Abstract 109: Integrative analyses of the cfDNA fragmentome and TCR repertoires capture chemo-immunotherapy response in diffuse pleural mesothelioma.

Abstract Background: Immunotherapy-containing therapies have shown promise for patients with unresectable diffuse pleural mesothelioma (DPM), yet there are no reliable strategies to monitor therapy response. By expanding the compendium of cancer-associated alterations profiled, including genome-wide fragmentation patterns, cell-free DNA (cfDNA) whole genome sequencing (WGS) enables tracking of tumor dynamics. In tandem, while understudied, T cell clone dynamics may be informative in capturing early immunotherapy response. Methods: Using 314 tumor and peripheral blood biospecimes, we analyzed serial plasma cfDNA samples (n=135) from 55 patients with unresectable DPM, who received durvalumab with platinum-based chemotherapy (NCT02899195). Following cfDNA extraction and genomic library preparation, cfDNA at baseline (C1D1), Cycle 2 Day 1 (C2D1), and Cycle 5 Day 1 (C5D1) underwent low-coverage (1-2x) whole genome sequencing. Tumor- and mutation-naive estimates of tumor fraction were derived by applying the DELFI tumor score (DELFI-TS) model, which integrates genome-wide fragmentation patterns and chromosomal arm aneuploidy. In parallel, we performed TCR Vβ CDR3 next-generation sequencing on tumor (n=43) and peripheral serial blood (n=136) samples. The TCR repertoire was characterized using clonality, TCR clonotype/cluster dynamics, and the Morisita-Horn similarity index to assess repertoire similarity across samples. Clinical outcomes were assessed by radiographic response, progression-free (PFS), and overall survival (OS). Results: Patients with distant metastasis (M1) had higher DELFI-TS levels (p=0.038). At baseline, DELFI-TS levels were numerically higher for radiographic non-responders (SD/PD) vs responders (CR/PR). Using the 92th percentile of DELFI-TS in non-cancer cfDNA control samples to determine the limit of blank, patients with detectable baseline DELFI-TS (ctDNA+) had shorter PFS and OS (log-rank p0.001). Patients that attained a radiographic response had more clonal peripheral TCR repertoires at both baseline and on-therapy timepoints compared to non-responders (p=0.037 at C1D1; p=0.007 at C2D1; p=0.042 at C5D1). Morisita-Horn similarity between C1D1 and on-therapy was lower in non-responders than responders (p=0.019 for C1D1 vs C2D1; p=0.036 for C1D1 vs C5D1). In contrast, a more diverse intra-tumoral TCR repertoire was noted for patients with an OS of 12 or more months (p=0.018). Conclusions: Our findings provide proof-of-concept that cfDNA fragmentomic analyses can quantify pre-treatment cfDNA tumor fraction that may capture clinical outcomes with chemo-immunotherapy response for patients with DPM. Longitudinal analyses of peripheral TCR repertoires can further differentiate responding from non-responding DPM, supporting the notion that joint analyses may more accurately capture immunotherapy response. Citation Format: Jinny Huang, Jennifer Li, James R. White, Shashikant Koul, Gavin Pereira, Nisha Rao, Jennie Yao, Julie R. Brahmer, Robert B. Scharpf, Rachel Karchin, Victor E. Velculescu, Zhouxin Sun, Suresh S. Ramalingam, Patrick M. Forde, Noushin Niknafs, Valsamo (Elsa) K. Anagnostou. Integrative analyses of the cfDNA fragmentome and TCR repertoires capture chemo-immunotherapy response in diffuse pleural mesothelioma abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 109.