The clear cell sarcoma functional genomic landscape
Emanuele Panza, … , Mario R. Capecchi, Kevin B. Jones
Emanuele Panza, … , Mario R. Capecchi, Kevin B. Jones
Published June 22, 2021
Citation Information: J Clin Invest. 2021;131(15):e146301. https://doi.org/10.1172/JCI146301.
View: Text | PDF
Research Article Genetics Oncology

The clear cell sarcoma functional genomic landscape

Abstract

Clear cell sarcoma (CCS) is a deadly malignancy affecting adolescents and young adults. It is characterized by reciprocal translocations resulting in expression of the chimeric EWSR1-ATF1 or EWSR1-CREB1 fusion proteins, driving sarcomagenesis. Besides these characteristics, CCS has remained genomically uncharacterized. Copy number analysis of human CCSs showed frequent amplifications of the MITF locus and chromosomes 7 and 8. Few alterations were shared with Ewing sarcoma or desmoplastic, small round cell tumors, which are other EWSR1-rearranged tumors. Exome sequencing in mouse tumors generated by expression of EWSR1-ATF1 from the Rosa26 locus demonstrated no other repeated pathogenic variants. Additionally, we generated a new CCS mouse by Cre-loxP–induced chromosomal translocation between Ewsr1 and Atf1, resulting in copy number loss of chromosome 6 and chromosome 15 instability, including amplification of a portion syntenic to human chromosome 8, surrounding Myc. Additional experiments in the Rosa26 conditional model demonstrated that Mitf or Myc can contribute to sarcomagenesis. Copy number observations in human tumors and genetic experiments in mice rendered, for the first time to our knowledge, a functional landscape of the CCS genome. These data advance efforts to understand the biology of CCS using innovative models that will eventually allow us to validate preclinical therapies necessary to achieve longer and better survival for young patients with this disease.

Authors

Emanuele Panza, Benjamin B. Ozenberger, Krystal M. Straessler, Jared J. Barrott, Li Li, Yanliang Wang, Mingchao Xie, Anne Boulet, Simon W.A. Titen, Clinton C. Mason, Alexander J. Lazar, Li Ding, Mario R. Capecchi, Kevin B. Jones

×

Figure 5

Cre-mediated translocation model of clear cell sarcomagenesis mimics the transcriptome of the EWSR1-ATF1 expression model but has additional genome CNAs.

Options: View larger image (or click on image) Download as PowerPoint
Cre-mediated translocation model of clear cell sarcomagenesis mimics the...
(A) Graph of the RPM that aligned onto the human EWSR1-ATF1 fusion oncogene cDNA coding sequence expressed conditionally from the Rosa26 locus and from the HprtCre-induced translocation tumor. For reference, also noted are the RT-qPCR–calculated RPM levels of EWSR1-ATF1 expression from the human SU-CCS1 cell line and from 3 FFPE human CCS tumor specimens, using B2M as a control in the human samples and its average expression across the mouse samples to calculate an RPM estimate. (B) RPM alignments across the genomic sequence for Ewsr1 and Atf1, averaged across 8 translocation-generated tumors (dark blue) and 12 Rosa26-EA1 tumors (cyan), demonstrating overall lower expression (compared with cDNA expression in the EA1 tumors) and a reduced 3′ bias in the exons 3′ to the translocation point (arrow) of Ewsr1 relative to the same in Atf1 in the translocation-generated tumors, which may represent reduced expression of the exons 3′ to the translocation in Ewsr1 or increased expression of the exons 3′ to the translocation in Atf1. (C) PCA demonstrating relative clustering of 8 translocation-driven sarcomas with Rosa26-EA1–driven comparators, separate from the clusterings of other mouse cancer subtypes sequenced in the same batch as the EA1 tumors. SS, synovial sarcoma; OS, osteosarcoma; mel, melanoma. (D) Heatmap of the Pearson’s correlation distance between single-batch–sequenced transcriptomes of the Rosa26-EA1–driven (cyan diamonds) or HprtCre-induced translocation–driven (blue circles) sarcomas, as well as 1 control tissue sample. (E) PCA of the same transcriptomes as in D. (F) CNA analysis on 4 HprtCre-induced translocation tumors, using a low-read-depth whole-genome sequencing approach. The upper row shows higher-resolution images of chromosome 15 from the sequencing of each tumor, the middle row shows the CNAs across the entire genome, and lower row shows chromosome 11 from each.