Human embryonic stem cells (hESCs) provide an excellent model system for studying cellular differentiation and human development. These cells can give rise to cell types from all three germ layers, with numerous protocols for cell-specific populations. However, this system has been under-utilized to determine the effects of the environment, specifically regarding exposure to toxic agents that can have a detrimental effect. Here hESCs will be used to determine how polycyclic aromatic hydrocarbons (PAHs) alter the epigenome of hESCs and ESC-derived neural progenitor cells (NPCs) and if this in turn affects their differentiation capacity. As proof of principle the focus will be on the widely studied 7,8 dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene or BPDE. BPDE is known to form DNA adducts that can lead to mutational changes, but additional evidence has shown that such adducts are often targeted to methylated CpGs. As has been previously demonstrated, hESCs have very unique epigenomes through the global mapping and analysis of histone modifications and DNA methylation. It was determined that cytosine methylation patterns change in response to different concentrations of BPDE. Therefore, the intent here is to examine if exposure has a detrimental effect on the ability of hESCs and NPCs to differentiate, with regards to timing or efficiency of lineage specification. In addition, it is important to determine the specific genomic sites of BPDE-DNA adducts. Expertise in ChIP-seq will be leveraged to develop a global identification method of these adducts using antibodies against BPDE-DNA.
The investigators will establish human embryonic stem cells and neural progenitor cells as a system for determining the environmental epigenomic effects on these progenitor populations by exposure to the polycyclic aromatic hydrocarbon BPDE. They will determine if this affects the differentiation capacity and results in changes to global DNA methylation. The investigators will also develop a method to determine the genome-wide location of DNA adducts caused by BPDE, called BPDE-DNA-seq.