Abstract 3401: Comprehensive analysis of genetic alterations and intratumor heterogeneity in myxofibrosarcoma

Abstract

Abstract Myxofibrosarcoma (MFS) is a rare subtype of soft tissue sarcomas (STSs) preferentially affecting elderly. Histologically, MFS is distinct from other STSs, in that it is characterized by the proliferation of pleomorphic spindle cells with varying degrees of myxoid components. However, the molecular pathogenesis of MSF is poorly understood. In this study, we conducted an integrated molecular analysis of 44 samples from primary MFS patients, in which samples were analyzed by whole-genome sequencing (WGS) (n=2), whole-exome sequencing (WES) (n=44), RNA sequencing (n=3), DNA methylation array (n=16), and immunohistochemistry (IHC, n=27). Copy number alterations (CNAs) were identified by sequence based copy number analysis. The obtained genomic data were combined with those from STS cases from the Cancer Genome Atlas (TCGA) cohort, including 17 MSF samples and compared to the data from other STS samples (n=189). To further investigate the genetic basis of mixed histological components and chronological changes in MFS, we performed analysis from multi-regional and/or multi-time-point samples from 8 MSF cases. A total of 4,613 mutations were identified by WES in 61 primary MFS samples with a median of 44.0 mutations/sample. Mutations were dominated by age-related C to T transitions at CpG sites. Most frequently mutated genes included TP53 (n=21, 34.4%), ATRX (n=9, 14.8%), and RB1 (n=3, 4.9%). A fusion gene associated with TRIO was detected by RNA sequencing in a single case. Among other STSs, undifferentiated pleomorphic sarcoma (UPS) harbored the most similar genetic abnormalities (most frequently mutated genes included TP53 (40.9%), ATRX (29.5%), and RB1 (11.3%)), suggesting that these two subtypes are genetically closely related. Also combined cases with CNAs (n=35) and strong staining in IHC (n=13), TP53 abnormality was found in most cases (n=56, 91.8%). Two MSF cases evaluated by WGS showed complex structural abnormalities, where 491 and 198 somatic structural variations were detected suggestive of increased genetic instability. Multi-regional sampling (n=5) disclosed a high level of intratumor heterogeneity with less than 29.0% of mutations being shared by different samples. Multi-time points sampling (n=6) revealed that the number of mutations was significantly higher in relapse samples (odds ratio 1.6, p = 0.03). While in all cases, TP53 lesions were observed at the initial time-point, others were subclonal and acquired during the clinical course. Finally, in methylation analysis, 3,817 differentially methylated regions were detected (Stouffer's p < 0.05), based on which MFS were clustered into two distinct subtypes. In summary, the genetic profile of MFS is characterized by frequent abnormalities in TP53, ATRX, and RB1 and closely related to other STSs, especially to UPS. Clonal TP53 abnormalities resulted in complex chromosomal structure and a high degree of intratumor heterogeneity. Citation Format: Yasuhide Takeuchi, Annegret Kunitz, Hiromichi Suzuki, Kenichi Yoshida, Nobuyuki Kakiuchi, Yusuke Shiozawa, Akira Yokoyama, Yoichi Fujii, Tetsuichi Yoshizato, Kosuke Aoki, Keisuke Kataoka, Yasuhito Nannya, Yuichi Shiraishi, Teppei Shimamura, Kenichi Chiba, Hiroko Tanaka, Hideki Makishima, Satoru Miyano, Hironori Haga, Frederik Damm, Seishi Ogawa. Comprehensive analysis of genetic alterations and intratumor heterogeneity in myxofibrosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3401.