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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 30, 2021 |
Title |
RNA-seq profiling of Ewing sarcoma cells after TRIM8 knockout and EWS/FLI over-expression |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Fusion-transcription factors (fusion-TFs) represent a class of driver oncoproteins that are difficult to therapeutically target. Recently, protein degradation has emerged as a strategy to target these challenging oncoproteins. The mechanisms that regulate fusion-TF stability, however, are generally unknown. Using CRISPR-Cas9 screening, we discovered tripartite motif- containing 8 (TRIM8) as an E3 ubiquitin ligase that ubiquitinates and degrades EWS/FLI, a driver fusion-TF in Ewing sarcoma. Moreover, we identified TRIM8 as a selective dependency in Ewing sarcoma compared to >700 other cancer cell lines. Mechanistically, TRIM8 knockout led to an increase in EWS/FLI protein levels that was not tolerated. EWS/FLI acts as a neomorphic substrate for TRIM8, defining the selective nature of the dependency. Our results demonstrate that fusion-TF protein stability is tightly regulated and highlight fusion-oncoprotein specific regulators as selective therapeutic targets. This study provides a tractable strategy to therapeutically exploit oncogene overdose in Ewing sarcoma and potentially other fusion-TF driven cancers.
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Overall design |
TC71 Ewing sarcoma cells engineered to express FKBP12F36V-HA-TRIM8 was treated with either DMSO control or dTAGV-1 for 24 hours to induce TRIM8 degradation. In addition, TC71 Ewing sarcoma cells engineered to express doxycycline-inducible EWS/FLI-HA was treated with either water control or doxycycline (500ng/mL) for 8 hours. Triplicates for all groups were used for paired-end RNA-sequencing.
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Contributor(s) |
Seong BA, Dharia NV, Lin S, Donovan KA, Chong S, Robichaud A, Conway A, Hamze A, Ross L, Alexe G, Adane B, Nabet B, Ferguson F, Stolte B, Wang EJ, Sun J, Darzacq X, Piccioni F, Gray NS, Fischer ES, Stegmaier K |
Citation(s) |
34329586 |
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Submission date |
May 11, 2020 |
Last update date |
Sep 29, 2021 |
Contact name |
Neekesh V. Dharia |
E-mail(s) |
neekeshdharia@gmail.com
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Organization name |
Dana-Farber Cancer Institute
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Department |
Pediatric Oncology
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Lab |
Kimberly Stegmaier
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Street address |
350 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 (12)
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Relations |
BioProject |
PRJNA631627 |
SRA |
SRP261076 |
Supplementary file |
Size |
Download |
File type/resource |
GSE150244_TRIM8_BN_DM_24h_DESeq2_DESeq2_LFC_apeglm.txt.gz |
607.0 Kb |
(ftp)(http) |
TXT |
GSE150244_TRIM8_BN_DM_24h_DESeq2_log2p1_tpm_data.txt.gz |
688.2 Kb |
(ftp)(http) |
TXT |
GSE150244_TRIM8_iEFdox_DESeq2_DESeq2_LFC_apeglm.txt.gz |
857.0 Kb |
(ftp)(http) |
TXT |
GSE150244_TRIM8_iEFdox_DESeq2_log2p1_tpm_data.txt.gz |
954.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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