临床基因组学和功能基因组学支持ARID1A缺失在促结缔组织增生性小圆细胞肿瘤进展中的作用

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.