Changes in Circulating Tumor DNA Reflect Clinical Benefit Across Multiple Studies of Patients With Non-Small-Cell Lung Cancer Treated With Immune Checkpoint Inhibitors

PURPOSE

As immune checkpoint inhibitors (ICI) become increasingly used in frontline settings, identifying early indicators of response is needed. Recent studies suggest a role for circulating tumor DNA (ctDNA) in monitoring response to ICI, but uncertainty exists in the generalizability of these studies. Here, the role of ctDNA for monitoring response to ICI is assessed through a standardized approach by assessing clinical trial data from five independent studies.

PATIENTS AND METHODS

Patient-level clinical and ctDNA data were pooled and harmonized from 200 patients across five independent clinical trials investigating the treatment of patients with non-small-cell lung cancer with programmed cell death-1 (PD-1)/programmed death ligand-1 (PD-L1)-directed monotherapy or in combination with chemotherapy. CtDNA levels were measured using different ctDNA assays across the studies. Maximum variant allele frequencies were calculated using all somatic tumor-derived variants in each unique patient sample to correlate ctDNA changes with overall survival (OS) and progression-free survival (PFS).

RESULTS

We observed strong associations between reductions in ctDNA levels from on-treatment liquid biopsies with improved OS (OS; hazard ratio, 2.28; 95% CI, 1.62 to 3.20; P < .001) and PFS (PFS; hazard ratio 1.76; 95% CI, 1.31 to 2.36; P < .001). Changes in the maximum variant allele frequencies ctDNA values showed strong association across different outcomes.

CONCLUSION

In this pooled analysis of five independent clinical trials, consistent and robust associations between reductions in ctDNA and outcomes were found across multiple end points assessed in patients with non-small-cell lung cancer treated with an ICI. Additional tumor types, stages, and drug classes should be included in future analyses to further validate this. CtDNA may serve as an important tool in clinical development and an early indicator of treatment benefit.

Evaluation of lung densitometric and volumetric changes in silicosis patients using three-dimensional software for multidetector CT and the relationship with profusion scores

AIM

To evaluate the density and volume changes in the lungs of silicosis patients and their relationship with the disease severity classification of the International Labor Organization (ILO).

MATERIALS AND METHODS

The multidetector computed tomography (CT) images of 44 patients diagnosed with silicosis and 32 controls that underwent thoracic CT due to trauma were evaluated. Patients with silicosis were divided into three categories according to the ILO classification. Data related to the total lung volume, total lung mean density, lung opacity score, percentage of lung high opacity, and mean density in the lower and upper lobes were obtained using three-dimensional (3D) software.

RESULTS

There was no significant difference between the total lung mean densities of the silicosis and control groups (p=0.213); however, a significant difference was observed between the two groups in terms of the total lung volume (p<0.0001). According to the ILO classification, there was a significant difference between the disease severity categories in relation to the percentage of lung high opacity (p=0.000005). A strong correlation was detected between disease severity and high opacity percentage (p<0.0001, r=0.804). According to the ILO classification, there was also a significant difference between disease severity categories in terms of the lung opacity score (p=0.000144), as well as a moderate correlation between disease severity and opacity score (p<0.0001, r=0.580).

CONCLUSION

Total lung volume is a CT finding that shows variation in exposure to crystalline silica. The percentage of high opacity determined using multidetector CT is an effective parameter in evaluating disease severity.

Early Assessment of Molecular Progression and Response by Whole-genome Circulating Tumor DNA in Advanced Solid Tumors

Treatment response assessment for patients with advanced solid tumors is complex and existing methods require greater precision. Current guidelines rely on imaging, which has known limitations, including the time required to show a deterministic change in target lesions. Serial changes in whole-genome (WG) circulating tumor DNA (ctDNA) were used to assess response or resistance to treatment early in the treatment course. Ninety-six patients with advanced cancer were prospectively enrolled (91 analyzed and 5 excluded), and blood was collected before and after initiation of a new, systemic treatment. Plasma cell-free DNA libraries were prepared for either WG or WG bisulfite sequencing. Longitudinal changes in the fraction of ctDNA were quantified to retrospectively identify molecular progression (MP) or major molecular response (MMR). Study endpoints were concordance with first follow-up imaging (FFUI) and stratification of progression-free survival (PFS) and overall survival (OS). Patients with MP (n = 13) had significantly shorter PFS (median 62 days vs. 310 days) and OS (255 days vs. not reached). Sensitivity for MP to identify clinical progression was 54% and specificity was 100%. MP calls were from samples taken a median of 28 days into treatment and 39 days before FFUI. Patients with MMR (n = 27) had significantly longer PFS and OS compared with those with neither call (n = 51). These results demonstrated that ctDNA changes early after treatment initiation inform response to treatment and correlate with long-term clinical outcomes. Once validated, molecular response assessment can enable early treatment change minimizing side effects and costs associated with additional cycles of ineffective treatment.

Abstract P5-01-13: Longitudinal changes in whole-genome (WG) cell-free DNA (cfDNA) and methylation as a blood-based biomarker to identify early disease progression in advanced breast cancer

Background: Liquid biopsies have potential clinical utility as dynamic biomarkers for treatment response in advanced breast cancer. We evaluated a plasma-only assay to track serial changes in WG cfDNA to identify disease progression prior to routine imaging.

Methods: We prospectively enrolled and serially collected blood from 25 patients with advanced breast cancer. Blood was drawn and collected in Streck tubes prior to start of a new treatment, after the first cycle (median 22 days), and/or second cycle (median 52 days). 4 mL of plasma was separated from peripheral blood, after which cfDNA was isolated from plasma and used to prepare libraries (11 with bisulfite conversion) for WG sequencing (median 20x depth). Based on a patient-specific profile of WG features, including copy-number alterations and cfDNA fragment length, the fraction of tumor-derived cfDNA (ctDNA) was quantified over the initial course of treatment. For a subset of the cohort (11 of 25 patients), we also quantified changes in genome-wide methylation levels from baseline to subsequent timepoints to classify patients as progressors or non-progressors. Imaging was performed per standard practice with treatment response determined by an independent radiologist according to RECIST 1.1 guidelines.

Results: Median age of patients in the cohort was 65 (range 30-83) and included all subtypes—HR+ (n=14), HR+ & HER2+ (n=6), and triple negative (n=5). 52% of patients were on their third line of therapy (range 1-5). On-study therapies were chemotherapy alone (8), targeted + hormone therapy (5), hormone therapy alone (4), targeted + chemotherapy (5), targeted therapy alone (1), or immune checkpoint + HDAC inhibitors (2). Patients with predicted progression by cfDNA (n=5), indicated by an increase in tumor fraction at either post-treatment blood collection, had worse progression-free survival (median 67 days) compared to patients who did not show an increase (n=20; median 207 days) (hazard ratio 7.9, [95% CI 2.2-28.5], log-rank p=3 × 10-4). For the patients who were predicted to progress, the ctDNA assay preceded clinical evaluation by a median of 53 days. All patients with predicted progression were later confirmed to progress at the first follow-up evaluation (5/5, 100% positive predictive value). For the remaining patients, 15 of 20 did not progress (75% negative predictive value). Therefore, sensitivity for the assay was 50% and specificity was 100%. Comparing molecular predictions for 11 of 25 patients based on genomic versus methylation features, 8 non-progressors were classified correctly by both types of features. For the 3 progressors, 2 were predicted correctly based solely on methylation, increasing the sensitivity to detect progression early in the treatment course.

Conclusions: Analyzing ctDNA early in the course of a new therapy holds promise to identify patients with early disease progression across multiple types of treatment. The assay accurately identified patients with no durable clinical benefit earlier, indicating potential clinical utility to change therapy and to limit unnecessary side effects and costs associated with ineffective treatments, if validated in a prospective clinical trial.​ Finally, integrating methylation-based changes with information about genomic alterations may increase performance of ctDNA-based response monitoring.

Citation Format: Andrew A Davis, David Chan, Michael S Oh, Robert W Lentz, Neil Peterman, Alex Robertson, Rohith Srivas, Abhik Shah, Nicole Lambert, Ayse Tezcan, Haluk Tezcan, Young Kwang Chae. Longitudinal changes in whole-genome (WG) cell-free DNA (cfDNA) and methylation as a blood-based biomarker to identify early disease progression in advanced breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-01-13.

Abstract 2279: Serial changes in tumor-derived whole-genome cfDNA fraction to identify early disease progression prior to imaging

Background:

Response to cancer treatment is usually determined by clinical exam and imaging assessment. Here, we analyzed changes in tumor-derived whole-genome cell-free DNA (cfDNA) at baseline and after treatment initiation to determine response to treatment prior to routine imaging.

Methods:

We prospectively enrolled and serially collected blood from 54 patients with metastatic malignancies (21 lung, 20 breast, 13 other tumor types). Baseline blood samples were drawn prior to initiation of a new treatment and at one or two additional time points, after the first cycle (median 21 days) and the second cycle (median 42 days). 4 mL of plasma was separated from peripheral blood collected in Streck Cell-Free DNA Blood Collection Tubes, and cfDNA was isolated from plasma aliquots using Qiagen QIAmp extraction kits. To prepare sequencing libraries, a method optimized for whole genome sequencing (WGS) was used based on the Kapa HyperPrep chemistry. WGS was performed at approximately 25X depth on the Illumina HiSeq X. Based on a patient-specific profile of whole genome features, changes in the fraction of tumor-derived cfDNA were quantified over the initial course of treatment. Imaging was performed per standard practice with treatment response determined by RECIST.

Results:

Median number of prior treatment lines was 1 [range 0-6]. Patients were treated with the following therapies: chemotherapy (27), immunotherapy (14), hormone therapy (7), or targeted therapy (6). For the entire cohort, patients with predicted progression by cfDNA (n=11), indicated by an increase in tumor fraction at either post-treatment blood collection, had worse event-free survival compared to patients that did not show an increase (n=43) (hazard ratio 8.0, [95% CI 3.4-19.2], log-rank p=4.5 x 10-8). For the patients who were predicted to progress, the cfDNA assay preceded clinical evaluation by a median of 39 days. Median progression-free survival was 62 days for patients with predicted progression versus 232 days for others. All patients with predicted progression were later confirmed to progress at the first follow-up evaluation (11/11, 100% positive predictive value). For the remaining patients, 32 of 43 did not progress (74% negative predictive value). Therefore, sensitivity for the assay was 50% and specificity was 100%.

Conclusions:

Analyzing tumor-derived cfDNA early in the course of a new therapy holds promise to identify patients with early disease progression across a variety of tumor histologies and types of treatment. Early identification of patients who are not benefitting from treatment will enable initiation of other potentially effective therapies, and reduce unnecessary side effects and cost associated with these treatments. Further studies are warranted to validate these findings in larger cohorts and to confirm the histology and treatment-independent nature of the approach.

Citation Format: Andrew A. Davis, Wade T. Iams, David Chan, Michael S. Oh, Robert W. Lentz, Neil Peterman, Alex Robertson, Abhik Shah, Rohith Srivas, Nicole Lambert, Tim Wilson, Peter George, Becky Wong, Ayse Tezcan, Ram Yalamanchili, Ken Nesmith, John C. Spinosa, Haluk Tezcan, Young Kwang Chae. Serial changes in tumor-derived whole-genome cfDNA fraction to identify early disease progression prior to imaging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2279.

Whole-genome cell-free DNA (cfDNA) changes as a dynamic blood-based biomarker for early response assessment of advanced tumors

3041

Background: Liquid biopsies have potential clinical utility as dynamic biomarkers for treatment response. We analyzed serial changes in whole-genome (WG) cfDNA to identify patients with disease progression prior to routine imaging. Methods: We prospectively collected clinical data and blood from 69 advanced cancer patients (28 lung, 25 breast, 16 other). Blood was collected at baseline prior to initiation of a new treatment and at one or two additional timepoints (median 21 and 42 days). We isolated plasma cfDNA and prepared sequencing libraries for WG sequencing or WG bisulfite sequencing (median depth 20X). We quantified changes in the fraction of tumor-derived cfDNA over the initial course of treatment to predict progression vs. no progression. Treatment response at first post-treatment imaging was determined by RECIST 1.1 and clinical assessment. Study endpoints were agreement with first post-treatment imaging and progression-free survival (PFS) by cfDNA prediction. Results: Median age of patients was 70 and 59% were female. Patients were treated with the following therapies: chemotherapy (37), immunotherapy (17), endocrine (9), or targeted therapy (6). Patients with predicted progression by cfDNA (14), indicated by an increase in tumor fraction at either post-treatment blood collection, had shorter PFS (median 63 days) compared to patients without an increase (N = 55; median 255 days), with hazard ratio of 10.3 (95% confidence interval 4.6-23.4, log-rank P = 1x10-11). Positive predictive value was 100% for disease progression and negative predictive value was 78%. These findings were consistent in subset analyses of patients with lung (log-rank P = 2x10-5), breast (log-rank P = 3x10-4), and those treated with immunotherapy (log-rank P = 5x10-6). Conclusions: Our results show the ability to detect early disease progression with high fidelity using WG cfDNA prior to first imaging. These findings were consistent across multiple tumor types and treatments, including immunotherapy patients. Once validated, this dynamic, predictive, blood-based biomarker could aid in clinical decision making for early treatment change as a novel and cost-effective approach.

A prospective study tracking longitudinal changes in genome-wide cell-free DNA (cfDNA) methylation to identify early nonresponders to cancer treatment

3042

Background: Methylation is an epigenetic modification linked to cancer pathogenesis. The aim was to determine if changes in cfDNA methylation patterns before and after initiation of treatment could predict non-response to treatment prior to routine imaging and clinical follow-up. Methods: We prospectively collected clinical data and blood from 28 patients with metastatic malignancies (13 lung, 11 breast, 4 other). Blood was drawn prior to start of a new treatment, after first cycle (median 30 days), and/or second cycle (median 57 days). We performed whole-genome (WG) bisulfite sequencing (median depth 18X) on plasma cfDNA to determine methylation levels. By tracking how methylation levels deviate from unaffected individuals, from baseline to subsequent timepoints, we classified patients as either progressors (greater deviance) or non-progressors. Treatment response at first follow-up imaging (FUI) was determined by RECIST 1.1. Study endpoints were agreement with first FUI and progression-free survival (PFS) by cfDNA classification. Results: The cohort consisted of 68% females and the median age was 70. Main treatment regimens were chemo- (N = 12), immuno- (6), endocrine (5), or targeted-therapy (5). PFS was significantly shorter (log-rank p = 8 x 10-7) in patients classified as progressors by cfDNA (N = 8; median: 62 days) compared to non-progressors (N = 20, median: 263 days). For patients classified as progressors, the cfDNA assay preceded imaging and clinical evaluation by a median of 34 days. 7 out of 8 patients classified as cfDNA progressors were later confirmed to progress at first follow-up evaluation (88% positive predictive value). The one patient who was classified as progressor based on cfDNA was stable based on FUI (day 93 of treatment) but was later confirmed as progression on day 128 by FUI. For the remaining patients, 18 of 20 did not progress (90% negative predictive value). Thus, sensitivity for the assay for identifying progression was 78% and specificity was 95%. Conclusions: Our results show that WG cfDNA methylation change is a novel signature with potential to identify patients whose treatment regimen is ineffective prior to imaging.

Effects of the blockade of cardiac sarcolemmal ATP-sensitive potassium channels on arrhythmias and coronary flow in ischemia–reperfusion model in isolated rat hearts

Activation of ATP-sensitive K+ channels (K ATP) during ischemia leads to arrhythmias and blockade of these channels exert antiarrhythmic action. In this study, we investigated the effects of HMR1098, a sarcolemmal K ATP channel blocker and 5-hydroxydeconoate (5-HD), a mitochondrial K ATP channel blocker on cardiac function and arrhythmias in isolated rat hearts. The hearts were subjected to 30 min coronary occlusion, followed by 30 min reperfusion. In the preischemic period, both HMR 1098 and 5-HD slightly increased coronary perfusion pressure. Coronary occlusion increased the perfusion pressure and decreased the left ventricular developed pressure (LVDP) in both control and drug-treated hearts. However, inhibition of LVDP was greater and recovery of the perfusion pressure was lower in 30 micromol/l HMR1098 and 100 micromol/l 5-HD-treated hearts compared to control (P < 0.05). HMR1098, at 3 micromol/l, but not at 30 micromol/l, significantly reduced the ratio of bigeminis, couplets and salvos (P < 0.05). Ventricular tachycardia and ventricular fibrillation were not prevented by HMR1098, at both concentrations, and with 5-HD (100 micromol/l). These results suggest that blockade of sarcK ATP and mitoK ATP channels exert weak antiarrhythmic action, but reduce the recovery of coronary perfusion and contractile force, implying that both types of K(ATP) channels have beneficial role in the recovery of ischemic rat myocardium.