Molecular-genetic characteristics of soft tissue sarcomas associated with the development of chemotherapy resistance.

Abstract

11550 Background: The development of resistance is the one of the reason for ineffective treatment of soft tissue sarcomas (STSs). The search for new molecular-biological targets, both for the personalized selection of novel targeted drugs and for predicting chemoresistance of STSs to individual antitumor agents and their combinations, is a pressing task. Methods: In this study, an experimental in vitro chemoresistance analysis, whole-genome sequencing, and single-cell sequencing of tumors in patients (N = 9) with undifferentiated pleomorphic sarcomas were performed. Chemotherapy resistance indices were determined for the obtained samples. Results: Whole-genome DNA sequencing yielded data on the type and frequency of somatic mutations in undifferentiated pleomorphic sarcomas, and driver genes of carcinogenesis were identified, among which the most frequently occurring were FCGBP, PARP4, TP53, RGPD3, PDE4DIP, and RB1. Correlations between the presence of genetic alterations and the response to chemotherapy in the in vitro test were sought. Thus, in samples resistant to the combination of doxorubicin and ifosfamide, the presence of mutations in the PEG3, USP8, NT5C3A, and WAS genes was characteristic. Bioinformatic analysis of single-cell transcriptome sequencing data, aimed at characterizing the population composition and transcriptomic landscape of undifferentiated pleomorphic sarcoma cells, revealed 15 normal and 8 tumor cell populations. Among the populations of normal cells, the following clusters were identified: M2 and M1 macrophages, T-cells, matrix-remodeling fibroblasts and myofibroblasts, monocytes, stromal cells, endothelial cells, and osteoblasts. Among tumor cells, clusters of proliferating cells, hypoxic cells, matrix-interacting cells, and tumor cells with a stem-like phenotype were identified. The most common clusters in all samples were M2 macrophages, endothelial cells, and one of the clusters of tumor cells interacting with the matrix. Comparison of the expression profiles of cells from patients with different responses to chemotherapy allowed identification and characterization of clusters associated with chemosensitivity and chemoresistance. These included clusters of macrophages, tumor cells, fibroblasts, and endothelial cells. In addition, genes common to all clusters associated with resistant samples were identified (ARGLU1, JUND, TNNT3, RHOB, CCNL2, LENG8, LUC7L3, KLF9, RSRP1, RNF213, SERPINE1, CDK5RAP3). Conclusions: The data obtained in this study will expand the understanding of the pathogenesis of undifferentiated pleomorphic sarcomas and the mechanisms underlying their development of chemotherapy resistance. In the future, this will serve as the basis for creating a test system to evaluate the expression levels of genes whose activation/repression is associated with the development of drug resistance in STSs.