Circulating Tumor DNA Dynamics Predict Benefit from Consolidation Immunotherapy in Locally Advanced Non-Small Cell Lung Cancer

Abstract

Circulating tumor DNA (ctDNA) molecular residual disease (MRD) following curative-intent treatment strongly predicts recurrence in multiple tumor types, but whether further treatment can improve outcomes in patients with MRD remains unclear. We applied CAPP-Seq ctDNA analysis to 218 samples from 65 patients receiving chemoradiation therapy (CRT) for locally advanced NSCLC, including 28 patients receiving consolidation immune checkpoint inhibition (CICI). Patients with undetectable ctDNA after CRT had excellent outcomes whether or not they received CICI. Among such patients, one died from CICI-related pneumonitis, highlighting the potential utility of only treating patients with MRD. In contrast, patients with MRD after CRT who received CICI had significantly better outcomes than patients who did not receive CICI. Furthermore, the ctDNA response pattern early during CICI identified patients responding to consolidation therapy. Our results suggest that CICI improves outcomes for NSCLC patients with MRD and that ctDNA analysis may facilitate personalization of consolidation therapy.

Extended Data Fig. 1:. Validation of predictive value of ctDNA MRD after chemoradiation therapy (CRT) alone.

a, Event chart showing timing of therapy, progression based on RECIST 1.1 evaluation of imaging, and results of ctDNA testing for each patient. b, Kaplan-Meier analysis of freedom from progression stratified by ctDNA detection within 4 months of completing CRT (n=6 not detected, n=6 detected). P values were calculated using a two-sided log-rank test.

Extended Data Fig. 2:. ctDNA dynamics during consolidation immune checkpoint inhibition (CICI) after chemoradiation therapy (CRT) predicts disease progression.

Kaplan-Meier analysis of (a) freedom from progression and (b) freedom from distant progression in patients with ctDNA decreasing early on-CICI (n=5) and ctDNA increasing early on-CICI (n=5). P values were calculated using two-sided log-rank tests.

Extended Data Fig. 3:. Pretreatment tumor mutational burden is not significantly correlated with response to chemoradiation or consolidation immune checkpoint inhibition (CICI).

Pretreatment tumor mutational burden in non-synonymous mutations per megabase extrapolated from CAPP-Seq in (a) patients with ctDNA detected (n=26) and not detected (n=25) after chemoradiation therapy and (b) patients with ctDNA increasing early on-CICI (n=5) and decreasing early on-CICI (n=5). P values were calculated using two-sided Mann-Whitney tests. Bars represent medians.

Fig. 1:. Study schema and pretreatment genotypes for patients with locoregionally advanced non-small cell lung cancer treated with chemoradiation and consolidation immunotherapy.

a, Schematic of treatment, genotyping, and ctDNA monitoring for the two patient cohorts. Tumor genotyping was performed using tumor tissue if available or pretreatment plasma in combination with peripheral blood leukocytes. Plasma samples were collected for ctDNA quantification pretreatment and within 4 months of completing all planned radiation and chemotherapy (post-CRT) in patients treated without consolidation immune checkpoint inhibition (No CICI cohort). In patients who received consolidation immune checkpoint inhibition (CICI cohort), plasma samples were collected pretreatment, a median of 1 week after completing chemoradiation before starting consolidation immune checkpoint inhibition (Pre-CICI), and a median of 11 weeks into consolidation immune checkpoint inhibition (Early On-CICI). b, Plot of patient characteristics and tumor variants for patients in both cohorts with variants identified from tumor tissue or pretreatment plasma. Each column represents pretreatment information for a single patient. The top heat maps depict key patient characteristics. The middle bar graph displays tumor mutational burden (TMB) extrapolated from the mutation rate measured by CAPP-Seq. The bottom heat maps show mutations in candidate driver genes along with total number of single nucleotide variants detected.

Fig. 2:. ctDNA changes during therapy are associated with outcomes in NSCLC patients treated with chemoradiation therapy (CRT) and consolidation immune checkpoint inhibition (CICI).

a, Event chart showing timing of therapy, progression based on RECIST 1.1 evaluation of imaging, and results of ctDNA testing for each patient in the CICI cohort. b, Proportion of patients with ctDNA detected or not detected pretreatment, pre-CICI, and early on-CICI in the CICI cohort who developed progressive disease during follow-up. The number of patients in each group is displayed on the graph. P values were calculated using two-sided Fisher’s exact tests. c, Kaplan-Meier analysis of freedom from progression in the CICI cohort stratified by ctDNA detection in the early on-CICI sample (n=15 not detected, n=7 detected). P value was calculated using a two-sided log-rank test.

Fig. 3:. Patients with ctDNA not detected after chemoradiation therapy (CRT) may not benefit from consolidation immune checkpoint inhibition (CICI).

a, Example of longitudinal CT imaging with sum of target lesion longest diameters measured according to RESIST 1.1 (RECIST SLD, right y-axis) and ctDNA concentrations (left y-axis) for a patient in the CICI cohort with ctDNA not detected after CRT. ctDNA remained not detected early on-CICI and at last follow-up with no evidence of disease. Tumors are outlined in blue on the CT images. A total of 10 patients in the CICI cohort had similar ctDNA testing and clinical outcomes. b, Example of longitudinal CT imaging and ctDNA concentrations for the one patient in the CICI cohort with ctDNA not detected after CRT who developed grade 5 pneumonitis during CICI. Pneumonitis is outlined in orange on the CT image. c, Kaplan-Meier analysis of freedom from progression in patients with ctDNA not detected pre-CICI treated with CICI (n=13) and patients with ctDNA not detected post-CRT treated without CICI (n=12). P value was calculated using a two-sided log-rank test.

Fig. 4:. ctDNA dynamics predict benefit from consolidation immune checkpoint inhibition (CICI) after chemoradiation therapy (CRT).

a, Kaplan-Meier analysis of freedom from progression in patients with ctDNA detected pre-CICI treated with CICI (n=9) and patients with ctDNA detected post-CRT treated without CICI (n=17). P value was calculated using a two-sided log-rank test. b, ctDNA concentrations for the two ctDNA patterns observed in patients from the CICI cohort with ctDNA detected in the pre-CICI or early on-CICI samples. “Increasing”: ctDNA concentration increases early on-CICI. “Decreasing”: ctDNA concentration decreases early on-CICI. Only patients with evaluable pre-CICI and early on-CICI samples are included. Patients with disease progression in the follow-up period are denoted with a solid line, and patients without disease progression are denoted with a dashed line. c, Percentage of patients and median freedom from progression (mFFP) for each ctDNA pattern. d, Example of longitudinal CT imaging and ctDNA concentrations for a patient with the ctDNA “Increasing” pattern. ctDNA was detected pre-CICI and increased during CICI in a patient who developed pleural metastases, suggesting ctDNA can identify a lack of response to CICI. A total of 4 patients in the CICI cohort had similar ctDNA testing and clinical outcomes. e, Kaplan-Meier analysis of freedom from progression in patients with the ctDNA “Increasing” pattern during CICI (n=5) and patients with ctDNA detected post-CRT treated without CICI (n=17). P value was calculated using a two-sided log-rank test.

Fig. 5:. Decreasing ctDNA concentration during consolidation immune checkpoint inhibition (CICI) identifies MRD-positive patients with improved outcomes.

a-b, Kaplan-Meier analysis of (a) freedom from progression and (b) freedom from distant progression in patients with ctDNA detected after chemoradiation therapy with the ctDNA “Decreasing” pattern during CICI (n=5) and patients with ctDNA detected after chemoradiation therapy not treated with CICI (n=17). P values were calculated using a two-sided log-rank test. c, Proportion of patients with ctDNA detected after chemoradiation therapy not treated with CICI or patients with the ctDNA “Decreasing” pattern during CICI who developed any disease progression and distant progression. The number of patients in each group is displayed on the graph. P values were calculated using two-sided Fisher’s exact tests. d-e, Longitudinal CT imaging, sum of target lesion longest diameters measured by RESIST 1.1 (RECIST SLD, right y-axis), and ctDNA concentrations (left y-axis) for two patients with the ctDNA “Decreasing” pattern during CICI. A total of 5 patients in the CICI cohort had similar ctDNA testing with 1 of 5 patients developing disease progression. d, ctDNA was detected following CRT and converted to not detected during CICI in a patient with no evidence of disease progression at last follow-up. e, ctDNA was detected following CRT and temporarily became not detected during CICI with two cycles of concurrent carboplatin and paclitaxel (CT) before increasing 14 months prior to progression in a patient with an isolated local failure 22 months after starting CRT. Tumors are outlined in blue on the CT images.