ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours

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Abstract

Gastrointestinal stromal tumour (GIST) is the most common human sarcoma and is primarily defined by activating mutations in the KIT or PDGFRA receptor tyrosine kinases1,2. KIT is highly expressed in interstitial cells of Cajal (ICCs)—the presumed cell of origin for GIST—as well as in haematopoietic stem cells, melanocytes, mast cells and germ cells2,3. Yet, families harbouring germline activating KIT mutations and mice with knock-in Kit mutations almost exclusively develop ICC hyperplasia and GIST4,5,6,7, suggesting that the cellular context is important for KIT to mediate oncogenesis. Here we show that the ETS family member ETV1 is highly expressed in the subtypes of ICCs sensitive to oncogenic KIT mediated transformation8, and is required for their development. In addition, ETV1 is universally highly expressed in GISTs and is required for growth of imatinib-sensitive and resistant GIST cell lines. Transcriptome profiling and global analyses of ETV1-binding sites suggest that ETV1 is a master regulator of an ICC-GIST-specific transcription network mainly through enhancer binding. The ETV1 transcriptional program is further regulated by activated KIT, which prolongs ETV1 protein stability and cooperates with ETV1 to promote tumorigenesis. We propose that GIST arises from ICCs with high levels of endogenous ETV1 expression that, when coupled with an activating KIT mutation, drives an oncogenic ETS transcriptional program. This differs from other ETS-dependent tumours such as prostate cancer, melanoma and Ewing sarcoma where genomic translocation or amplification drives aberrant ETS expression9,10,11. It also represents a novel mechanism of oncogenic transcription factor activation.

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Figure 1: ETV1 is universally highly expressed and required for tumour growth and survival in GIST.
Figure 2: Etv1 is expressed in the subtypes of ICCs susceptible to oncogenesis and is required for their development.
Figure 3: ETV1 regulates GIST-signature genes predominantly through enhancer binding.
Figure 4: KIT signalling synergizes with ETV1 in GIST tumorigenesis by stabilization of ETV1 protein.

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Primary accessions

Gene Expression Omnibus

Data deposits

All microarray and ChIP-Seq data are deposited in Gene Expression Omnibus under accession number GSE22852.

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Acknowledgements

This work was supported in part by the National Cancer Institute (K08CA140946, to Y.C.), (5F32CA130372, to P.C.), (CA47179, to C.R.A. and R.G.M.), (CA148260, to R.G.M.), US National Institute of Mental Health (R21MH087840, to D.Z.), National Cancer Institute–American Society of Clinical Oncology Cancer Foundation Clinical Investigator Team Leadership Supplemental Award (to R.G.M.), American Society of Clinical Oncology Young Investigator Award (to P.C.), the Doris Duke (to C.L.S.), Charles H Revson (to Y.C.) and Charles A. Dana (to Y.C.) foundations, The Rockefeller University Fund (to C.D.A.), American Cancer Society Mentored Research Scholar Grant CCE-106841 (to C.R.A.), P01CA47179 (to C.R.A. and R.G.M.), the Life Raft Group (to C.R.A.), the GIST Cancer Research Fund (to C.R.A.), the Shuman Family Fund for GIST Research (to P.C., C.R.A. and R.G.M.), Cycle for Survival (to R.G.M.), Startup Funds from the Albert Einstein College of Medicine (to D.Z.), National Institutes of Health (GM40922, to C.D.A.) and the Starr Cancer Consortium (to P.C., Y.C., C.L.S. and C.D.A.). We thank the International Genomics Consortium for generating ExpO data. We thank G. Wang, P. Iaquinta, and H. Hieronymus for discussions, and especially T. M. Jessell and J. N. Betley for providing and breeding Etv1−/− mice.

Author information

Author contributions P.C., Y.C., C.D.A. and C.L.S. designed the experiments. R.G.M. and C.R.A. provided advice about experimental design. P.C. and Y.C. performed most of the experiments, including data mining, data analysis, tissue culture experiments, tissue processing, immunofluorescence microscopy, colony formation assays and ChIP-Seq experiments. J.W. and T.S. performed xenograft and some qRT-PCR experiments. L.Z. and C.R.A. provided human tumour samples and performed fluorescence in situ hybridization and immunohistochemistry on them. S.D. performed the Solexa sequencing and genomic alignment, and X.G. and D.Z. analysed ChIP-Seq data. J.A.F. provided key experimental reagents. P.C., Y.C., C.D.A. and C.L.S. wrote the manuscript. All authors discussed results and edited the manuscript.

Correspondence to C. David Allis or Charles L. Sawyers.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-17 with legends. (PDF 14059 kb)

Supplementary Table 1

This table shows a complete gene lists of three GIST-signature gene sets and ICC-MY and ICC-DMP-signature gene sets. Probe ID, gene symbol, average Z-score of expression, and Z-score difference are shown. (XLS 81 kb)

Supplementary Table 2

This table shows gene sets with FDR < 0.25 for overrepresented among downregulated by ETV1 knockdown by GSEA - gene set name, size, enrichment score, normalized enrichment score, p-value, and FDR are shown. (XLS 47 kb)

Supplementary Movie 1

Whole Mount Reconstruction of Kit IF in Etv1+/+ Large Intestine - the movie focuses from the ICC-MY layer through the ICC-IM layer, ending with the ICC-SMP layer. Image is 176x132 μm. (MOV 284 kb)

Supplementary Movie 2

Whole Mount Reconstruction of Kit IF in Etv1-/- Large Intestine ? the movie focuses from the ICC-MY layer through the ICC-IM layer, ending with the ICC-SMP layer. Image is 176x132 μm. (MOV 81 kb)

Supplementary Movie 3

Whole Mount Reconstruction of Kit IF in Etv1+/+ Small Intestine ? the movie focuses from the ICC-MY layer into the ICC-DMP layer. Image is 59x44 μm. (MOV 81 kb)

Supplementary Movie 4

Whole Mount Reconstruction of Kit IF in Etv1-/- Small Intestine - the movie focuses from the ICC-MY layer into the ICC-DMP layer. Image is 59x44 μm. (MOV 25 kb)

Supplementary Movie 5

Whole Mount Reconstruction of Kit IF in Etv1+/+ Cecum - the movie focuses from the ICC-MY layer into the ICC-IM layer. Image is 176x132 μm. (MOV 124 kb)

Supplementary Movie 6

Whole Mount Reconstruction of Kit IF in Etv1-/- Cecum. Movie focuses from the ICC-MY layer into the ICC-IM layer. Image is 176x132 μm. (MOV 26 kb)

Supplementary Movie 7

Whole Mount Reconstruction of Kit IF in Etv1+/+ Gastric Fundus. Movie focuses from the outer longitudinal intramuscular ICC layer into the inner circular intramuscular ICC layer. Image is 176x132 μm. (MOV 104 kb)

Supplementary Movie 8

Whole Mount Reconstruction of Kit IF in Etv1-/- Gastric Fundus. Movie focuses from the outer longitudinal intramuscular ICC layer into the inner circular intramuscular ICC layer. Image is 176x132 μm. (MOV 45 kb)

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Chi, P., Chen, Y., Zhang, L. et al. ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature 467, 849–853 (2010) doi:10.1038/nature09409

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