Research in the Morris Lab
An overview of our research
Cell fate is flexible
The generation of clinically relevant cells, such as neurons, cardiomyocytes, and hepatocytes, in vitro offers potential for regenerative therapy and permits disease modeling, toxicology testing and drug discovery. Cell differentiation had long been thought a unidirectional process toward restricted potential and increased specialization. In the past half-century this has been challenged: Mature somatic cells can be returned to a pluripotent state, and subsequently differentiated to desired cell types. Alternatively, mature cells can be ‘directly converted’ from one mature state to another via transcription factor overexpression, bypassing pluripotency. Many approaches are employed to generate defined fate in vitro, however the resultant cells often appear developmentally immature or incompletely specified, limiting their utility.
Challenges of engineering cell fate
The evaluation of cell fate has been confounded the the lack of any systematic means by which to assess the fidelity of engineered cells. We were involved in the development of ‘CellNet’, a network biology-based computational platform that accurately evaluates cell fate through gene regulatory network reconstruction and generates hypotheses for improving cell differentiation protocols (see Cahan et al., Cell 2014, and Morris et al., Cell 2014). Using this platform we surveyed a range of engineered cells and found that cells derived via directed differentiation more faithfully recapitulated target cell identity than cells generated by direct conversion. These directly converted cells commonly failed to silence expression programs of the original cell type, and illicit gene expression programs were frequently induced. Employing induced hepatocytes (iHeps) generated from fibroblasts as a prototypical conversion, our computational and functional analyses showed that iHeps behave as embryonic progenitors with the potential to functionally engraft both the liver and colon. We found that these engineered cells resembled mature colonic epithelium only after transplantation into the colon niche.
Major themes of the Morris Lab
Our research centers on the study of gene regulatory networks to dissect and engineer cell fate of clinically relevant tissues such as the liver. This focus integrates three major themes: First, we aim to understand how transcription factor overexpression drives changes in the transcriptional program to remodel cell identity, and how we can exploit this to derive desired cell types. Second, we transplant engineered cells into the in vivo niche, tracking their maturation in order to understand the steps required to fully differentiate cells in vitro. Finally, we employ single cell transcriptomics to understand how cell fate is specified in the developing embryo, formulating a blueprint of cell identity to help engineer fate in vitro. Ultimately, we wish to translate new insights in cell fate specification into better human models of gastrointestinal disease and eventually into the development of novel therapeutic strategies.
See below for more information on the themes of the Morris Lab.
Mapping the Transcriptional Landscape of Development
Our analyses using CellNet in combination with functional studies of fibroblasts converted to induced hepatocytes (iHeps) showed that these converted cells behave as embryonic progenitors with the potential to functionally engraft both the liver and colon. This is supported by many examples suggesting that engineered cells are developmentally immature. CellNet-guided efforts to enhance hepatic identity of iHeps have met with only moderate success, potentially because the engineered cells are several differentiation steps removed from adult liver, our only reference at present. It is currently unknown if, and how our engineered cells relate to any populations in the developing embryo.
To address this, we are applying high-throughput single cell RNA sequencing to the developing mouse endoderm. Through this approach, we will map the transcriptional landscape of endoderm ontogeny. GRN reconstruction of defined populations at defined stages will act as a roadmap to assist in the assessment and maturation of iHeps, and will also facilitate the differentiation of hepatocytes generated from embryonic stem cells in vitro. Furthermore, we hope to uncover and characterize unique progenitor populations in the developing embryo. In addition to utilizing the mouse as a model system, we are now also moving into human systems with the intent to generate better models of liver development and disease in order to develop novel therapeutic strategies.
Cell fate engineering: manipulating gene regulatory networks
Cells produced both by directed differentiation and direct conversion are immature. Our previous computational and functional analyses demonstrated that in almost all fate conversions employing transcription factor overexpression, gene regulatory networks (GRNs) of alternate lineages are specified, compromising desired functions of the engineered cells. This was particularly evident in the conversion of fibroblasts to induced hepatocytes (iHeps), where the generated cells possessed both hepatic and intestinal potential. We are investigating how the transcription factors utilized in these conversion protocols impact the GRN of the host cell to drive changes in cell identity. We are particularly interested in pioneer factors, capable of remodeling chromatin and often re-purposed during development. To study the mechanism of conversion we use a combination of transcriptional, epigenetic, and functional analyses. This understanding will help us guide the activity of conversion factors and unlock further progenitor potential of engineered cells. In addition, this line of investigation will be broadly applicable to the cell fate engineering field and may also shed light on the activity of transcription factors during development.
Regeneration as a guide for cell fate maturation
Our earlier studies have demonstrated that iHeps cultured in vitro possess partial hepatic and intestinal fate. We went on to show that iHeps have intestinal potential and can functionally engraft a mouse model of acute colitis. After 12 days in the colon niche, recovered iHeps were almost indistinguishable from native colonic epithelium. This maturation of engineered hepatocytes following transplantation suggests that full potential can be unlocked from engineered cells. We are tracking the maturation of iHeps in the liver and colon at the single cell level following transplantation. Mapping these in vivo differentiation steps will help guide maturation in vitro and also assist in identifying factors to promote liver repopulation and maturation. This line of investigation will aid in answering important questions about silencing of the donor cell program and establishment of the target cell GRNs.