Cell-type dependent enhancer binding of the EWS/ATF1 fusion gene in clear cell sarcomas

Shingo Komura,Takatoshi Ohno,K Hashimoto ,Kenichi Sekiguchi ,Tomoyo Ukai,Junya Toguchida,Kenji Ito,Katsuji Shimizu,Hirofumi Shibata,Katsunori Semi,Yutaka Matsuda,Sho Ohta,Knut Woltjen,Mio Kabata,Manabu Ozawa,Haruhiko Akiyama,Fumiaki Itakura,Takuya Yamamoto,Masamitsu Sone,Norihide Jo,Yoshihiko Yamada

doi:10.1038/s41467-019-11745-1

Abstract

Clear cell sarcoma (CCS) is a rare soft tissue sarcoma caused by the EWS/ATF1 fusion gene. Here, we established induced pluripotent stem cells (iPSCs) from EWS/ATF1-controllable murine CCS cells harboring sarcoma-associated genetic abnormalities. Sarcoma-iPSC mice develop secondary sarcomas immediately after EWS/ATF1 induction, but only in soft tissue. EWS/ATF1 expression induces oncogene-induced senescence in most cell types in sarcoma-iPSC mice but prevents it in sarcoma cells. We identify Tppp3-expressing cells in peripheral nerves as a cell-of-origin for these sarcomas. We show cell type-specific recruitment of EWS/ATF1 to enhancer regions in CCS cells. Finally, epigenetic silencing at these enhancers induces senescence and inhibits CCS cell growth through altered EWS/ATF1 binding. Together, we propose that distinct responses to premature senescence are the basis for the cell type-specificity of cancer development.

Highlights

Clear cell sarcoma (CCS) is a rare soft tissue sarcoma caused by the EWS/ATF1 fusion gene
To establish induced pluripotent stem cells (iPSCs), we introduced OCT3/4, SOX2, KLF4 and cMYC into a murine CCS cell line (G1297) containing doxycycline (Dox)-controllable EWS/ATF1 alleles9. iPSC-like colonies were picked up to establish iPSC-like cell lines (Fig. 1a)
Taking advantage of the model, we here propose that Tppp3-expressing neural crest-derived cells are a cell of origin for mouse CCS cells and epigenetic regulation at the cell of origin affects the binding patterns of a key driver oncogenic protein, which leads to the establishment of a sarcoma-specific super-enhancer

Summary

Introduction

Clear cell sarcoma (CCS) is a rare soft tissue sarcoma caused by the EWS/ATF1 fusion gene. Given that epigenetic regulations play a central role in differentiation and cell fate maintenance, these findings suggest that a coordinated action of the cancer genome and cellular context-dependent epigenetic regulations is required for cancer development. We establish induced pluripotent stem cells (iPSCs) from murine CCS cell lines that harbor sarcomaassociated genetic abnormalities and differentiate them into a wide variety of cell types in vivo via the generation of chimeric mice. Utilizing the one-step and cell-type-specific sarcoma model, we identify Tppp3-expressing peripheral nerve cell as a cell type that gives rise to CCSs and demonstrate that cellular context-dependent epigenetic regulations, in conjunction with genetic abnormalities, play a fundamental role in the maintenance of the malignant phenotype and can be a therapeutic target in sarcoma cells

Methods

Results

Conclusion