Abstract A031: Splicing-derived neoantigens in DLBCL reveal subtype- and cell-type-specific predicted neoantigen targets
Reid Shaw, Eric Perkey, Justin KlineAbstract
Background:
Splicing-derived neoantigens represent a largely unexplored class of immunotherapy targets in diffuse large B-cell lymphoma (DLBCL). While mutation-derived neoantigens have been extensively studied, aberrant splicing can generate tumor-specific peptides absent from normal tissues. The SSNIP pipeline identified tumor-specific splice junctions as a prevalent source of neoantigens in solid cancers but did not include DLBCL.
Methods:
We analyzed RNA-seq from 775 DLBCL transcriptomes (phs000235), identifying tumor-specific junctions by filtering against 1,303 GTEx normal lymphoid samples and validating against 17 FACS-sorted tonsillar B-cell populations spanning naive through memory stages. Neopeptides (8-11 mers) were predicted from junction-spanning reading frames, with MHC-I binding and antigen processing scores assessed via MHCflurry 2.1 across 19 HLA alleles. Immune cell fractions (quanTIseq) and purity-adjusted partial correlations inferred cellular origin. Somatic mutations from 739 samples assessed mutation independence. Samples were classified by DLBCL-IQ immune subtype and LymphGen.
Results:
From 125,062 protein-coding junctions, 7,260 (5.8%) were tumor-specific; none were detected in normal B-cell samples spanning all differentiation stages. After expression filtering, 3,494 neojunctions produced 47,849 predicted MHC binders (IC50 ≤500 nM) and 7,871 strong binders (IC50 ≤50 nM) across 712 genes. Neojunction-producing and somatically mutated genes were largely non-overlapping (11/805, 1.4%), and junction burden correlated with splicing factor expression (152/174 significant, led by HNRNPK, rho=0.50) rather than mutation load (rho=-0.01), establishing neojunctions as a mutation-independent antigen class. Immune deconvolution identified M1 macrophage infiltration as the dominant cell-type signal (87.5% of 1,188 significant associations), suggesting most high-prevalence neojunctions reflect tumor-associated macrophage activity. CD79A, an essential BCR component, showed the strongest correlation with the B-cell fraction (r=0.36, FDR=1.3×10-21) and produced 9 predicted strong MHC binders, identifying it as a candidate tumor-intrinsic neoantigen. Immune quadrant stratification revealed quadrant-specific candidates: GCB-Hot (MBOAT7, 71 strong binders, processing score=0.90); ABC-Hot (UBE2F, IC50=9.9 nM); GCB-Cold (SPIDR, 55 strong binders, processing score=0.92); ABC-Cold (TARS1). Hot-enriched genes included LAIR1 (49% prevalence, 39 strong binders, processing score=0.91); GCB-enriched genes included LMO2 and RRAS2.
Conclusions:
Splicing-derived neoantigens in DLBCL are abundant, mutation-independent, and stratified by immune subtype, cell-of-origin, and inferred cellular origin. CD79A emerges as a priority tumor-intrinsic candidate, while the dominant M1 macrophage signal suggests many candidates may be amenable to myeloid-directed strategies. These findings define a subtype-specific neoantigen landscape for immunotherapeutic investigation in DLBCL.
Citation Format:
Reid Shaw, Eric Perkey, Justin Kline. Splicing-derived neoantigens in DLBCL reveal subtype- and cell-type-specific predicted neoantigen targets [abstract]. In: Proceedings of the Fifth AACR International Meeting on Advances in Malignant Lymphoma: From Discovery to Clinical Impact; 2026 Jun 24-27; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2026;7(3_Suppl):Abstract nr A031.