Molecular and Pathological Profiling of Corresponding Treatment-Naïve and Neoadjuvant Pazopanib-Treated High-Risk Soft Tissue Sarcoma Samples of the GISG-04/NOPASS Study

Abstract

In the framework of the German Interdisciplinary Sarcoma Group GISG-04/NOPASS trial, we evaluated soft tissue sarcoma samples taken before and after neoadjuvant pazopanib therapy using histopathology and next generation sequencing (NGS) to find potential predictive biomarkers. We also aimed to improve the genetically based sarcoma classification and to elucidate additional potentially druggable mutations. In total, 30 tumor samples from 18 patients consisting of 12 pre-therapeutic biopsies and 18 resection specimens following neoadjuvant pazopanib therapy were available for analyses. NGS was performed with the Oncomine Focus Assay (Ion Torrent) covering 0.03 Mb of DNA and enabled the detection of genetic variants in 52 cancer-relevant genes. Pathological analysis showed significant regression (≥50%) after pazopanib treatment in only one undifferentiated (pleomorphic) sarcoma. NGS analyses revealed a very high frequency of CDK4 amplification (88%; 7/8) in the group of dedifferentiated liposarcoma. In addition, two potentially druggable mutations, a MAP2K1 missense mutation (E203K) and a BRAF missense mutation (V600E), were traceable in two undifferentiated (pleomorphic) sarcoma patients (11%; 2/18). Our findings demonstrate that NGS testing is a powerful technology helping to improve diagnostic accuracy and offering some patients the chance for personalized medicine even in a “mutation unlikely” cohort like STS.

Advances in sarcoma molecular diagnostics

“…78,79 Notably, this assay identified four fusion-positive cases that were false negatives by FISH and RT-PCR. 78 82 These results demonstrate the utility of MPS in improving diagnostic accuracy and the opportunity for personalized medicine in treating soft tissue sarcoma. 82 Advancements in amplicon-based MPS, such as single primer extension (SPE) MPS, have been developed to reduce bias and errors and to increase multiplexing capacity.…”

“…78 82 These results demonstrate the utility of MPS in improving diagnostic accuracy and the opportunity for personalized medicine in treating soft tissue sarcoma. 82 Advancements in amplicon-based MPS, such as single primer extension (SPE) MPS, have been developed to reduce bias and errors and to increase multiplexing capacity. SPE uses barcoding molecules to tag targets prior to sequencing, which can be paired with unique molecular indices in MPS to correct for PCR amplification and library bias.…”

“…Gampawar et al found AmpliSeq to have sensitivity and positive predictive values of >93% when compared to the reference DNA 81 . Gaiser et al used the Focus Assay to assess tumor samples from 18 patients for potential predictive biomarkers and found high frequencies of CDK4 amplification in 7/8 cases of dedifferentiated liposarcoma, and potentially druggable mutations in two cases of undifferentiated (pleomorphic) sarcoma 82 . These results demonstrate the utility of MPS in improving diagnostic accuracy and the opportunity for personalized medicine in treating soft tissue sarcoma 82 …”