Chow et al. BMC Medical Genetics (2020) 21:101 https://doi.org/10.1186/s12881-020-01034-w RESEARCH ARTICLE Open Access Recurrent secondary genomic alterations in desmoplastic small round cell tumors Warren A. Chow1* , Jiing-Kuan Yee2, Walter Tsark3, Xiwei Wu4, Hanjun Qin4, Min Guan1, Jeffrey S. Ross5,6, Siraj M. Ali5 and Sherri Z. Millis5 Abstract Background: Desmoplastic small round cell tumor (DSRCT) is a rare, highly aggressive, translocation-associated soft- tissue sarcoma that primarily affects children, adolescents, and young adults, with a striking male predominance. It is characterized by t(11;22) generating a novel EWSR1-WT1 fusion gene. Secondary genomic alterations are rarely described. Methods: Tumor tissue from 83 DSRCT patients was assayed by hybrid-capture based comprehensive genomic profiling, FoundationOne® Heme next generation sequencing analysis of 406 genes and RNA sequencing of 265 genes. Tumor mutation burden was calculated from a minimum of 1.4 Mb sequenced DNA. Microsatellite instability status was determined by a novel algorithm analyzing 114 specific loci. Results: Comprehensive genomic profiling identified several genomically-defined DSRCT subgroups. Recurrent genomic alterations were most frequently detected in FGFR4, ARID1A, TP53, MSH3,andMLL3 genes. With the exception of FGFR4, where the genomic alterations predicted activation, most of the alterations in the remaining genes predicted gene inactivation. No DSRCT were TMB or MSI high. Conclusions: In summary, recurrent secondary somatic alterations in FGFR4, ARID1A, TP53, MSH3,andMLL3 were detected in 82% of DSRCT, which is significantly greater than previously reported. These alterations may have both prognostic and therapeutic implications. Keywords: Desmoplastic small round cell tumor, Sarcoma, Genomic profiling, FGFR4 Background sarcoma RNA binding protein 1 gene, EWSR1 (termed Desmoplastic small round cell tumor (DSRCT) is a EWS) to the C-terminus of the Wilms tumor (WT1) rare, highly aggressive, translocation-associated soft- gene, creating a novel fusion chimera EWS-WT1 gene tissue sarcoma of children, adolescents, and young [2]. The most common chimera is an in-frame fusion of adults with a striking ∼85% male bias. Because DSRCT exons 1–7ofEWS, encoding the potential transcription typically presents with diffuse involvement of the ab- modulating domain, and exons 8–10 of WT1, encoding dominal and/or pelvic peritoneum, the 5-year mortality the last three zinc fingers of the DNA-binding domain is ~ 85% despite intensive multimodality therapy [1]. (reviewed by Loktev et al.) [3]. The cell of origin remains unknown, but all cases of Despite our understanding of the genomic underpin- DSRCT harbor a balanced, reciprocal t(11;22) (p13; ning of DSRCT, attempts to create a transgenic q12), resulting in fusion of the N-terminus of the Ewing DSRCT genetically-engineered mouse model (GEMM) using homologous murine Ewsr1 fused to human WT1 have been unsuccessful [4]. Similarly, overexpression * Correspondence: [email protected] 1Department of Medical Oncology & Therapeutics Research, City of Hope, of EWS-WT1 failed to transform wild-type (wt) pri- 1500 E. Duarte Rd, Duarte, CA 91010, USA mary mouse embryonic fibroblasts (pMEFs), whereas Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Chow et al. BMC Medical Genetics (2020) 21:101 Page 2 of 8 itsoverexpressioninpMEFswithamutationinatleast was calculated from a minimum of 1.4 Mb sequenced DNA one allele of transformation related protein 53 (Trp53) and reported as mutation/Mb. Microsatellite instability sta- enhanced proliferation, clonogenic survival, and anchorage- tus (MSI) was determined by a novel algorithm including independent growth, consistent with malignant transform- 114 specific loci. The clinical status of the patients regard- ation [5]. This suggests that additional unknown somatic ing the source and timing of the specimen acquisition only aberrations in addition to the EWS-WT1 chimera gene con- (primary tumor, metastasis, or recurrence) was provided to tribute to oncogenesis. Strikingly however, DSRCTs harbor a Foundation Medicine, however further information regard- low frequency of somatic aberrations [6–9]. For example, ing the subsequent clinical outcomes were primarily Shukla et al. reported 0 somatic mutations in 24 DSRCT tu- unknown. Approval for this study, including a waiver of in- mors analyzed by targeted exon sequencing [6]. Similarly, formed consent and a HIPAA waiver of authorization, was Jiang et al. reported 2/10 secondary somatic mutations in obtained from the Western Institutional Review Board their DSRCT series (MET N375S and PIK3C M1040I) using (Protocol No. 20152817). multiple sequencing methods, Silva et al. noted 1/1 AURKB RNA sequencing (seq) was performed on a single DSRCT and MCL1 amplification, and Bulbul et al. reported 1/15 tissue sample under a City of Hope Investigational Review (TP53 G245G) and 1/3 (FOXO3 L382fs) with a 592-gene Board approved protocol after written consent was ob- next-generation exome sequencing platform [7–9]. This dis- tained (COH IRB# 15243). The sample was immediately tinctly contrasts with the 32% frequency of TP53 mutations stored in liquid nitrogen after surgery at the COH Tissue reported present in other soft-tissue sarcomas [10]. More re- Biorepository. This sample was one of the 83 samples se- cent reports using next generation sequencing (NGS) only quenced at Foundation Medicine. RNA was isolated using have reported modestly higher rates of somatic genomic al- RNeasy MINI kit (Qiagen, Valencia, CA), and RNA-seq terations. Using whole exome sequencing (WES), Ferreira was performed at the COH Integrative Genomics Core. et al. noted 1/1 DSRCT with 12 predominantly synonymous RNA-seq libraries were prepared using KAPA Hyperprep and missense somatic mutations [11]. More recently, Devec- RNA-seq kit following manufacturer’s recommendations. chi et al. performed WES on 7 DSRCT and reported 8–33 The libraries were qualified and loaded to Hiseq 2500 flow- mutations per case [12]. A total of 137 unique somatic muta- cells for single end 51 bp sequencing. The raw sequences tions were detected, of which 133 were case-specific, and 2 were quality filtered and aligned to human genome using were mutated in two cases but in different positions. Most of Tophat. The expression levels of RefSeq Genes were the affected genes involved in DNA damage-response counted using HTSeq-count. The counts were normalized network, mesenchymal-epithelial reverse transition (MErT)/ and differential expression analysis were conducted using epithelial-mesenchymal transition (EMT), and immune re- Bioconductor package “edgeR”. Pathway analysis and func- sponse. We describe herein frequent, recurrent, and mostly tional annotation of the gene expression data were using previously undescribed secondary genomic alterations in GSEA and DAVID, as well as Ingenuity Pathway Analysis. DSRCT in the largest clinical database. Results Methods Tissue from 83 DSRCT clinical samples were analyzed DSRCT patients whose formalin-fixed and paraffin- at Foundation Medicine. The diagnosis was confirmed embedded (FFPE) tissue was sent for genomic testing by the presence of the EWS-WT1 chimera gene in all between 2012 and 2018 in the course of standard clinical cases by NGS. The demographics of the 83 patient co- care to Foundation Medicine were included in the ana- hort is shown in Table 1. As expected, there was a sig- lysis. Regardless of prior testing for status of EWS-WT1, nificant male bias with 81% of the samples from male only patients whose EWS-WT1 pathognomonic EWS- patients. The median age of the patients was 25 years WT1 chimera gene status was confirmed during Founda- (range, 6–67). The majority of patients were in the ado- tion Medicine testing were included in the cohort. The lescent and young adult (AYA) population (54%). Metas- analysis included both DNA sequencing of 406 cancer- tases were clinically documented in 60% of the cases. related genes and RNA sequencing of 265 genes com- The distribution of the specimen sites is shown in Fig. 1. monly rearranged in cancer, as previously described [13]. The majority of the biopsy samples were taken from the > 50 ng of DNA and 250 ng of RNA were extracted from abdomen (16%), soft-tissue (13%), omentum (12%), and the FFPE tissue and assayed by hybrid-capture based lymph nodes (11%). The remainder of the biopsied sites next generation sequencing