Prognostic and predictive value of ultrasensitive ctDNA monitoring in a metastatic pan-cancer cohort treated with immune checkpoint inhibitors in the context of phase 1 clinical trials.
Authors: Toledo Rodrigo De Almeida , Calahorro García Alma M , Mirallas Oriol , Moreno Ana , Galvao Vladimir , Alonso Guzmán , Vieito Maria , Brana Irene , Oberoi Arjun , Lostes-Bardaji M. Julia , Jimenez Jose , Sanz Marta , Viaplana Cristina , Perez-Lopez Raquel , Nuciforo Paolo , Abbott Charles , Pugh Jason , Chen Richard , Boyle Sean Michael , Garralda Elena 
Published: June 2024

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Background: Determining which patients will achieve clinical benefit from immune checkpoint inhibition (ICI) therapy remains an open question. Liquid biopsy tests to assess baseline and early dynamics of circulating tumor DNA (ctDNA) may allow clinicians to track response more granularly and predict ICI response or resistance prior to imaging. However, lack of sensitivity may hinder accurate detection of low ctDNA levels in tumors with low shedding rates or during substantial drops and clearance in response. Methods: This study represents a cohort of 175 patients with refractory metastatic tumors from 18 different cancer types, who received 1-3 successive lines of ICI treatment in the context of phase-1 clinical trials. Thus far, 609 plasma samples from 90 stage-IV cancer patients receiving immune checkpoint inhibitor (ICI) treatment have been processed. ctDNA was profiled using the NeXT Personal assay, a liquid biopsy platform that leverages whole-genome sequencing of tumor and normal samples to create custom, patient-specific panels that include up to 1,800 somatic variants. This enables the detection of molecular residual disease (MRD) down to a detection threshold of 1 part per million (PPM) of ctDNA. Results: NeXT Personal assay detected positive levels of ctDNA in 99% (81/82) of plasma baseline samples, with a wide dynamic range, extending from 4.2 PPM (~0.00042% TF) to ~640,000 PPM (~64% TF) (median limit of detection = 2 PPM, 0.0002% TF). Lower ctDNA values at baseline were correlated with increased duration of PFS (log-rank p=0.017, HR=0.57, 95% CI 0.36-0.91) and extended OS (log-rank p=0.002, HR=0.46, 95% CI 0.28-0.75). Early reduction in ctDNA level from baseline to treatment cycle 3 was associated with significant increases in PFS (log-rank p=0.001, HR=0.36, 95% CI 0.19-0.67) and OS (log-rank p=0.015, HR=0.44, 95% CI 0.22-0.87), representing a >3-fold increase in both median PFS and OS. ctDNA clearance resulted in significant improvement in both PFS and OS (PFS: log-rank p=0.002, HR=0.24, 95% CI 0.09-0.62; OS: log-rank p=0.01, HR=0.29, 95% CI 0.1-0.8). All plasma timepoints from periods of durable complete response (CR) assessed via RECIST 1.1 were ctDNA-negative, with a molecular clearance lead time of 277 days over radiographically confirmed CR. Conclusions: We demonstrate that early ctDNA dynamics are predictive of long-term ICI response in the advanced, pan-cancer ECT setting. Even in this refractory advanced cancer cohort, an ultra-sensitive assay was required for accurate MRD status determination, with low ctDNA detections down to 4.2 PPM that might otherwise have been missed. Taken together, these findings suggest a high sensitivity ctDNA assay is crucial for accurate monitoring of ICI response, providing information for more accurate patient management.