The Germline SH2B3rs111340708 Splicing Variant Drives Intron Retention and Protein Instability by Impacting Clinical Outcomes in Core Binding Factor AML.

The SH2B3 gene, also known as LNK, encodes an adaptor protein that negatively regulates key hematopoietic signaling pathways, including JAK-STAT, MAPK, and PI3K/AKT, thereby maintaining hematopoietic homeostasis. SH2B3 interacts with major signaling regulators such as JAK2, MPL, FLT3, and KIT. Loss-of-function alterations have been reported in several hematologic malignancies, supporting its role as a leukemia predisposition gene. We previously identified a germline start-loss mutation (c.3G > A) in SH2B3 in a family with early-onset myeloproliferative neoplasm, demonstrating that this variant causes SH2B3 haploinsufficiency. In the present study, next-generation sequencing of 149 de novo AML patients identified a frequent intronic polymorphism (rs111340708), located within intron 6 (IVS6) of SH2B3. Although this variant has a reported minor allele frequency (MAF) of approximately 12% in European populations, it was enriched in our AML cohort, reaching 34.2% in Core Binding Factor leukemias (CBFLs). The presence of the rs111340708 variant was associated with inferior overall survival, whereas no significant association with progression-free survival was observed. Functional analyses demonstrated that this polymorphism promotes aberrant IVS6 intron retention in AML cells, resulting in reduced abundance of correctly spliced SH2B3 transcripts and predicted generation of truncated peptides and/or nonsense-mediated decay. Consistently, immunoblot analyses of AML patient samples and hematologic cell lines revealed heterogeneous SH2B3 protein expression, including additional SH2B3-immunoreactive species in variant carriers, together with reduced levels of the canonical SH2B3 protein. Collectively, these findings identify a common germline splicing polymorphism as a novel mechanism contributing to SH2B3 functional impairment in AML and highlight the potential relevance of non-coding variants in leukemia pathogenesis, with possible implications for risk stratification and future therapeutic strategies.