Integrated multi-omic profiling reveals two distinct splenic marginal zone lymphoma subgroups with prognostic relevance

Splenic marginal zone lymphoma (SMZL) is a rare B-cell malignancy with notable genetic, epigenetic, and clinical heterogeneity. This study utilized coding and non-coding sequencing (n=74), including whole-genome sequencing (WGS) on 24 paired tumour-normal samples, targeted sequencing (n=55) and DNA methylation in 126 cases to characterize the disease. From WGS, we identified recurrent, predominantly clonal, coding mutations in KLF2 (50%), KMT2D (25%) and NOTCH2 (25%), alongside rare mutations in FLNC (8%), novel mutations in FAM135B (17%) and non-coding mutational hotspots in BCL6, PAX5 and BACH2, linked to aberrant somatic hypermutation. At least one non-coding hotspot was detected in 69% of cases. Copy-number aberrations (CNAs) were present in 73% of cases, including del(7q) (27%), gain(3q) (17%) and trisomy 12 (13%). DNA methylation profiling revealed two epigenetic subgroups: SMZL-HR (high-risk, n=67) and SMZL-LR (low-risk, n=59). SMZL-HR was associated with adverse features such as female sex, IGHV1-2*04 usage, KLF2 mutations, del(7q), shorter telomeres, and elevated epiCMIT scores. Transcriptomic analysis highlighted enhanced cell proliferation in SMZL-HR, with enrichment of E2F and G2M checkpoint pathways and epigenetic regulation via EZH2. SMZL-HR patients had significantly shorter time to first treatment (TTFT) (HR: 1.9, p=.003) and reduced overall survival (HR: 2.5, p=.039): 85% of SMZL-HR patients required treatment and showed a higher frequency of transformation (p=.007) and mortality (p<.001). Multivariate analysis confirmed SMZL-HR as an independent predictor of shorter TTFT (HR: 2.4, p=.001). These findings demonstrate the role of DNA methylation and molecular profiling in SMZL risk stratification.