Genomic analysis in patients with soft tissue sarcoma to examine gene mutations involved in chromosome segregation, mitotic spindle assembly, and degradation.
Authors: Takahashi Katsuhito , Higuchi Hajime , Komohara Yoshihiro , Aida Shinsuke , Yashima Jun , Yamamoto Hiromasa , Suzawa Ken , Takahashi Yuko , Toyooka Shinichi , Narahara Hiroyuki , Yotsumoto Junko , Miyaji Yasutomo , Oyama Yu , Ono Yasuo , Teraoka Satoshi 
Published: June 2023

e23523

Background: Soft tissue sarcoma (STS) is a rare cancer with few drug discovery. Recent genomic analysis of STS revealed a high degree of chromosomal instability (CIN) including genome-wide copy number alterations, aneuploidy, whole genome doubling and chromothripsis. In STS patients, we have reported extensive somatic LOH in tumors, a hallmark of CIN, represented by haploid of germline mutations/variants in cancer-related genes. CIN of STS implicates abnormalities in chromosome segregation, spindle assembly and degradation in mitosis but few studies have examined the impact of gene mutations involved in the pathological mitotic processes in STS. Methods: We recruited 155 patients with metastatic/recurrent STS (135 female and 20 male, mean age 51 at analysis, 100 LMS, 19 LPS, 4 ESS, 3 UPS, 3 AS, 3 MPT and others) with information of familial cancer burden. Whole exome sequencing and analysis were performed in both blood and tumor samples as described in 2018ASCO. Results: STS Patients with tumors harboring less than 33% somatic LOH (n = 54) in a total of somatic and LOH mutations/variants in 595 COSMIC genes have a better prognosis than those (34-66%, n = 49, 67-100%, n = 52) with more LOH genes (5-year OS; 72% vs 53% or 40%, p = 0.0499, p = 0.0023, respectively). LOH was associated with neither TMB nor MSI status but with a total number of somatic and germline mutations (R = 0.874). Of the genes involved in chromosome segregation and mitosis, we found that a family of ARHGAP genes which play a role in the spindle degradation and Aurora A kinase activation was most frequently mutated in tumor and germline genomes (n = 102 in a total of 155, n = 71 in 100 LMS). Damaging ARHGAP mutations/variants are correlated with higher LOH values (54.1±2.8%, n = 102 vs. 33.1±3.8%, n = 53, mean±SE, p < 0.001, for LMS, 63.3±2.9%, n = 71 vs. 36.7±5.4%, n = 29, mean±SE, p < 0.001) and poor prognosis of patients (5-year OS; 48% n = 102 vs. 71% n = 53, p = 0.0107). We also found damaging mutations/variants in a family of CAPN (calpain) genes involved in cleavage of the cohesion ring for chromosome separation (n = 73 in 155) and CENPT gene essential for bridging between kinetochore and microtubules via NDC80 (n = 43 in 155). For CENPT, loss of wild type allele at codons encoding functional Ser121 and Arg122 was found in 10 patients with LMS and DSRCT. Damaging CAPN mutations/variants are correlated with higher LOH values (60.6±3.0%, n = 73 vs. 34.8±3.2%, n = 82, mean±SE, p < 0.001). Conclusions: This study demonstrates extensive genomic abnormalities involved in the pathways of chromosome segregation and mitosis in STS. Recent studies, including ourselves, confirmed overexpression of KIF18A, NDC80 and NUF2 in STS, lethal targets for KIF18A and CHD (Calponin Homology Domain) inhibitors in CIN tumors. Together, our results will open a new avenue evolving treatment landscape of STS.