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TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma.

Cancer cell | 2021

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 with >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.

Pubmed ID: 34329586 RIS Download

Associated grants

  • Agency: NCI NIH HHS, United States
    Id: R01 CA204915
  • Agency: NCI NIH HHS, United States
    Id: R35 CA210030
  • Agency: NCI NIH HHS, United States
    Id: U54 CA231637
  • Agency: NCI NIH HHS, United States
    Id: U54 CA231641

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This is a list of tools and resources that we have found mentioned in this publication.


Gene Set Enrichment Analysis (tool)

RRID:SCR_003199

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

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Novus Biologicals (tool)

RRID:SCR_004286

Commercial antibody vendor which supplies antibodies and other products to life science researchers.

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STAR (tool)

RRID:SCR_004463

Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.

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Bioconductor (tool)

RRID:SCR_006442

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

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Subread (tool)

RRID:SCR_009803

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

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LIMMA (tool)

RRID:SCR_010943

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

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featureCounts (tool)

RRID:SCR_012919

A read summarization program, which counts mapped reads for the genomic features such as genes and exons.

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BD Biosciences (tool)

RRID:SCR_013311

An Antibody supplier

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New England Biolabs (tool)

RRID:SCR_013517

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FastQC (tool)

RRID:SCR_014583

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

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MultiQC (tool)

RRID:SCR_014982

Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.

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DESeq2 (tool)

RRID:SCR_015687

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

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Microsoft Excel (tool)

RRID:SCR_016137

Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.

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SARTools (tool)

RRID:SCR_016533

Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.

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clusterProfiler (tool)

RRID:SCR_016884

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

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Cancer Dependency Map Portal (tool)

RRID:SCR_017655

Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication.

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TC-71 (tool)

RRID:CVCL_2213

Cell line TC-71 is a Cancer cell line with a species of origin Homo sapiens (Human)

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A-673 (tool)

RRID:CVCL_0080

Cell line A-673 is a Cancer cell line with a species of origin Homo sapiens (Human)

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HEK293T (tool)

RRID:CVCL_0063

Cell line HEK293T is a Transformed cell line with a species of origin Homo sapiens (Human)

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HEK293T (tool)

RRID:CVCL_0063

Cell line HEK293T is a Transformed cell line with a species of origin Homo sapiens (Human)

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U-937 (tool)

RRID:CVCL_0007

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HA-Tag (C29F4) Rabbit mAb (antibody)

RRID:AB_1549585

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RRID:AB_675526

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RRID:AB_2716558

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TRIM8 Antibody (B-3) (antibody)

RRID:AB_2889167

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anti-ERG (A7L1G) (antibody)

RRID:AB_2721841

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GFP Antibody (antibody)

RRID:AB_10692764

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V5-Tag (D3H8Q) Rabbit Antibody (antibody)

RRID:AB_2687461

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β-Actin (E4D9Z) (antibody)

RRID:AB_2750839

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RRID:AB_10699459

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HA-Tag (6E2) Mouse mAb (antibody)

RRID:AB_10691311

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FLI1 antibody - ChIP Grade (antibody)

RRID:AB_301825

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Anti-Nkx2.2 antibody [NX2/294] (antibody)

RRID:AB_2889166

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Proteome Discoverer (software resource)

RRID:SCR_014477

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Crl:NU-Foxn1nu (organism)

RRID:IMSR_CRL:088

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NOD.Cg-Prkdcscid Il2rg/SzJ (organism)

RRID:IMSR_JAX:005557

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