Create marker gene lists for tumor cell states in Ewing sarcoma

[allyhawkins]

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#696

Describe the goals of the changes to the analysis module.

We are hoping to annotate clusters of tumor cells in the Ewing sarcoma samples based on the tumor cell state. In order to do that, we need to obtain a list of expected cell states and associated gene sets or gene signatures with those cell states. Ewing sarcoma cells lie on a continuum based on their EWS-FLI1 expression. The level of EWS-FLI1 expression then alters the cell phenotype, so we can search for enrichment of specific phenotypes to classify cells into EWS-FLI1 high, middle/hybrid, and low. In my preliminary search, we should expect to see the following cell states present:

• EWS-FLI1 high: High expression/repression of EWS-FLI1 targets, High HIF1alpha activity, low EMT-like phenotype (low migration, adhesion), low ECM expression, low CD73 expression
• EWS-FLI1 low: Expression of EWS-FLI1 repressed genes, mesenchymal-like, high EMT-like phenotype (high migration, adhesion), increased ECM expression, high CD73 expression, high HOXD13 activity
• EWS-FLI1 middle/hybrid: Proliferative

What will your pull request contain?

To address this we should create a TSV file with all marker genes for all cell states we would consider. We should comb through the literature to identify possible cell states and any marker genes that have been published to be associated with those cell states.

Will you require additional software beyond what is already in the analysis module?

No, right now just creating the TSV file.

Will you require different computational resources beyond what the analysis module already uses?

No

If known, when do you expect to file the pull request?

January 2025