Comprehensive Molecular Profiling of Desmoplastic Small Round Cell Tumor

Abstract

Desmoplastic small round cell tumor (DSRCT) is characterized by the EWSR1–WT1 t(11;22) (p13:q12) translocation. Few additional putative drivers have been identified, and research has suffered from a lack of model systems. Next-generation sequencing (NGS) data from 68 matched tumor-normal samples, whole-genome sequencing data from 10 samples, transcriptomic and affymetrix array data, and a bank of DSRCT patient-derived xenograft (PDX) are presented. EWSR1–WT1 fusions were noted to be simple, balanced events. Recurrent mutations were uncommon, but were noted in TERT (3%), ARID1A (6%), HRAS (5%), and TP53 (3%), and recurrent loss of heterozygosity (LOH) at 11p, 11q, and 16q was identified in 18%, 22%, and 34% of samples, respectively. Comparison of tumor-normal matched versus unmatched analysis suggests overcalling of somatic mutations in prior publications of DSRCT NGS data. Alterations in fibroblast growth factor receptor 4 (FGFR4) were identified in 5 of 68 (7%) of tumor samples, whereas differential overexpression of FGFR4 was confirmed orthogonally using 2 platforms. PDX models harbored the pathognomic EWSR1–WT1 fusion and were highly representative of corresponding tumors. Our analyses confirm DSRCT as a genomically quiet cancer defined by the balanced translocation, t(11;22)(p13:q12), characterized by a paucity of secondary mutations but a significant number of copy number alterations. Against this genomically quiet background, recurrent activating alterations of FGFR4 stood out, and suggest that this receptor tyrosine kinase, also noted to be highly expressed in DSRCT, should be further investigated. Future studies of DSRCT biology and preclinical therapeutic strategies should benefit from the PDX models characterized in this study. Implications: These data describe the general quiescence of the desmoplastic small round cell tumor (DSRCT) genome, present the first available bank of DSRCT model systems, and nominate FGFR4 as a key receptor tyrosine kinase in DSRCT, based on high expression, recurrent amplification, and recurrent activating mutations.

Multi-site desmoplastic small round cell tumors are genetically related and immune-cold

“…1a ), which is similar to other fusion-driven sarcomas such as Ewing sarcoma 22 , 23 , synovial sarcoma 24 , and rhabdomyosarcoma 25 . Our observed mutation rate was similar to those observed in DSRCT by Devecchi et al 21 and Slotkin et al 19 , but much lower than that seen by Bulbul et al (4–8 mutations per Mb) 17 . Mutation signature analysis 26 was not performed owing to the potential analysis biases resulting from the low mutation burden that was detected.…”

“…MUC19) were also identified in two of the six patients in the cohort studied by Devecchi et al 21 . In addition, two patients each harbored one mutation in ARID1A : one missense change in the BAF250_C domain and one splicing site mutation near the AT-rich interaction domain 1 A. Inactivating mutations in ARID1A are recurrent in other studies: 11% of 85 DSRCT patients, 7% of 68 DSRCT patients, with other case reports where one deleterious mutation and one variant of uncertain significance have also been observed 18 , 19 , 21 , 28 . ARID1A is a subunit of the SWI/SNF epigenetic regulator that is frequently altered in cancer.…”

“…Some inhibitors of these targets have anti-cancer effects in other cancer types and could provide potential therapeutic benefits for DSRCT patients (Table 3 ). For instance, FGFR4 is amplified in 8% of 83 DSRCT patients in one study and amplified in 7% of 67 DSRCT samples in another study, resulting in high levels of expression as compared to other fusion-driven sarcomas 18 , 19 . FGFR4 , which is involved in regulating cell proliferation, cell differentiation, and cell migration, is induced by the EWSR1-WT1 fusion in DSRCT cell lines, possibly through binding of EWSR1-WT1 within its coding regions 16 , 42 .…”

“…Genes related to mesenchymal cell differentiation or mesenchymal-epithelial reverse transition (MErT)/epithelial–mesenchymal transition (EMT) have been found to be altered as non-silent somatic mutations or gains in chromosome 1 20 , 21 . Copy number gains were seen in chromosomes 5 and 18, as well as copy number losses at 11p, 13q, and 22q 19 , 20 . Loss of the entire chromosome 6 where immune-regulatory genes are located have also been recorded 21 .…”

“…Owing to the rarity of the disease, limited genomic sequencing on single DSRCT specimens has been performed to identify critical genetic alterations other than the EWSR1-WT1 fusion. Analyses of sequencing panels, exomes, and genomes have identified recurrent secondary mutations in AR, FGFR4 , ARID1A , TERT , TP53 , MSH3 , HRAS , TOP2A , TOPO1 , PTEN , mucin genes, and others 17 – 19 . Genes related to mesenchymal cell differentiation or mesenchymal-epithelial reverse transition (MErT)/epithelial–mesenchymal transition (EMT) have been found to be altered as non-silent somatic mutations or gains in chromosome 1 20 , 21 .…”