Abstract 7271: Clinical genomic and functional genomic support for a role of ARID1A loss in progression of desmoplastic small round cell tumor

Abstract Background. Desmoplastic small round cell tumor (DSRCT) is a rare, lethal sarcoma defined and driven by the EWSR1::WT1 fusion. DSRCT has a very low tumor mutational burden (TMB) and few recurrent secondary somatic mutations. Often, the EWSR1::WT1 fusion is the sole identifiable genetic alteration. We leveraged the Memorial Sloan Kettering Cancer Center (MSK) sarcoma sequencing cohort to conduct a comprehensive profiling of 110 DSRCT cases to better define the genomic landscape and evolution of DSRCT. Methods. DSRCT samples underwent matched tumor:normal DNA sequencing on the MSK-IMPACT platform (01/2014-12/2023). All cases harbored the EWSR1::WT1 fusion. A genome-wide, pooled CRISPR-cas9 loss-of-function screen was conducted in 2 DSRCT cell lines (Brunello library, 4 sgRNAs per gene, targeting 19,114 genes). Immunohistochemistry (IHC) was used to assess ARID1A protein expression. Results. We identified 110 DSRCT samples from 82 patients (pts) after robust filtering and quality control from a starting cohort of 198 samples (123 pts). Pts were predominantly male (85.4%) with a male-to-female ratio of 5.8:1 and a median age of 21.5 yrs (range: 6.5-55.9 yrs). At diagnosis, 50% had localized disease (stage I-II), 28.05% had liver metastasis (stage III), and 21.95% presented with extra-abdominal disease (stage IV). DSRCT samples had a median TMB of 0.8 mutations/Mb (range: 0.0-6.6); indeed, 47.3% had no detectable mutations (muts) among the 505 genes profiled. The most frequent secondary alterations were ARID1A inactivating muts (12.2%), followed by FGFR4 activating muts (7.3%), TERT promoter muts (6.1%), and TP53 muts (4.9%). In the knockout screen, ARID1A, TP53, and PTEN ranked among the top positively selected hits, providing functional genomic support for the clinical genomic findings. Notably, ARID1A muts were more common in metastatic lesions (18.5%) than in primary intraabdominal tumors (9.8%), suggesting a role in disease progression. To explore their evolutionary timing, we performed clonal decomposition using cancer cell fraction (CCF) analysis: metastatic samples had significantly higher CCF values (p=0.0067), and clonal muts were predominantly found in metastases (5/7), while subclonal variants were mainly observed in primary tumors (6/8; p=0.021) and their subclonality confirmed by IHC for ARID1A. Two ARID1A-mutated patients had both primary and metastatic samples; in one, an ARID1A nonsense mutation shifted from subclonal (CCF=0.286) in the primary to clonal (CCF=1.0) in the metastasis. In the 2nd patient, an ARID1A frameshift mutation appeared only in the metastatic lesion. Conclusions. Late acquisition and metastatic selection of ARID1A mutations point to a role for loss of this BAF complex component in DSRCT progression. Future studies will investigate the pathobiology and therapeutic vulnerabilities associated with ARID1A loss in DSRCT. Citation Format: Tom Zhang, Andrea Gazzo, Christopher A. Febres-Aldana, Juan Luis Gomez Martis, Lee Spraggon, Romel Somwar, Marc Ladanyi. Clinical genomic and functional genomic support for a role of ARID1A loss in progression of desmoplastic small round cell tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7271.