Circulating Tumor DNA Mutations in Progressive Gastrointestinal Stromal Tumors Identify Biomarkers of Treatment Resistance and Uncover Potential Therapeutic Strategies.

Tun Kiat Ko,Nagavalli Somasundaram,Elizabeth Lee,Cedric Chuan-Young Ng,Valerie Shiwen Yang,Jason Yongsheng Chan,Mohamad Farid,Bin Tean Teh

doi:10.3389/fonc.2022.840843

Abstract

Liquid biopsy circulating tumor DNA (ctDNA)-based approaches may represent a non-invasive means for molecular interrogation of gastrointestinal stromal tumors (GISTs). We deployed a customized 29-gene Archer® LiquidPlex™ targeted panel on 64 plasma samples from 46 patients. The majority were known to harbor KIT mutations (n = 41, 89.1%), while 3 were PDGFRA exon 18 D842V mutants and the rest (n = 2) were wild type for KIT and PDGFRA. In terms of disease stage, 14 (30.4%) were localized GISTs that had undergone complete surgical resection while the rest (n = 32) were metastatic. Among ten patients, including 7 on tyrosine kinase inhibitors, with evidence of disease progression at study inclusion, mutations in ctDNA were detected in 7 cases (70%). Known somatic mutations in KIT (n = 5) or PDGFRA (n = 1) in ctDNA were identified only among 6 of the 10 patients. These KIT mutants included duplication, indels, and single-nucleotide variants. The median mutant AF in ctDNA was 11.0% (range, 0.38%–45.0%). In patients with metastatic progressive KIT-mutant GIST, tumor burden was higher with detectable KIT ctDNA mutation than in those without (median, 5.97 cm vs. 2.40 cm, p = 0.0195). None of the known tumor mutations were detected in ctDNA for localized cases (n = 14) or metastatic cases without evidence of disease progression (n = 22). In patients with serial samples along progression of disease, secondary acquired mutations, including a potentially actionable PIK3CA exon 9 c.1633G>A mutation, were detected. ctDNA mutations were not detectable when patients responded to a switch in TKI therapy. In conclusion, detection of GIST-related mutations in ctDNA using a customized targeted NGS panel represents an attractive non-invasive means to obtain clinically tractable information at the time of disease progression.

Highlights

Gastrointestinal stromal tumor (GIST) is the commonest mesenchymal neoplasm originating from the gastrointestinal tract
Most patients benefit from targeted therapy using the tyrosine kinase inhibitor (TKI) imatinib, though acquired resistance and disease progression associated with the development of secondary mutations usually occur after 18 to 24 months
Our results showed that known tumor mutations, including both KIT and PDGFRA, were detectable in circulating tumor DNA (ctDNA) only among patients with metastatic GIST with measurable disease progression

Summary

INTRODUCTION

Gastrointestinal stromal tumor (GIST) is the commonest mesenchymal neoplasm originating from the gastrointestinal tract. For ctDNA samples where no significant variants were detected by the default setting, we would manually check all the mapped NGS reads for the presence of KIT, PDGFRA, or other variants that were previously detected by Sanger sequencing of the corresponding tumor. If such variant was detected, it would only be reported as a significant variant if AF outlier p-value < 0.05. All tests were performed using MedCalc statistical Software for Windows version 19.0.4 (MedCalc Software, Ostend, Belgium)

RESULTS

DISCUSSION

ETHICS STATEMENT