MDPI Cancers Magazine – Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility (Bishop Lab)


by  Henry E. Miller 1,2, Aparna Gorthi 1,2, Nicklas Bassani 2, Liesl A. Lawrence 1,2, Brian S. Iskra 1,2 and Alexander J. R. Bishop 1,2,*

This study aims at defining the features of the cell of origin for Ewing sarcoma through comparative bioinformatics analysis of normal tissues with Ewing sarcoma. Key findings are that the EWSR1-FLI1 “genesets” are really indicators of a normal developmental trajectory from pluripotent stem cell to more differentiated mesoderm and with expression of EWSR1-FLI1, Ewing sarcoma cells are kept in a more pluripotent state that normally activates R-loop resolving processes such as Fanconi anemia pathway and FEN1.


Ewing sarcoma is an aggressive pediatric cancer of enigmatic cellular origins typically resulting from a single translocation event t (11; 22) (q24; q12). The resulting fusion gene, EWSR1-FLI1, is toxic or unstable in most primary tissues. Consequently, attempts to model Ewing sarcomagenesis have proven unsuccessful thus far, highlighting the need to identify the cellular features which permit stable EWSR1-FLI1 expression. By re-analyzing publicly available RNA-Sequencing data with manifold learning techniques, we uncovered a group of Ewing-like tissues belonging to a developmental trajectory between pluripotent, neuroectodermal, and mesodermal cell states. Furthermore, we demonstrated that EWSR1-FLI1 expression levels control the activation of these developmental trajectories within Ewing sarcoma cells. Subsequent analysis and experimental validation demonstrated that the capability to resolve R-loops and mitigate replication stress are probable prerequisites for stable EWSR1-FLI1 expression in primary tissues. Taken together, our results demonstrate how EWSR1-FLI1 hijacks developmental gene programs and advances our understanding of Ewing sarcomagenesis.

Keywords: Ewing sarcoma; EWSR1-FLI1; transcriptomics; manifold learning; single-cell biology; R-loops; replication stress; sarcomagenesis; developmental trajectories; cell identity

Video: 3D PHATE reveals Ewing sarcoma’s developmental context 

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Please note: Brian S. Iskra 1,2 is an MD/Ph.D. student and member in the Gregory J. Aune MD/Ph.D Lab


1. Department of Cell Systems and Anatomy, The University of Texas Health at San Antonio, San Antonio, TX 78229, USA
2. Greehey Children’s Cancer Research Institute, The University of Texas Health at San Antonio, San Antonio, TX 78229, USA
*  Author to whom correspondence should be addressed.

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