William Stanford

Tissue-specific stem cells are required developmentally to generate a tissue or organ in the fetus and for many tissues, they function to maintain tissue homeostasis during the lifetime of the individual. We are interested in understanding the molecular control of cell fate decisions in development and homeostasis to better understand human development and disease, particularly cancer as this disease is largely driven by aberrant activation of developmental pathways. We use an unbiased “systems” or “integrative” approach to build models of cell fate decisions which we then test using reductionist approaches like CRISPR-mediated genome engineering and gene knockouts. Because the epigenome integrates external signals such as growth factors as inputs into gene regulatory networks, much of our interest in recent years has revolved around epigenetic regulation of cell fate in development and disease. Our three primary projects at this time are:
   
1)    Modeling and therapeutic development for the rare lung tumour lymphangioleiomyomatosis (LAM) and related tuberous sclerosis complex (TSC) tumours such as brain tumours known as SEGAs. Because LAM tumours cannot be propagated outside of the patient, we have used reprogramming of patient cells into induced pluripotent stem cells and CRISPR-mediated genome engineering to a library of mutant pluripotent stem cells that we have differentiated into the affected lineages to model these cancers. We are the first lab to develop non-transformed human cell models of LAM. Together Molly Shoichet’s lab in Toronto, we have developed a lung-like 3D environment to grow these tumours and performed screens that have identified a drug family capable of specifically kill our LAM model cells. Current projects include translating these novel drug hits in vivo, teasing apart disease mechanisms and a CRISPR-based synthetic lethal screen of TSC2 null cells to identify new drug targets.

2)    The epigenetic control of hematopoietic stem cells (HSCs) and leukemic stem cells (LSCs). Using a combination of pluripotent stem cells, hematopoietic stem cells, and bone marrow cells from patients with acute myeloid leukemia (AML), we identified an epigenetic reader protein known as MTF2/PCL2 that recruits the Polycomb repressive complex 2 (PRC2) to regulatory sites in erythroid progenitors and an HSCs. We found that epigenetic repression of MTF2 in AML leads to epigenetic reprogramming of AML into therapy-resistant, aggressive disease, revealing a primary mechanism of refractory AML. Importantly, by drafting the gene regulatory network of MTF2 we found a therapeutic vulnerability in refractory AML, which is being tested by a phase 1b clinical trial. We are currently testing other therapeutic targets. We are exploring additional drivers of refractory AML and therapeutic vulnerabilities discovered from our gene regulatory network analyses and a CRISPR-based synthetic lethal screen.

3)    Defective epigenetic inheritance in vascular disease and aging. The transmission of epigenetic marks to daughter cells during replication, termed epigenetic inheritance, is critical for tissue homeostasis; epigenetic drift is the failure of epigenetic inheritance leading to altered epigenetic landscapes and a hallmark of cellular aging, chronic disease and oncogenesis. While this process is largely believed to be a random process, studying a rare premature aging disease known as progeria, we have found evidence that epigenetic inheritance is driven by the DNA damage response. We are using a variety of cutting edge techniques to model chromatin dynamics during vascular aging and epigenetic drift, and testing these models on cardiovascular disease patient samples.  

The focus of my laboratory is to understand and manipulate the behavior of pluripotent and somatic stem cells to understand mechanisms of human disease and develop novel therapeutics. Our research utilizes systems biology to tease apart cell behavior and pathophysiology. We often use pluripotent embryonic stem cells (ESCs) as a model stem cell system because they are easier to grow and manipulate in culture than somatic stem cells. In fact, pluripotent stem cells have become the “new yeast”, enabling researchers to analyze mammalian development at the transcriptome (mRNA & miRNA), proteome, methylome, etc. systems level. Of course, yeast do not encode miRNA so this is an critical difference supporting the use of human ESC research. Importantly, we are now combining these systems approaches to study human disease using induced pluripotent stem cells (iPSCs).  We believe such a systems genetics strategy will identify novel therapeutic targets and therapeutics for many diseases including cancer.  

This work complements our previous endeavors which focused extensively on using the mouse as a model for human disease and generated novel gene trap vectors and a resource of more than 23,000 sequence annotated gene trap mouse embryonic stem cell lines that represents mutations in more than 4500 unique genes as well as numerous targeted clones as part of the CMHD and NorCOMM resources (http://www.norcomm.org/index.htm). This resource is freely available to academic researchers as part of the international mouse knockout project.