Monitoring Circulating Tumor DNA During Surgical Treatment in Patients with Gastrointestinal Stromal Tumors

Abstract

The majority of patients diagnosed with advanced gastrointestinal stromal tumor (GIST) are successfully treated with a combination of surgery and tyrosine kinase inhibitors (TKIs). However, it remains challenging to monitor treatment efficacy and identify relapse early. Here, we utilized a sequencing strategy based on molecular barcodes and developed a GIST-specific panel to monitor tumor-specific and TKI resistance mutations in cell-free DNA and applied the approach to patients undergoing surgical treatment. Thirty-two GIST patients were included, and 161 blood plasma samples were collected and analyzed at routine visits before and after surgery and at start, during, and end of surgery. Patients were included regardless of their risk category. Our GIST-specific sequencing approach allowed detection of tumor-specific mutations and TKI resistance mutations with mutant allele frequency < 0.1 %. Circulating tumor-DNA (ctDNA) was detected in at least one timepoint in 9 out of 32 patients, ranging from 0.04% to 93% in mutant allele frequency. High-risk patients were more often ctDNA-positive than other risk groups (p < 0.05). Patients with detectable ctDNA also displayed higher tumor cell proliferation rates (p < 0.01) and larger tumor sizes (p < 0.01). All patients who were ctDNA-positive during surgery became negative after surgery. Finally, in two patients who progressed on TKI treatment, we detected multiple resistance mutations. Our data show that ctDNA may become a clinically useful biomarker in monitoring treatment efficacy in high-risk GIST patients and can assist in treatment decision making.

Development of Highly Sensitive Digital Droplet PCR for Detection of cKIT Mutations in Circulating Free DNA That Mediate Resistance to TKI Treatment for Gastrointestinal Stromal Tumor (GIST)

“…Both PCR-based techniques and NGS were shown to exhibit high analytical sensitivity [ 23 , 24 , 30 , 33 , 48 , 50 ]. Particularly, BEAMing and ddPCR are characterized by sensitivities reaching levels between 0.01 and 0.1% [ 30 , 33 , 48 ].…”

“…Particularly, BEAMing and ddPCR are characterized by sensitivities reaching levels between 0.01 and 0.1% [ 30 , 33 , 48 ]. Technical developments within the last few years have raised the sensitivity of NGS to similar levels [ 23 , 24 , 50 , 51 ]. NGS harbors a range of advantages compared to ddPCR, in particular the unbiased detection of multiple ctDNA mutations in parallel.…”

“…Techniques for ctDNA detection can be divided into targeted, single-mutation approaches (PCR: qPCR, BEAMing, ddPCR) or more unbiased approaches by means of targeted next-generation sequencing (NGS) [ 9 , 22 ]. NGS is more advantageous than single-mutation assays, as it allows for simultaneous genome-wide testing in a single assay [ 23 ] and it was shown to mirror ctDNA clonal heterogeneity in GIST patients [ 11 , 24 , 25 , 26 , 27 , 28 , 29 ]. On the other hand, NGS-based approaches are expensive and time-consuming and still demand an extensive bioinformatic analysis [ 30 , 31 , 32 , 33 ].…”

Plasma Sequencing for Patients with GIST—Limitations and Opportunities in an Academic Setting

“…However, this was mainly during surgery or progression but not after complete resection using simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing (SiMSen-Seq). Primary mutations were detectable in two patients at the time of progression [ 28 ]. Using NGS, Kang et al were able to detect KIT mutations in 13/18 cases before treatment and surgery.…”

The Need to Pair Molecular Monitoring Devices with Molecular Imaging to Personalize Health

“…Other predictive biomarkers (i.e., those that are cancer-predictive but not necessarily cancer-associated) have been identified and demonstrated in electrochemical devices including platelet factor 4 (PF-4), interleukin 6 (IL-6), interleukin 8 (IL-8), and carcinoembryonic antigen (CEA). Thus, during treatment, molecular sensors can be used to monitor the effects of therapies, providing rapid feedback to better direct clinical decisions [28][29][30]. Advances in molecular imaging and sensing can radically alter clinical workflows, with molecular sensors replacing intermittent invasive clinical monitoring and molecular imaging providing accurate, noninvasive, diagnoses.…”