Circulating tumor DNA to monitor treatment response and detect acquired resistance in patients with metastatic melanoma

Abstract

Repeat tumor biopsies to study genomic changes during therapy are difficult, invasive and data are confounded by tumoral heterogeneity. The analysis of circulating tumor DNA (ctDNA) can provide a non-invasive approach to assess prognosis and the genetic evolution of tumors in response to therapy. Mutation-specific droplet digital PCR was used to measure plasma concentrations of oncogenic BRAF and NRAS variants in 48 patients with advanced metastatic melanoma prior to treatment with targeted therapies (vemurafenib, dabrafenib or dabrafenib/trametinib combination) or immunotherapies (ipilimumab, nivolumab or pembrolizumab). Baseline ctDNA levels were evaluated relative to treatment response and progression-free survival (PFS). Tumor-associated ctDNA was detected in the plasma of 35/48 (73%) patients prior to treatment and lower ctDNA levels at this time point were significantly associated with response to treatment and prolonged PFS, irrespective of therapy type. Levels of ctDNA decreased significantly in patients treated with MAPK inhibitors (p < 0.001) in accordance with response to therapy, but this was not apparent in patients receiving immunotherapies. We show that circulating NRAS mutations, known to confer resistance to BRAF inhibitors, were detected in 3 of 7 (43%) patients progressing on kinase inhibitor therapy. Significantly, ctDNA rebound and circulating mutant NRAS preceded radiological detection of progressive disease. Our data demonstrate that ctDNA is a useful biomarker of response to kinase inhibitor therapy and can be used to monitor tumor evolution and detect the early appearance of resistance effectors.

Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma

“…However, a subsequent scan revealed tumor shrinkage, demonstrating that ctDNA had accurately predicted this delayed response to immunotherapy. A similar observation was recently reported in another patient with a delayed immunotherapy response ( 44 ), so together these data suggest that ctDNA could be particularly valuable in patients with delayed responses to immunotherapy.…”

Clinical significance of BRAFV600E mutation in circulating tumor DNA in Chinese patients with melanoma

“…In prior reports, the concordance between BRAF V600E in ctDNA and BRAF V600E in tissue samples was ~70% and the sensitivity was 38-79% (9,(11)(12)(13). The concordance and sensitivity between ctDNA and tumor tissue in our study were 70.2 and 76%, which were higher than those of prior reports.…”

“…The main reason for this observation is that our study uniquely used 3D dPCR, which is highly sensitive, quantitative, and real-time. Unlike other detection methods, such as Beads Emulsion Amplification Magnetics (BEAMing), Amplification Refractory Mutation System (ARMS), and Next Generation Sequencing (NGS) (9,(11)(12)(13), each reaction of 3D dPCR has 20,000 wells and each well is isolated from its neighbors. This ensures the high sensitivity and accuracy of 3D dPCR.…”

“…The concordance between ctDNA for BRAF V600E and BRAF V600E status in tissue has been shown to be ~70%. CtDNA for BRAF V600E has a sensitivity of 38-79% and a specificity of 40-100% (9,(11)(12)(13). BRAF V600E mutated DNA was detected in CTCs of 77% of melanoma patients with recorded mutated tumor tissues (14).…”

Targeted agents and immunotherapies: optimizing outcomes in melanoma

“…The clinical feasibility of clinical trials is, however, daunting: the degree of heterogeneity of resistance observed between patients, as well as within different tumours in the same patient, is a major barrier to therapeutic progress. This hurdle could potentially be overcome through real-time monitoring for changes associ ated with resistance to BRAF-MEK-inhibitor therapy (for example, analysis of the predominant melanoma-cell clone at progression), and reactive use of targeted therapeutics based on the biological changes observed 122 . Such an approach would necessitate intermittent assessment of the ongoing status of the tumour; therefore, the substantial progress that has been made in the development of non-invasive monitoring technologies, such as 'liquid biopsy' of circulating tumour cells (CTC) 123 and circulating cell-free tumour DNA (ctDNA) 124 , is note worthy.…”