We are interested in understanding how individual cells form complex tissues and organs. Our foundational hypothesis is that multi-scale interactions between cells, their internal regulatory networks, and the external microenvironment shape cell fate and functional tissue development. 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. Our goal is to simulate, manipulate and prospectively control these networks to reveal fundamental new rules that govern organogenesis and to accelerate progress to regenerative therapeutics, with an emphasis on the blood-forming system. Our research program is based on four pillars:

1. Multi-scale simulation of human tissue- and organo-genesis:
Understanding de novo blood development requires connecting stem cell regulatory networks to blood-forming multi-cellular niches and functional blood cells. We lead the stem cell field in developing mathematical models of the intracellular signaling networks that regulate pluripotency and early mesoderm differentiation. We have pioneered the development of intercellular (between cell) simulation networks, particularly with respect to hematopoiesis. Recently, we have directed our efforts to gene regulatory network (GRN) inference and simulation strategies. We are developing new and more predictive Boolean modeling, graph theory-based and other approaches to simulate the GRN responses of pluripotent stem cells (PSCs) and blood stem cells to microenvironmentally coded input signals, and link these responses to stem cell fate transitions. We are extending our expertise in normal blood development to leukemogenesis to identify key intracellular and intercellular nodes that differentially target leukemia-initiating cells and environments. We are building models that connect single cell GRNs (normal, aberrant or engineered) and the cellular microenvironment to dynamic cell and tissue development. Our new capabilities in agent-based multicellular modeling (being developed by PDF Himanshu Kaul) add further innovation to these efforts.


2. Synthetic cells for regenerative medicine:

Current directed stem cell differentiation protocols use cytokine and small molecule supplementation to mimic in vivo environments and developmental events. For example PSC-derived blood development typically involves directing cells into mesoderm, hemogenic endothelium (HE) and blood progenitor cells, with heterogeneous outputs and yields at each stage. We have used reporter PSC lines to analyze and enrich for different stages of blood development, however recent advances in synthetic gene networks represent an exciting opportunity to engineer detection, selection and control of functional tissue development from PSCs. One example synthetic framework we are implementing in PSCs, termed bow-tie (developed by PDF Laura Prochazka), allows recognition of multiple input molecules (endogenous cell-specific miRNA), integration of these signals in AND-like logic functions, and production of user-selected multiple output molecules (e.g. mCherry to turn the network into a sensor, or specific genes to modify the stem cell GRN and cell fate). This strategy will be applied to PSC-derived blood differentiation and T-cell development in hPSC platform lines that can be shared as a community resource.


3. Synthetic niches to guide human tissue- and organo-genesis:
We have pioneered the use of synthetic stem cell niche engineering strategies to impose strict control of extracellular signaling, spatial organization and cell interactions on blood and pluripotent stem cells. Established capabilities include 2D hPSC micropatterning to study gastrulation-like events and hemogenic endothelium (HE) induction to definitive blood, as well as controlled 3D cell organization to promote hPSC differentiation to HE and guide hydrogel-mediated progenitor T (Pro-T) cell development. Similarly, we continue to advance systems to monitor and control the concentration, timing and identity of molecules that promote and inhibit blood stem cell expansion to maximize yields or guide differentiation. Currently, we are advancing our stem cell niche engineering capabilities by controlling the spatial organization of multiple cell types, as well as their temporally-modulated exposure to exogenous signals. For example, in 2D we are developing technologies to dynamically pattern surfaces and allow spatial positioning of multiple cell types, while in 3D systems we are working on using functionalized hydrogel bio-printing to model specific stages of embryonic development and blood cell emergence.


4. New therapeutics for blood disease:
Transplantation of blood stem cells is in routine clinical use, yet limited availability and variable quality of donor tissue prevent the wider application of this cell-based therapy. Blood stem cell-derived T-cells typically appear as late as nine months after transplantation and take over a year to completely restore the polyclonal repertoire. This post-transplant T-cell deficiency is associated with an increased risk for opportunistic infections and graft failure. A key strength of our program is our ability to leverage both cord blood- and hPSC-derived blood development to advance RM and cancer therapeutics. We have already launched, with Excellthera, a phase I/II clinical trial for the treatment of blood cancers using blood stem cell expansion technologies developed in our lab. This expertise is enabling new applications using blood stem cells, such as pro-T cell generation for cancer and infectious disease immunotherapy. For example, using our niche engineering platform (Pillar 3) we have developed an artificial thymus-like niche capable of presenting new ligand combinations to blood SC to induce pro-T cells under clinically relevant conditions. Translation of our protocols we develop in Pillars 1-3 will focus on generating the pre-clinical data that demonstrates the utility of normal and engineered PSC–derived blood cells in animal models of disease, as well as the effectiveness of our engineered blood stem cells and thymic niches to improve blood stem cell transplants and enhance in vivo pro-T cell yields. In addition, we will apply our computational pipeline (Pillar 1) to develop clinical assays for therapeutic stratification of blood cancer patient conditioning regimes.