Application of Circulating Cell-Free Tumor DNA Profiles for Therapeutic Monitoring and Outcome Prediction in Genetically Heterogeneous Metastatic Melanoma

Abstract

PURPOSE Circulating cell-free tumor DNA (ctDNA) reflects the heterogeneous spectrum of tumor-specific mutations, especially in systemic disease. We validated plasma-based assays that allow the dynamic quantitative detection of ctDNA as a prognostic biomarker for tumor load and prediction of therapy response in melanoma. MATERIALS and METHODS We analyzed plasma-derived ctDNA from a large training cohort (n = 96) of patients with advanced-stage melanoma, with assays for the BRAFV600E and NRASQ61 driver mutations as well as TERTC250T and TERTC228T promoter mutations. An independent patient cohort (n = 35) was used to validate the utility of ctDNA monitoring under mitogen-activated protein kinase–targeted or immune checkpoint therapies. RESULTS Elevated plasma ctDNA level at baseline was an independent prognostic factor of disease progression when compared with serum S100 and lactate dehydrogenase levels in multivariable analyses (hazard ratio [HR], 7.43; 95% CI, 1.01 to 55.19; P = .05). The change in ctDNA levels during therapy correlated with treatment response, where increasing ctDNA was predictive for shorter progression-free survival (eg, for BRAFV600E ctDNA, HR, 3.70; 95% CI, 1.86 to 7.34; P < .001). Increasing ctDNA levels predicted disease progression significantly earlier than did routine radiologic scans ( P < .05), with a mean lead time of 3.5 months. NRAS-mutant ctDNA was detected in a significant proportion of patients with BRAF-mutant tumors under therapy, but unexpectedly also at baseline. In vitro sensitivity studies suggested that this represents higher-than-expected intratumoral heterogeneity. The detection of NRASQ61 ctDNA in baseline samples of patients with BRAFV600E mutation who were treated with mitogen-activated protein kinase inhibitors significantly correlated with shorter progression-free survival (HR, 3.18; 95% CI, 1.31 to 7.68; P = .03) and shorter overall survival (HR, 4.08; 95% CI, 1.57 to 10.58; P = .01). CONCLUSION Our results show the potential role of ctDNA measurement as a sensitive monitoring and prediction tool for the early assessment of disease progression and therapeutic response in patients with metastatic melanoma.

Inflammatory Cytokines and ctDNA Are Biomarkers for Progression in Advanced-Stage Melanoma Patients Receiving Checkpoint Inhibitors

“…We observed that undetectable ctDNA at 6–8 weeks of therapy predicted longer PFS, verifying that ctDNA can be a valuable biomarker in melanoma patients receiving checkpoint inhibitors. This is in agreement with other studies showing that ctDNA is a predictor for PFS in melanoma patients treated with checkpoint inhibitors but also targeted therapy [ 12 , 13 , 15 , 16 , 41 ]. We did not find an association between ctDNA detection at baseline and PFS, a finding that is both in agreement with [ 13 ] and in contrast to findings of other studies [ 12 , 14 ].…”

“…Analysis of ctDNA can identify tumor-specific mutations and has been shown to correlate with tumor burden and clinical outcome [ 9 , 10 ]. Several studies have found that undetectable ctDNA prior to or early after initiating treatment is associated with improved progression-free survival (PFS) and OS [ 11 , 12 , 13 , 14 , 15 , 16 ]. Furthermore, ctDNA can also be used to uncover mechanisms of acquired resistance at the time of disease progression, allowing therapy to be adapted accordingly [ 12 , 16 ].…”

Clinical significance of clonal hematopoiesis in the interpretation of blood liquid biopsy

“…In this regard, the minimally invasive nature of liquid biopsy overcomes these issues. Recent studies have shown the potential of genomic analysis of plasma cell-free DNA (cfDNA) to facilitate early cancer detection (Bettegowda et al, 2014;Cree et al, 2017;Lam et al, 2018), residual disease detection (Chaudhuri et al, 2017;Tie et al, 2016), and disease and treatment monitoring (Demuth et al, 2018;Long-Mira et al, 2018;V araljai et al, 2019) that could lead to the era of precision oncology.…”

Detection of Circulating Tumor DNA in Solid Tumors

“…A study reported a correlation between alterations in the ctDNA levels during therapy and the tumor response, with an increase in the levels being predictive of disease progression and a decrease being predictive of treatment response. Detection of NRAS Q61 ctDNA in the baseline samples of patients with BRAF V600E mutation who were treated with MAPK inhibitors was reported to be associated with shorter PFS [119]. Another recent study corroborated this finding by demonstrating that increasing levels of ctDNA during melanoma treatment with targeted therapy or immunotherapy could predict disease progression prior to the progression becoming apparent in radiological imaging [120].…”

“…Interestingly, a recent study reported plasma-based comprehensive genomic sequencing of 8,388 consecutively-tested advanced NSCLC using the NGS platform Guardant 360 [115]. The ctDNA analysis revealed somatic alterations in 86% of these cases, with the identification of therapeutically targetable and resistant mutations [119]. On the basis of these data, the use of comprehensive ctDNA testing was proposed for the NSCLC patients who are incompletely tested at the time of diagnosis and for those who are in progression on targeted therapies [115].…”