Identification of checkpoint inhibitor resistance mechanisms in leiomyosarcoma through enrichment of active chromatin-associated cell-free DNA.

Abstract

11545 Background: Leiomyosarcoma (LMS) is a sarcoma subtype with poor metastatic outcomes and limited treatment options. Checkpoint inhibitors (CPI) combination therapy may benefit LMS patients (pts). We previously showed (Lopes, ASCO 2025) that a liquid biopsy assay enriching for active chromatin–associated cell-free DNA (cfDNAac) identified biomarkers predicting clinical benefit in LMS pts treated with durvalumab plus olaparib or cediranib (NCT03851614). Here, we report longitudinal cfDNAac findings at baseline and progression. Methods: Plasma samples at baseline (n=30) and disease progression (n=22) were analyzed using a cfDNAac capture platform. Univariate analysis and recursive feature elimination identified genomic features associated with clinical benefit rate (CBR; complete response/partial response or stable disease >6 months). Molecular transcriptomic profiles, pathway enrichment, and copy number variation (CNV) were analyzed and correlated with CBR and progression-free survival (PFS). Linear mixed-effects models assessed temporal differences in cfDNAac-derived biomarkers between CBR and non-CBR groups. Results: A total of 1,570 baseline cfDNAac features distinguished pts who achieved CBR from those who did not (n=8 vs 22, p < 0.01). Pts with CBR exhibited enrichment of immune-related signatures (i.e., B and T-cell activation, lymphocyte differentiation, and a decrement of extracellular matrix organization [ECM]), all of which were individually significantly associated with longer PFS (p < 0.05). Upon progression, B-cell and T-cell activation significantly decreased, whereas ECM-related signatures increased in CBR compared to non-CBR group, the latter of which remained stable. A higher baseline tumor fraction (>5%) was also associated with reduced CBR (p < 0.05) and shorter PFS (HR = 3.33; CI: 1.32-8.40 p < 0.01). Recurrent CNV losses on chromosome 15 correlated with improved PFS (HR = 2.48; 95% CI: 0.99-6.22; p = 0.052) and CBR (p = 0.0073). At progression, these CNV reverted in CBR pts but remained stable in non-CBR patients. Conclusions: This active chromatin-associated cell-free DNA profiling enables a non-invasive monitoring of dynamic tumor microenvironment remodeling over time and provides insights into emerging mechanisms of resistance to CPI in LMS pts.