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Updated: May 24, 2025
Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
Published on: June 27, 2020
Single-Cell RNA Sequencing of Ewing Sarcoma Tumors Demonstrates Transcriptional Heterogeneity and Clonal Evolution
Andrew Goodspeed1,2, Avery Bodlak3, Alexis B Duffy4
1University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
Purpose:
Ewing sarcoma is the second most common bone cancer in children, accounting for 2% of pediatric cancer diagnoses. Patients who present with metastatic disease at the time of diagnosis have a dismal prognosis compared with the >70% 5-year survival of those with localized disease. Novel therapeutic approaches that can impact metastatic disease are desperately needed, as well as a deeper understanding of the heterogeneity of Ewing sarcoma tumors.
Experimental Design:
In this study, we utilized single-cell RNA sequencing to characterize the transcriptional landscape of primary Ewing sarcoma tumors and the surrounding tumor microenvironment in a cohort of seven untreated patients with Ewing sarcoma, as well as in circulating tumor cells (CTC). A potential CTC therapeutic target was evaluated through immunofluorescence of fixed CTCs from a separate cohort.
Results:
Primary tumor samples demonstrate a heterogeneous transcriptional landscape with several conserved gene expression programs, including those composed of genes related to proliferation and Ewing sarcoma gene targets, which were found to correlate with overall survival. Copy-number analysis identified subclonal evolution within patients prior to treatment. Analyses of the immune microenvironment reveal an immunosuppressive microenvironment with complex intercellular communication among the tumor and immune cells. Single-cell RNA sequencing and immunofluorescence of CTCs at the time of diagnosis identified TSPAN8 as a potential therapeutic target.
Conclusions:
Ewing sarcoma tumors demonstrate significant transcriptional heterogeneity as well as a complex immunosuppressive microenvironment. This work evaluates several proposed targets that warrant further exploration as novel therapeutic strategies.
Insights
This study reveals significant transcriptional heterogeneity and an immunosuppressive microenvironment in Ewing sarcoma tumors. TSPAN8 is identified as a potential therapeutic target for this pediatric cancer.
Area of Science:
- Oncology
- Genomics
- Immunology
Background:
- Ewing sarcoma is a rare but aggressive pediatric bone cancer.
- Metastatic disease at diagnosis significantly worsens patient prognosis.
- Understanding tumor heterogeneity and the microenvironment is crucial for developing new therapies.
Purpose of the Study:
- To characterize the transcriptional landscape of primary Ewing sarcoma tumors and their microenvironment using single-cell RNA sequencing.
- To investigate circulating tumor cells (CTCs) in Ewing sarcoma patients.
- To identify potential therapeutic targets for Ewing sarcoma.
Main Methods:
- Single-cell RNA sequencing of primary tumors and CTCs from seven untreated patients.
- Copy-number analysis to assess subclonal evolution.
- Immunofluorescence of CTCs to evaluate potential therapeutic targets.
Main Results:
- Ewing sarcoma tumors exhibit a heterogeneous transcriptional landscape with conserved gene expression programs linked to survival.
- Subclonal evolution was observed within tumors prior to treatment.
- An immunosuppressive tumor microenvironment with complex cell-cell communication was identified.
- TSPAN8 was identified as a potential therapeutic target on CTCs.
Conclusions:
- Ewing sarcoma tumors display significant transcriptional heterogeneity and a complex immunosuppressive microenvironment.
- The findings highlight TSPAN8 as a promising target for novel therapeutic strategies.
- Further research into these targets could lead to improved treatments for Ewing sarcoma.
