Abstract 1109: BN2 subtype of diffuse large B-cell lymphoma is characterized by distinct alternative splicing
Authors: Sanyeowool An, Ja Min Byun, Youngil Koh, Sung-Soo Yoon
Journal: Cancer Research (2025)

Abstract Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous cancer with unique genetic subtypes and clinical profiles. Alternative splicing (AS) is pivotal in regulating cellular growth, tissue invasion, disease progression, and immune evasion in cancer. However, its specific contributions and associations with the molecular subtypes of DLBCL, remain inadequately characterized.Using RNA sequencing (RNA-Seq) and whole-exome sequencing (WES) data from 620 DLBCL patients, we analyzed splicing activity across genetic subtypes classified by the LymphGen algorithm. Splicing-related pathways were assessed using mean z-scores calculated from normalized expression values (log2(TPM + 0.01)). rMATS was used to quantify splicing events in terms of percent spliced in (PSI) values by comparing each subtype with the combined group of all other subtypes. Notably, splicing-related pathways showed relative activation in the BN2 subtype compared to other subtypes, suggesting a distinct role for splicing dysregulation in its molecular phenotype. Principal component analysis (PCA) of PSI values across all AS events further highlighted BN2’s distinct molecular profile, with BN2 samples forming a separated cluster from other subtypes. These findings suggest that splicing dysregulation in the BN2 subtype, defined by translocations in BCL6, a well-established transcriptional regulator, may potentiate the downstream effects of disrupted transcriptional control.rMATS analysis revealed significant splicing alterations in RPLP0 (retained introns), ACTG1 (alternative 5' splice sites and retained introns), ACTB (retained introns), and CD74 (skipped exons), highlighting disruptions in ribosomal stability, cytoskeletal organization, and immune regulation (P-value &amp;lt; 0.05). Differential Transcript Usage (DTU) analysis further validated that isoform-level changes in BN2 corresponded to significant events identified by rMATS. Splicing alterations in RPLP0, a ribosomal stability regulator, suggest potential impairments in protein synthesis and cellular homeostasis, while dysregulation of ACTB and ACTG1, critical cytoskeletal proteins, may enhance cellular motility and invasiveness. These housekeeping genes showed disease-specific splicing in BN2, highlighting their biomarker potential and role in pathogenesis. Similarly, CD74, which plays a key role in antigen presentation and immune modulation, showed splicing changes that may contribute to the unique molecular and immune characteristics of BN2.By integrating pathway analyses, PCA, and splicing data, this study highlights BN2-specific molecular vulnerabilities and provides insights into the development of splicing-targeted therapeutic interventions. Future research should focus on validating these findings in preclinical models to evaluate their potential as diagnostic markers or therapeutic targets in DLBCL. Citation Format: Sanyeowool An, Ja Min Byun, Youngil Koh, Sung-Soo Yoon. BN2 subtype of diffuse large B-cell lymphoma is characterized by distinct alternative splicing [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 1109.