Impact of the germline SH2B3 RS111340708 splicing variant on clinical outcomes and signaling deregulation in core binding factor acute myeloid leukemia

Background SH2B3 (LNK) encodes a key adaptor protein that negatively regulates hematopoietic signaling pathways (JAK-STAT, MAPK, and PI3K/AKT) by interacting with mediators such as JAK2, MPL, FLT3, and KIT. While loss-of-function mutations in SH2B3 are known to predispose to myeloid malignancies, the role of recurrent germline variants in modulating signaling deregulation and clinical outcomes in Acute Myeloid Leukemia (AML) remains poorly defined. Aims We aimed to characterize the distribution of the SH2B3 rs111340708 polymorphism across AML molecular subtypes and evaluate its impact on splicing, protein expression, and survival, specifically focusing on Core Binding Factor Leukemias (CBFLs). Methods Samples from 149 AML patients (CBFL, non-CBFL, and CEBPA-mutated) were analyzed using Next-Generation Sequencing (Oncomine Myeloid Research Assay). Functional consequences were assessed via in vitro assays and immunoblotting in primary samples and cell lines. Clinical impact in the CBFL cohort (n=32) was evaluated using Kaplan-Meier survival analysis and log-rank tests (significance at p < 0.05). Results The intronic variant SH2B3 rs111340708 (a deletion within IVS6) was significantly enriched in our AML cohort, appearing in 49% of patients with an allele frequency of 32.9% in CBFLs, markedly higher than the ~12% reported in European populations. In the CBFL subgroup, carriers of the variant had significantly shorter overall survival (OS) compared to non-carriers (median OS 866 days vs. not reached; p=0.011), while progression-free survival (PFS) showed a negative trend (median 285 vs. 998 days; p=0.15). Functional analyses demonstrated that this polymorphism promotes aberrant IVS6 retention, which predictably introduces premature stop codons. Consistently, immunoblotting revealed markedly reduced levels of functional SH2B3 and the expression of protein isoforms with altered molecular weights in carrier patients and cell lines. Summary/Conclusion The SH2B3 rs111340708 splicing polymorphism represents a novel germline mechanism of SH2B3 inactivation in AML. By compromising hematopoietic homeostasis, this high-frequency variant contributes to leukemogenesis and may identifies a high-risk subgroup within CBFL. These findings highlight SH2B3 as a significant prognostic biomarker and suggest that targeting downstream pathways, such as JAK signaling, may provide a tailored therapeutic strategy for SH2B3-deficient leukemias.