Abstract 1942: Copy number aberrations in the ctDNA uncover clinical and biological heterogeneity in aggressive B-cell lymphomas

Abstract Introduction: Circulating tumor DNA (ctDNA) has emerged as a valuable tool in revealing molecular heterogeneity and risk factors of large B-cell lymphoma (LBCL). Several ctDNA estimates, such as variant profiling and minimal residual disease kinetics, have been thoroughly dissected, while multiple other molecular aspects accessible in the liquid biopsy (LB), such as DNA copy number aberrations (CNAs) and changes in serum proteome, remain to be disclosed. We studied CNAs from the ctDNA of LBCL patients treated in a Nordic phase II trial to expand the clinically applicable LB repertoire. Materials and methods: The patients (n=123) included in the study were young (18-64 years), had clinically high-risk LBCL and were treated in a Nordic LBC-06 trial with dose-dense immunochemotherapy. A duplex adapter informed 750 kb gene panel was applied to pretherapeutic plasma ctDNA samples, and variants and CNAs were called using Illumina's DRAGEN pipeline. Clinical data, ctDNA variants (n=123), and serum protein levels, including inflammatory (PD-L1, IL10, IL18, and CXCL9) and subtype-specific (TARC and TACI) markers measured with Luminex assay (n=122) were explored in the context of CNAs. Results: Profiling of ctDNA revealed CNAs (range 1-38) in 80 (65%) patients. The detection of CNAs was affected by ctDNA variant allele frequency. The most recurrently altered regions included gains in the REL (2:p16) and BCL6 (3:q27) genes and losses in the CDKN2A/B (9p:21) and histone (6p:22) loci. Comparison of TP53 status (loss in 11 (9%) patients) with clinical data uncovered that TP53 assessment from the LB was more predictive than routinely performed FISH-informed TP53 analysis for overall survival (OS; HR 7.23, p = 0.001 vs HR 2.84, p = 0.09). Moreover, loss of TP53 correlated with P53 immunohistochemistry positivity (p < 0.001) and remained prognostic for OS in multivariable analysis together with age-adjusted International Prognostic Index (HR 8.49, p < 0.001). Correlation with serum protein profiles showed associations between high levels of inflammatory proteins and CNAs in key oncogenic pathways. These included gains in the NFκB pathway genes MALT1 (p < 0.001) and REL (p <0.01), immune evasion genes, such as CD274 (p < 0.05), and losses in the tumor suppressor genes PRDM1 (p < 0.05) and CDKN2A (p < 0.05). Furthermore, extended LB analysis of serum TARC levels, ctDNA variants, and CNAs revealed a subgroup of patients initially diagnosed as diffuse LBCL with a primary mediastinal B-cell lymphoma-like molecular fingerprint. Conclusions: Together, we show that minimally invasive CNA profiling improves risk stratification and molecular characterization of LBCL subtypes. By integrating several LB approaches, we present CNA landscapes that reflect immune evasion and a more aggressive clinical course of the disease and provide potential actionable vulnerabilities for clinical decision-making. Citation Format: Maare Arffman, Leo Meriranta, Judit Jørgensen, Marja-Liisa Karjalainen-Lindsberg, Klaus Beiske, Mette Pedersen, Kristina Drott, Øystein Fluge, Sirkku Jyrkkiö, Peter Brown, Harald Holte, Sirpa Leppä. Copy number aberrations in the ctDNA uncover clinical and biological heterogeneity in aggressive B-cell lymphomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1942.