Hypermutated Circulating Tumor DNA: Correlation with Response to Checkpoint Inhibitor-Based Immunotherapy

Abstract

Purpose: Tumor mutational burden detected by tissue next-generation sequencing (NGS) correlates with checkpoint inhibitor response. However, tissue biopsy may be costly and invasive. We sought to investigate the association between hypermutated blood-derived circulating tumor DNA (ctDNA) and checkpoint inhibitor response.Experimental Design: We assessed 69 patients with diverse malignancies who received checkpoint inhibitor-based immunotherapy and blood-derived ctDNA NGS testing (54-70 genes). Rates of stable disease (SD) ≥6 months, partial and complete response (PR, CR), progression-free survival (PFS), and overall survival (OS) were assessed based on total and VUS alterations.Results: Statistically significant improvement in PFS was associated with high versus low alteration number in variants of unknown significance (VUS, >3 alterations versus VUS ≤3 alterations), SD ≥6 months/PR/CR 45% versus 15%, respectively; P = 0.014. Similar results were seen with high versus low total alteration number (characterized plus VUS, ≥6 vs. <6). Statistically significant OS improvement was also associated with high VUS alteration status. Two-month landmark analysis showed that responders versus nonresponders with VUS >3 had a median PFS of 23 versus 2.3 months (P = 0.0004).Conclusions: Given the association of alteration number on liquid biopsy and checkpoint inhibitor-based immunotherapy outcomes, further investigation of hypermutated ctDNA as a predictive biomarker is warranted. Clin Cancer Res; 23(19); 5729-36. ©2017 AACR.

FIGURE 1. PFS and OS for VUS >3 versus ≤3 Groups

Panel A: Progression-free survival (PFS) is shown for 69 patients treated with checkpoint inhibitor-based immunotherapy. Comparison groups are those with >3 variants of unknown significance (VUS) circulating tumor DNA (ctDNA) alterations (in blue) versus ≤3 VUS ctDNA alterations (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients who are still progression free at the designated time; they were censored at that point. Panel B: Overall survival (OS) is shown for 69 patients treated with checkpoint inhibitor-based immunotherapy. Comparison groups are those with >3 VUS ctDNA alterations (in blue) versus ≤3 VUS ctDNA alterations (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients still alive at the designated time; they were censored at that point.

FIGURE 2. Landmark Analyses of PFS at 2 Months for Responders and Non-Responders, VUS >3 versus ≤3 Groups

Panel A: A 2-month landmark study for PFS is shown for 15 patients treated with checkpoint inhibitor-based immunotherapy who had >3 VUS ctDNA alterations. Comparison groups are those who achieved response (CR or PR) (in blue) versus those who did not achieve response (SD or PD) (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients who are still progression free at the designated time; they were censored at that point. Panel B: A 2-month landmark study for PFS is shown for 26 patients treated with checkpoint inhibitor-based immunotherapy who had ≤3 VUS ctDNA alterations. Comparison groups are those who achieved response (CR or PR) (in blue) versus those who did not achieve response (SD or PD) (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients who are still progression free at the designated time; they were censored at that point. Panel C: A 2-month landmark study for PFS is shown for 15 patients treated with checkpoint inhibitor-based immunotherapy who had achieved response (CR or PR). Comparison groups are those with >3 VUS ctDNA alterations (in blue) versus ≤3 VUS ctDNA alterations (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients who are still progression free at the designated time; they were censored at that point. Panel D: A 2-month landmark study for PFS is shown for 26 patients treated with checkpoint inhibitor-based immunotherapy who had not achieved response (SD or PD). Comparison groups are those with >3 VUS ctDNA alterations (in blue) versus ≤3 VUS ctDNA alterations (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients who are still progression free at the designated time; they were censored at that point.

FIGURE 3. Landmark Analyses at 2 Months for OS in Responders and Non-Responders, VUS >3 versus ≤3 Groups

Panel A: A 2-month landmark study for OS is shown for 18 patients treated with checkpoint inhibitor-based immunotherapy who had >3 VUS ctDNA alterations. Comparison groups are those who achieved response (CR or PR) (in blue) versus those who did not achieve response (SD or PD) (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients still alive at the designated time; they were censored at that point. Panel B: A 2-month landmark study for OS is shown for 36 patients treated with checkpoint inhibitor-based immunotherapy who had ≤3 VUS ctDNA alterations. Comparison groups are those who achieved response (CR or PR) (in blue) versus those who did not achieve response (SD or PD) (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients still alive at the designated time; they were censored at that point. Panel C: A 2-month landmark study for OS is shown for 15 patients treated with checkpoint inhibitor-based immunotherapy who had achieved response (CR or PR). Comparison groups are those with >3 VUS ctDNA alterations (in blue) versus ≤3 VUS ctDNA alterations (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients still alive at the designated time; they were censored at that point. Panel D: A 2-month landmark study for OS is shown for 39 patients treated with checkpoint inhibitor-based immunotherapy who had not achieved response (SD or PD). Comparison groups are those with >3 VUS ctDNA alterations (in blue) versus ≤3 VUS ctDNA alterations (in red). Data is calculated by method of Kaplan Meier, with log-rank p values. Course 1, day 1 of first immunotherapy represents starting point. Tick marks represent patients still alive at the designated time; they were censored at that point.