Evolutionary pressures shape soft tissue sarcoma development and radiotherapy response

Abstract

Abstract Evolutionary pressures play a key role in tumorigenesis, progression, and response to therapy. However, the selection pressures and subclonal dynamics of soft tissue sarcomas during their natural history remain to be defined. Additionally, although radiotherapy plays a crucial role in obtaining local control for many solid tumors, the effect of radiation on tumor evolution has been challenging to study due to a lack of longitudinal tumor samples before and after treatment. We integrated temporal genomic profiling of 120 spatially distinct tumor regions from 20 patients with pleomorphic sarcomas, longitudinal circulating tumor DNA (ctDNA) analysis, in silico tumor simulation, and evolutionary biology computational pipelines to study sarcoma evolution both during tumorigenesis and in response to radiotherapy. We found that the majority of unirradiated sarcomas displayed initial linear evolution followed by subsequent branching evolution with distinct mutational processes during early and late sarcoma development. We observed evidence of strong selection pressures during sarcoma development with further selection for resistant subclonal populations during radiotherapy using metrics of genetic divergence between regions. We demonstrated dramatic changes in subclone abundance following radiotherapy with subclone contraction tied to alterations in calcium signaling. Finally, ctDNA analysis accurately measured tumor subclone abundance and enabled non-invasive longitudinal monitoring of subclonal changes. These results highlight the natural history of soft tissue sarcomas and suggest that targeting resistant subclonal populations could improve outcomes in patients treated with radiotherapy.