Our group has pioneered in the field of STEM CELL BIOENGINEERING,an area that applies

engineering principles to stem cell biology.

To download articles on our published work please visit PubMed or Google Scholar


Our work aims to yield fundamental new insight into cell fate control in early human development, and translational technologies and novel approaches directly applicable to regenerative medicine,drug screening, and cellular therapeutic strategies. We are fundamentally interested in how complex tissues and organs develop from somatic and pluripotent stem cells (PSC). At the foundation of our research is the hypothesis that multiscale feedback interactions between cells’ internal regulatory networks and the external microenvironment shape functional tissue and organ development. By simulating, manipulating and prospectively controlling these networks our goals are to reveal new fundamental rules that govern organogenesis and to accelerate progress to regenerative therapeutics, with an emphasis on the blood-forming system. Our work will reveal new rules that govern tissue development, generate new technologies for RM applications, and yield new SC-based therapies. Our work contributes to the CIHR mission to improve the health and welfare of Canadians.

Our approach is based on three complementary thrusts:

1. BLOOD RESEARCH: We are interested in understanding the process by which individual cells form complex tissues and organs, and in utilizing this knowledge for therapeutic benefit. At the foundation of our research is the hypothesis that multi-scale interactions between cells, their internal regulatory networks, and the external microenvironment shape cell fate and functional tissue development. Our expertise in stem cell (SC) bioengineering and both somatic and pluripotent stem cell (PSC)-driven hematopoiesis serve as a clinically-relevant and unifying systems which form the basis of our research. We develop statistical and mechanistic mathematical models to reveal how these levels of biological organization interact to guide development, test our model predictions using synthetically-engineered cells and niches, and mobilize the knowledge gained to generate therapeutically-relevant blood cell types from stem cells.



Hematopoietic stem cells (HSCs) give rise to all blood cell types through the process of haematopoiesis. The clinical utility of HSCs arises from their ability to engraft and sustain the production of blood cells in compromised patients. Umbilical cord blood (UCB) is a very attractive source of HSCs, but has limited use for hematopoietic transplantation due to the restricted number of stem and progenitor cells obtained from each UCB collection. To alleviate this barrier, we have examined the role of cell population dynamics in the expansion of HSC-derived cells sourced from UCB, and used the resulting knowledge to develop automated systems of soluble protein delivery able to manipulate subpopulations of cells. Our predominant observation from this work is that blood stem cell growth in vitro, and perhaps also in vivo, is limited by feedback networks from differentiated cells.


Blood Comp



Our lab has also been instrumental in advancing “niche engineering” - the fabrication of controlled cellular environments that mimic those of functional tissues and organs. To test the hypothesis that generating adult-like cells and tissues from pluripotent stem cells (PSC) requires appropriate niche signals, we build multicellular environments that mimic the spatial, temporal and biochemical configuration of early developmental tissues that give rise to the first definitive blood cells. We recently showed that this approach dramatically enhances blood generation from human PSC. Importantly, the strict microenvironmental control achieved by niche engineering permits experimental validation of our computational model predictions. Our foundational work in PSC-derived mesoderm and blood development complements our leadership in establishing new technologies to accelerate the therapeutic use of human umbilical cord blood (UCB) derived blood stem cells. In collaboration with the Sauvageau lab (Montreal), we pioneered clinical strategies for the production of these cells in automated feedback controlled bioreactors. In complementary efforts with the Dick lab (UHN), our informatics tools are being used to map cell interactions that regulate normal and leukemic hematopoiesis, uniquely positioning us to compare properties and responses of blood cells generated from PSCs to those propagated from UCB. Finally, our ability to efficiently and scalably generate adult and PSC-derived blood progenitor cells opens exceptional opportunities to generate functional differentiated cell types.



Current SC-based cell therapies use cytokine and small molecule supplementation to mimic in vivo environments and developmental events and result in heterogeneous outputs and yields. While reporter PSC lines can be used to analyze and enrich for different stages of blood development, we are using recent advances in engineering synthetic gene networks to directly measure and guide the development of functional cell types and tissues from PSC. Our long-term goal in this work is to be able to design and produce synthetic networks capable of selecting functional blood cell types, such as T-cells and haematopoietic stem progenitor cells (HPSC), in response to controllable signals arising within engineered cell niches.


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2. PLURIPOTENT STEM CELLS: research is focused on the development of strategies that identify intracellular control points critical to regulating pluripotency and the transition of pluripotent stem cells (PSC) to blood-forming mesoderm

Our work currently focuses on inferring the genetic regulatory networks (GRN) that control pluripotency maintenance and the transition to early developmental lineages in mouse and human. Additionally, we are developing spatially-explicit models that integrate these GRN with their associated morphogenetic signaling gradients in 2- and 3-dimensionally organized cell populations, thereby increasing the fidelity and power of our in silico predictions to increase understanding of organogenesis. These models will be used to identify the key molecular control points between the regulatory signaling gradients, and the cell fate-determining transcriptional networks, that influence normal and aberrant blood development and differentiation.









3. COMPUTATIONAL APPROACHES: We use computational approaches to enhance our abilities to explore and understand stem cell biology and regenerative medicine.

Our research combines approaches from computer science and bioinformatics, numerical simulation and visualization, and theoretical science to study basic and applied problems in stem cell biology. These methods are critical to our goal of understanding the development of the blood system so that we are better able to produce particular cell types for clinical use. To this end, we have developed a novel computational approach to determine the diffusible ligand-based cell interactions between cells in the blood developmental hierarchy, allowing us to determine how those interactions govern blood cell production within the adult hematopoietic system. Finally, we are also interested in how to simulate intracellular gene regulatory networks (GRNs) activation during the maintenance of stem cell pluripotency and how alterations in the network behaviour govern the transition to differentiated cell fates. Ongoing studies are particularly focused on developing spatially-explicit multiscale models of how diffusible factors secreted from individual cells influence surrounding cells, or initiate changes in their gene and signaling networks to induce cell fate transitions.





SIGNIFICANT RESEARCH CONTRIBUTIONS: Zandstra has led a fantastic team of graduate students, post-doctoral fellows and collaborators, to make discoveries using stem cell niche engineering (Discher Science 2009; Peerani J Clin Invest 2010) and computational modeling (Qiao CELL Stem Cell 2015) that advance our understanding of tissue and organ development from stem cells(Woodford Curr Opin Biotechnol 2012) and enable cell therapy manufacturing (Kirouac CELL Stem Cell 2009; Lipsitz Nat Biotechnol 2016).


Developed suspension bioprocesses for the production of pluripotent stem cell (PSC)-derived blood and cardiac cells (Song PNAS USA 2010; Bauwens Tissue Eng 2011; Fluri, Nat Methods 2012). These studies demonstrated the generation of PSC and PSC-derived cells for tissue engineering and pre-clinical testing (Thavandiran PNAS USA 2013; Shakiba Nat Commun 2015), and resulted in licensed patents such as the Aggrewell technology (Ungrin PLOS One 2008) sold by STEMCELL Technologies (Vancouver, B.C.) and a PSC expansion process licensed (via CCRM) to BlueRock Therapeutics (Toronto, ON). Discovered control of endogenous factor feedback networks from inhibitory cells enhance human blood stem cell growth (Csaszar CELL Stem Cell 2012). This discovery led to the development of a fed-batch system for suspension culture expansion of blood stem cells (Kirouac Mol Sys Biol 2009; Fares Science 2014). This technology has been licensed to Excellthera (Montreal, QC) and is being used in a phase 1/2 clinical trial for the treatment of leukemia (11 patients treated to date).



Developed high-throughput 2D approaches to mimic early embryogenesis and enable discovery of new molecules controlling stem cells during development (Peerani EMBO J 2007; Nazareth Nat Methods 2013). Using these micro-fabricated surfaces, we have shown cell patterning can be used to reprogram cell fate (Onishi Stem Cell Reports 2014), and have developed novel niche engineering surfaces capable of quantitatively immobilizing signaling proteins to guide stem cell self-renewal (Alberti Nat Methods 2009). Designed 3D micro-tissues to guide stem cell differentiation and mimic human tissue and organ function (Rahman Biomaterials 2010; Bratt-Leal Biomaterials 2011). Our capacity to generate different stem cell-derived cells allowed us to formulate human “micro-tissues” that are useful as mimetics to understand development (Varelas Nat Cell Biol 2008), optimize blood differentiation (Lee Stem Cell Res 2009; Mueller Sci Reports 2016), and screen for cell transplant and drug development strategies (Song PNAS USA 2009; Thavandiran PNAS USA 2013).


Computational models of cell and tissue development

Developed multi-scale computational models that connect gene and signaling networks to the cellular microenvironment (Davey FASEB 2007; Moledina PNAS USA 2012). We pioneered strategies for cell-cell interaction network modeling (Kirouac Mol Syst Biol 2010, 2011; Qiao Mol Syst Biol 2014; Yuzwa Neuron 2016) and developed statistical and computational approaches to simulate gene regulatory networks in heterogeneous cell populations (Varelas CELL 2008; Ng Nature 2016). This theoretical work, with our experimental methods, deepens our understanding of fundamental mechanisms that control stem cell fate.


Why Choose Us

We aim to yield new insights

into cell fate control in early human development, andtranslational technologies and novel approaches directly applicable to regenerative medicine, drugscreening, and cellular therapeutic strategies

We aim to develop cutting-edge technologies

that advance our understanding of stem cell developmental processes and that lead to the development of other technologies for the growth and differentiation of stem cells

We aim to understand the mechanisms of complex tissues

that develop from Stem Cells, and to use this understanding to advance new cell therapies and regenerative medicines