Project Details
Description
Abstract
Ewing sarcoma survival has not improved in decades despite long knowledge of its singular driving somatic
mutation, the pernicious EWS-FLI1 fusion oncoprotein. As an aberrant transcription factor EWS-FLI1 alters
expression of thousands of genes enacting a complex program toxic to most cell types, so much so that the cell
of origin for Ewing sarcoma is still a matter of debate. Ewing sarcoma occurs at starkly higher rates (roughly 10-
fold) in children of European ancestry compared to those with primarily African ancestry, while Latino children
have roughly ⅔ and Asian children ½ the risk of Ewing sarcoma than do white children. Ancestry is in fact the
strongest known risk factor for Ewing sarcoma, but the molecular basis of these differences in risk have been
investigated only sparingly. As the mechanisms by which EWS-FLI1 interacts with the genome have become
clear, it is feasible with an appropriate model to investigate how genomic ancestry in general and at specific loci
modulates EWS-FLI1 activity including its downstream effects on epigenetic and transcriptional programs. To
this end we have devised a strategy to introduce EWS-FLI1 in derivatives of induced pluripotent stem cells (iPSC)
in order to characterize downstream molecular and functional consequences of EWS-FLI1 expression. Using
accessible variant array data from several large stem cell repositories we identified banked iPSC lines derived
from individuals with a range of European, African, and Amerind ancestry. We will introduce EWS-FLI1
expression at intermediate stages of development relevant to Ewing sarcomagenesis—namely neural crest cells
and mesenchymal stem cells. Measures of functional tolerance and molecular state will be compared to
corresponding samples from subjects with solely European ancestry. Globally we will examine whether gene
expression and chromatin state exhibits similarity to the Ewing expression signature in proportion to European
ancestry percentage. Genome-wide chromatin occupancy of EWS-FLI1 will be profiled and its relationship to
local ancestry defined using long-read sequencing. Genes that are differentially influenced by EWS-FLI1 in
“permissive” (European ancestry), “moderately permissive” (Amerind ancestry) and “impermissive” (African
ancestry) genomes will be considered targets of potential therapeutic value and will undergo validation using
CRISPR/Cas9 genome engineering and functional assays. The resulting data will represent the first and only
effort, to our knowledge, to take advantage of the known differences in risk for Ewing sarcoma by ancestry to
study EWS-FLI1 binding and downstream effects. In addition, we will make available the genome-scale data
produced by our study and freely distribute our iPSC models for wider use by Ewing sarcoma researchers.
Status | Finished |
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Effective start/end date | 4/7/23 → 3/31/24 |
Funding
- National Cancer Institute: $625,106.00
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