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| Status |
Public on Jun 28, 2022 |
| Title |
EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma [CITE-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Posterior homeobox D genes, in particular HOXD13, are over-expressed by Ewing sarcoma, a tumor driven by the oncogenic fusion protein EWS-FLI1. Here, we have found that EWS-FLI1 maintains HOXD13 expression through a GGAA microsatellite enhancer in the developmental posterior HOXD regulatory domain. Activation of this enhancer is EWS-FLI1 dependent and epigenomic silencing of this region leads to loss of HOXD13 expression in Ewing sarcoma cells, but not in unrelated cells. To determine the function of HOXD13 activation in Ewing sarcoma we performed nascent RNA sequencing upon HOXD13 knockdown. We identified NT5E as a target induced by HOXD13. NT5E encodes for the cell surface marker CD73, so we used CITE-seq to profile these cells.
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| Overall design |
A673 and CHLA10 cells were labeled with an CD73-ADT antibody and a unique HTO antibody for 30 min at 4C. Cells were washed, counted and pooled at 1000 cells/uL. Libraries were prepared and sequenced by the University of Michigan Advanced Genomics core using the 10X genomics platform. Libraries generated using the 3’ V3 10X Genomics Chromium Controller following the manufacturer’s protocol (CG000183) and then paired end sequencing was ran on the NovaSeq 6000. Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger (3.1) Pipeline (10X Genomics) was used to align reads and generate count matrices.
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| Contributor(s) |
Apfelbaum A, Furlan S, Lawlor E |
| Citation(s) |
35653119 |
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| Submission date |
Feb 02, 2021 |
| Last update date |
Jul 01, 2022 |
| Contact name |
April Apfelbaum |
| E-mail(s) |
april_apfelbaum@dfci.harvard.edu
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| Organization name |
Dana-farber Cancer Institute
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| Department |
Pediatric Oncology
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| Lab |
Bandopadhayay Lab
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| Street address |
450 Brookline Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE182513 |
EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma |
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| Relations |
| BioProject |
PRJNA698816 |
| SRA |
SRP304255 |
