Sarcoma represents a highly heterogeneous group of tumours. We report here the first unbiased and systematic search for gene fusions combined with unsupervised expression analysis of a series of 184 small round cell sarcomas. Fusion genes were detected in 59% of samples, with half of them being observed recurrently. We identified biologically homogeneous groups of tumours such as the CIC-fused (to DUX4, FOXO4 or NUTM1) and BCOR-rearranged (BCOR–CCNB3, BCOR–MAML3, ZC3H7B–BCOR, and BCOR internal duplication) tumour groups. VGLL2-fused tumours represented a more biologically and pathologically heterogeneous group. This study also refined the characteristics of some entities such as EWSR1–PATZ1 spindle cell sarcoma or FUS–NFATC2 bone tumours that are different from EWSR1–NFATC2 tumours and transcriptionally resemble CIC-fused tumour entities. We also describe a completely novel group of epithelioid and spindle-cell rhabdomyosarcomas characterized by EWSR1– or FUS–TFCP2 fusions. Finally, expression data identified some potentially new therapeutic targets or pathways. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
|path5053-sup-0001-SupInfo.pdfPDF document, 2.2 MB||
Figure S1. Constitution of the cohorts
Figure S2. Detailed unsupervised analyses
Figure S3. Details of VGLL2–NCOA2/CITED2, CIC–NUTM1, BCOR-ITD, and EWSR1–PATZ1 fusion points
Figure S4. Sequence of the fusion points and genes expressed in FET–TFCP2-positive tumours
Figure S5. Expression of the most specific gene for each tumor entity (with more than two samples)
|path5053-sup-0002-TableS1.xlsExcel spreadsheet, 29 KB||Table S1. List of the fusion genes routinely tested by RT-PCR at the Institut Curie Unité de Génétique Somatique|
|path5053-sup-0003-TableS2.xlsExcel spreadsheet, 76.5 KB||Table S2. Description of the samples from the three cohorts|
|path5053-sup-0004-TableS3.xlsExcel spreadsheet, 3.1 MB||Table S3. Differentially expressed genes in the BGA and supervised analyses and Gene ontology/GSEA enrichment for all sarcomas subtypes|
|path5053-sup-0005-TableS4.xlsExcel spreadsheet, 228.5 KB||Table S4. Differentially expressed genes and gene ontology enrichment for FUS–NFATC2-positive versus EWSR1–NFATC2-positive tumours|
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
- 1. Round cell sarcomas beyond Ewing: emerging entities. Histopathology 2014; 64: 26–37.
- 2, , , et al. The Ewing family of tumors – a subgroup of small-round-cell tumors defined by specific chimeric transcripts. N Engl J Med 1994; 331: 294–299.
- 3, , , et al. Identification of novel genes, SYT and SSX, involved in the t(X;18)(p11.2;q11.2) translocation found in human synovial sarcoma. Nat Genet 1994; 7: 502–508.
- 4, , , et al. Fusion of a fork head domain gene to PAX3 in the solid tumour alveolar rhabdomyosarcoma. Nat Genet 1993; 5: 230–235.
- 5, , , et al. Fusion between CIC and DUX4 up-regulates PEA3 family genes in Ewing-like sarcomas with t(4;19)(q35;q13) translocation. Hum Mol Genet 2006; 15: 2125–2137.
- 6, , , et al. The NFATc2 gene is involved in a novel cloned translocation in a Ewing sarcoma variant that couples its function in immunology to oncology. Clin Cancer Res 2009; 15: 2259–2268.
- 7, , , et al. A new subtype of bone sarcoma defined by BCOR–CCNB3 gene fusion. Nat Genet 2012; 44: 461–466.
- 8, , , et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol 2011; 7: e1001138.
- 9, , , et al. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics 2011; 27: 1922–1928.
- 10, , , et al. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 2016; 34: 525–527.
- 11, , . Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009; 37: 1–13.
- 12, . Visualizing high-dimensional data using t-SNE. J Mach Learn Res 2008; 9: 2579–2605.
- 13, , , et al. A molecular study of pediatric spindle and sclerosing rhabdomyosarcoma: identification of novel and recurrent VGLL2-related fusions in infantile cases. Am J Surg Pathol 2016; 40: 224–235.
- 14, , , et al. New brain tumor entities emerge from molecular classification of CNS-PNETs. Cell 2016; 164: 1060–1072.
- 15, , , et al. ETV4 is a useful marker for the diagnosis of CIC-rearranged undifferentiated round-cell sarcomas: a study of 127 cases including mimicking lesions. Mod Pathol 2016; 29: 1523–1531.
- 16, , , et al. Novel BCOR-MAML3 and ZC3H7B-BCOR gene fusions in undifferentiated small blue round cell sarcomas. Am J Surg Pathol 2016; 40: 433–442.
- 17, , , et al. Recurrent BCOR internal tandem duplication and YWHAE-NUTM2B fusions in soft tissue undifferentiated round cell sarcoma of infancy: overlapping genetic features with clear cell sarcoma of kidney. Am J Surg Pathol 2016; 40: 1009–1020.
- 18, , , et al. BCOR overexpression is a highly sensitive marker in round cell sarcomas with BCOR genetic abnormalities. Am J Surg Pathol 2016; 40: 1670–1678.
- 19, , , et al. Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney. Nat Commun 2015; 6: 8891.
- 20, , , et al. The genomic landscape of the Ewing sarcoma family of tumors reveals recurrent STAG2 mutation. PLoS Genet 2014; 10: e1004475.
- 21, , , et al. A novel zinc finger gene is fused to EWS in small round cell tumor. Oncogene 2000; 19: 3799–3804.
- 22, , , et al. Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology. Acta Neuropathol (Berl) 2016; 131: 833–845.
- 23, , , et al. Comprehensive genomic profiling of 282 pediatric low- and high-grade gliomas reveals genomic drivers, tumor mutational burden, and hypermutation signatures. Oncologist 2017; 22: 1478–1490.
- 24. Mechanisms of human lymphoid chromosomal translocations. Nat Rev Cancer 2016; 16: 387–398.
- 25, , , et al. RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6–RUNX1 acute lymphoblastic leukemia. Nat Genet 2014; 46: 116–125.
- 26, , , et al. PGBD5 promotes site-specific oncogenic mutations in human tumors. Nat Genet 2017; 49: 1005–1014.
- 27, , , et al. A novel CIC-FOXO4 gene fusion in undifferentiated small round cell sarcoma: a genetically distinct variant of Ewing-like sarcoma. Am J Surg Pathol 2014; 38: 1571–1576.
- 28, , , et al. ERK/p90RSK/14-3-3 signalling has an impact on expression of PEA3 Ets transcription factors via the transcriptional repressor capicúa. Biochem J 2011; 433: 515–525.
- 29, , , et al. ATXN1L, CIC, and ETS transcription factors modulate sensitivity to MAPK pathway inhibition. Cell Rep 2017; 18: 1543–1557.
- 30, , , et al. Inactivation of Capicua drives cancer metastasis. Nat Genet 2017; 49: 87–96.
- 31, , , et al. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. Mol Cell Biol 2006; 26: 6880–6889.
- 32, , , et al. Characterization of the genomic structure, chromosomal location, promoter, and development expression of the alpha-globin transcription factor CP2. J Biol Chem 1994; 269: 11663–11671.
- 33, , . Characterization of a family of related cellular transcription factors which can modulate human immunodeficiency virus type 1 transcription in vitro. Mol Cell Biol 1994; 14: 1776–1785.
- 34, . Lineage-specific and ubiquitous biological roles of the mammalian transcription factor LSF. Gene 2004; 343: 23–40.
- 35, , , et al. Transcription factor Late SV40 Factor (LSF) functions as an oncogene in hepatocellular carcinoma. Proc Natl Acad Sci U S A 2010; 107: 8357–8362.
- 36, , , et al. Small molecule inhibitors of Late SV40 Factor (LSF) abrogate hepatocellular carcinoma (HCC): evaluation using an endogenous HCC model. Oncotarget 2015; 6: 26266–26277.
- 37, , , et al. Transcription factor LSF (TFCP2) inhibits melanoma growth. Oncotarget 2016; 7: 2379–2390.
- 38, , , et al. Antiproliferative small-molecule inhibitors of transcription factor LSF reveal oncogene addiction to LSF in hepatocellular carcinoma. Proc Natl Acad Sci U S A 2012; 109: 4503–4508.
- 39, , , et al. Clinical effect of molecular methods in sarcoma diagnosis (GENSARC): a prospective, multicentre, observational study. Lancet Oncol 2016; 17: 532–538.