and iPSCs) towards the hematopoietic (blood forming) lineage to produce T lymphocyte precursors. T cells mediate resistance to opportunistic infections and enhanced T cell reconstitution in immunocompromised patients could improve patient survival. ESCs have been shown to differentiate into committed hematopoietic progenitor cells (HPCs) in clinically viable serum-free conditions in our laboratory (Purpura, K.A., J. Morin and P.W. Zandstra. Exp Hematol 2008). The challenge remains to engineer a controlled serum-free cellular microenvironment with immobilized Delta-like 1 (DL1) ligand to direct the differentiation of ESC/iPSC-derived HPCs to the T cell lineage with high yield and efficiency. It is hypothesized that differentiation of T cells from stem cells can be accelerated by deriving iPSCs from T cells (or T-iPSCs) as they may retain epigenetic memory of the cell type from which they were derived. This hypothesis will be tested by differentiating ESCs and T-iPSCs in a novel hydrogel system with the presentation of immobilized DL1 ligand to robustly and reproducibly study the kinetics of T cell differentiation.
The somatic tissues of all species are formed by the initial formation of the three germ layers during development in an evolutionarily conserved principle called ‘Gastrulation’. In amniotes (birds and mammals, for example), the process of gastrulation is initiated by the induction of the primitive streak. Although the induction of the primitive streak is seen in gastrulating embryos of various species, the cell biological processes vary significantly. Studying the induction of the primitive streak, and the subsequent mesendodermal specification in human embryos is especially difficult because it requires an in vitro system that is able to pattern a complex, multi-cellular environment in a controlled manner. The focus of my research is to use micro-fabrication techniques to develop a platform that mimics the micro-environment present in vivo, and to use this platform to investigate the molecular mechanisms that control the events that govern this highly critical checkpoint involved in embryonic development.
Nimalan is designing stimulatory/sensory microbioreactor screening systems for investigating the mechanisms by which human Pluripotent Stem Cells (hPSC) differentiate into mature, adult-like cardiomyocytes within three-dimensional microenvironments (via cell-cell and cell-ECM interactions), and then how they proceed into disease-states caused by Myocardial Infarction (MI). The complex process by which hPSC fate toward a mature and functional heart cell is determined, all the while mediated by biochemical, mechanical, and electrical stimuli, each of which uniquely interact temporally and spatially to induce signaling cues and morphogenesis, still remains elusive. Additionally, it has proven difficult to accurately recapitulate MI in vitro through induction of the same apoptosis signaling pathways as observed in vivo. The goal is to use this microtissue-based high-content screening platform to discover and validate the efficacy and safety of novel small molecules which may be beneficial as cardioprotectants, anti-arrhythmogenics, and promoters of regeneration after MI.
I am working on a scalable method to differentiate three different human pluripotent stem cell lines (hPSC) into pancreatic progenitor cell populations. The cells generated in this protocol will be transplanted into mice to investigate their potential to differentiate to a beta-cell like population capable of controlling glucose levels. While developing a differentiation protocol for pancreatic progenitors, I am also addressing the variability of endogenous signaling in multiple hPSC cell lines. I am also investigating the effects of endothelial cells on the differentiation of hPSC to pancreatic progenitors. The study of endogenous signaling during differentiation for multiple hPSC lines with or without additional cell populations will reveal how to modify the endogenous signaling environment to induce efficient differentiation, addressing a major problem in current hPSC differentiation protocols. I completed a BASc in chemical engineering at the University of Waterloo, and I'm currently in the MD/PhD program at the University of Toronto.
Abstract: Myocardial infarction (MI) is now the leading cause of congestive heart failure and death in the world. Coronary occlusion and the resultant myocardial ischemia rapidly result in myocardial necrosis followed by scar formation. As a result, loss of cardiomyocytes in the adult heart is irreversible and leads to reduced cardiac function. While several studies have now shown that cell transplantation results in small improvements in the infarct area, major challenges such as increasing cell survival, engraftment and functional integration with the host tissue remain. Mouse embryonic stem cells (mESCs) are a promising source of cells as they can differentiate into cardiomyocytes well as into recently identified cardiac progenitor cells. Although, multiple cardiac progenitor stages can be generated, which one or which combination that will result in effective treatment of cardiac disease is uncertain.
Additionally, the ability to isolate and enrich for specific cell types is limited, especially at the progenitor cell stage. In order to address this problem my project involves the identification of new surface markers to allow for the isolation of specific progenitor cell types.
An emerging focus of the lab is to construct computational models to predict the influence of intrinsic and extrinsic factors on early stem cell fate decisions. Our group has recently developed a high throughput platform which provides the experimental setup necessary to thoroughly explore how microenvironmental attributes contribute to such fate decisions. My work focuses on developing software that will assist us in analyzing and visualizing our experimental data, and validating the predictions of our models.