Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA

Abstract

Purpose: Decisions to continue or suspend therapy with immune checkpoint inhibitors are commonly guided by tumor dynamics seen on serial imaging. However, immunotherapy responses are uniquely challenging to interpret because tumors often shrink slowly or can appear transiently enlarged due to inflammation. We hypothesized that monitoring tumor cell death in real time by quantifying changes in circulating tumor DNA (ctDNA) levels could enable early assessment of immunotherapy efficacy.Experimental Design: We compared longitudinal changes in ctDNA levels with changes in radiographic tumor size and with survival outcomes in 28 patients with metastatic non-small cell lung cancer (NSCLC) receiving immune checkpoint inhibitor therapy. CtDNA was quantified by determining the allele fraction of cancer-associated somatic mutations in plasma using a multigene next-generation sequencing assay. We defined a ctDNA response as a >50% decrease in mutant allele fraction from baseline, with a second confirmatory measurement.Results: Strong agreement was observed between ctDNA response and radiographic response (Cohen's kappa, 0.753). Median time to initial response among patients who achieved responses in both categories was 24.5 days by ctDNA versus 72.5 days by imaging. Time on treatment was significantly longer for ctDNA responders versus nonresponders (median, 205.5 vs. 69 days; P < 0.001). A ctDNA response was associated with superior progression-free survival [hazard ratio (HR), 0.29; 95% CI, 0.09-0.89; P = 0.03], and superior overall survival (HR, 0.17; 95% CI, 0.05-0.62; P = 0.007).Conclusions: A drop in ctDNA level is an early marker of therapeutic efficacy and predicts prolonged survival in patients treated with immune checkpoint inhibitors for NSCLC. Clin Cancer Res; 24(8); 1872-80. ©2018 AACR.

Conflict of interest statement

Conflicts of Interest: Patent applications have been filed covering aspects of the described ctDNA assay technology, with A.A.P. listed as an inventor.

©2018 American Association for Cancer Research.

Figures

Fig. 1. Schematic of ctDNA assay and representative patient cases

A, Schematic illustration of the enhanced Error Suppressed Deep Sequencing assay for circulating tumor DNA (ctDNA) quantitation. MLT, molecular lineage tag; BC, barcode. B and C, Plasma levels of ctDNA and measurements of radiographic tumor burden are plotted for two representative patients with metastatic NSCLC: a patient with treatment response and a patient with progressive disease. B, An 89 year-old woman who received anti-PD-1 immunotherapy as first-line treatment achieved undetectable ctDNA on day 42, and met radiographic response criteria on day 125. The patient received 27 cycles of immunotherapy, with treatment continuing as of the data cutoff date. Undetectable ctDNA is indicated by open diamonds. C, A 73 year-old woman who received first-line anti-PD-1 immunotherapy failed to meet criteria for radiographic or ctDNA response. Radiographic progression was noted on day 38 and therapy was stopped on day 73 (date of death). Radiographic and ctDNA measurements for the remaining 26 patients in the study are presented in Supplementary Fig. S1.

Figure 2. Concordance, Magnitude, and Timing of ctDNA and Radiographic Response to Immunotherapy

A, Agreement of ctDNA response and best radiographic response, defined as the lowest ratio of [tumor burden on any post-baseline scan] to [tumor burden at baseline] (26) (n = 24 patients). Tumor burden was measured according to RECIST, version 1.1 (19). Red outline indicates patients who achieved a ctDNA response. Dotted lines indicate a 30% decrease or 20% increase in RECIST sum of diameters. B and C, Percentage change in ctDNA level from baseline during the first 100 days of immunotherapy among patients with at least a 30% decrease (B, n = 10) or a 20% increase (C, n = 6) in RECIST-defined tumor burden. D, Lowest ctDNA level (percentage change from baseline) measured within the first 50 days after initiation of immunotherapy, for patients who achieved radiographic partial response vs. those who did not. Each dot represents one patient (n = 24). The median value for each group is indicated by a horizontal line. A dashed line indicates a 50% decrease in ctDNA level, which is the threshold for ctDNA response. P=0.002 by Wilcoxon rank sum test. E, Time to radiographic vs. ctDNA response among patients who achieved both types of response (n = 10). Dates of ctDNA and radiographic measurements meeting response criteria are shown. Also shown are preceding time points that failed to meet response criteria as well as confirmatory measurements for both ctDNA and imaging.

Figure 3. Duration of Treatment and Intervals of Radiographic and ctDNA Response

The relationship between duration of treatment benefit and achievement of radiographic or ctDNA response is shown (n = 28 patients). Immunotherapy treatment durations are plotted as horizontal bars, with arrows indicating ongoing therapy as of the data cutoff date. Overlying lines depict periods of radiographic and ctDNA response for each patient, and hash marks indicate measurement time points. Arrows denote ongoing ctDNA or radiographic response based on the last available measurement.

Figure 4. Progression-free and Overall Survival According to ctDNA Response

Extended Kaplan-Meier curves (20) provide estimates of (A) progression-free survival and (B) overall survival for all patients (n = 28). A time-varying categorization was used to designate patients as ctDNA responders or ctDNA non-responders. All patients were initially classified as non-responders because response could not be assessed until after treatment initiation. Patients were considered ctDNA responders if a ≥50% reduction of ctDNA was observed from baseline with a second consecutive confirmatory value. Patients were subsequently re-classified as non-responders if two consecutive measurements rose above the 50% threshold.