9P Early circulating tumor DNA (ctDNA) kinetics and gene expression analysis to predict treatment outcomes with anti-PD-1 therapy

ctDNA kinetics in the first 6 weeks and immune-related gene expression signatures can predict outcomes in patients (pts) treated with anti-PD-1 therapy. The earliest predictive timepoint in ctDNA kinetics for benefit to this therapy is unknown. Pts with recurrent/metastatic head and neck squamous cell carcinoma treated with pembrolizumab or nivolumab monotherapy were prospectively enrolled. Plasma was collected at baseline (B), 2, 3, 8, 15, 22 and 29 days after first dose. Whole exome sequencing (WES) and RNA-seq were performed in archival tumor. ctDNA was analyzed using a bespoke 16 gene panel based on matched WES (SignateraTM). Differential Gene Expression Analysis was performed with DESeq2. Gene Set Enrichment Analysis included different transcription factors (TF), molecular/immune pathways and PREDICT-IO signature (PMID 36055464). A total of 104 plasma samples from 15 pts were collected. ctDNA was detected in 90/104 (87%). Clinical Benefit (CB) rate, defined as complete (CR), partial response (PR) or stable disease (SD) > 6 months by RECIST 1.1, was 47% (1 CR, 3 PR, 3 SD). There were no differences in ctDNA quantity at B according to local/distant disease, primary site or PD-L1 status. A decrease in ctDNA at day 8 from B was associated with CB (100 vs 14%, p<0.01) and with longer progression-free survival (PFS) adjusted by Holm-correction for multiple comparisons (HR: 22.9 95%CI 2.5-211.3, p=0.02) compared to a stability/increase. This association was also seen at day 15, 22 and 29 but not at day 2 or 3. A steady decline in ctDNA beyond day 8 (↓ΔctDNA) was observed in 4 pts (3 PR, 1 SD). Immune-related pathways and TF were significantly enriched in CR/PR and ↓ΔctDNA. Oncogenic pathways and TF were enriched in pts with increase/stability beyond day 8 (↑ΔctDNA). PREDICT-IO High was associated with longer PFS (HR: 7.7 95%CI 1.5-38, p=0.005). All PREDICT-IO Low pts were ↑ΔctDNA (N=7). Within PREDICT-IO High pts, ↓ΔctDNA showed a trend to longer PFS than ↑ΔctDNA (HR: 6.9 95%CI 0.95-63, p=0.051). A decrease in ctDNA by day 8 of anti-PD1 therapy is associated with CB and longer PFS. ctDNA kinetics can improve predictive value of PREDICT-IO High signature. Validations in larger pan-cancer cohorts are needed.