Abstract
BackgroundChronic lymphocytic leukemia (CLL) is the most common adult leukemia. Mutations in splicing factor 3b subunit 1 (SF3B1), especially the K700E variant, are closely associated with aggressive progression and poor prognosis, though the underlying mechanisms remain unclear. SAT1 plays a pivotal role in polyamine metabolism, which is essential for cell growth and survival. This study investigates how the SF3B1 K700E mutation regulates SAT1 expression, leading to immune evasion in CLL.
Methods and ResultsWe first conducted RNA profiling on MEC-1 cells expressing SF3B1 K700E and primary CLL samples from SF3B1-mutated patients. Integrated expression and splicing analyses revealed upregulation of SAT1 in SF3B1-mutated samples, accompanied by exon 4 skipping and increased mRNA stability. We then employed targeted metabolomics to assess the impact of the spliced isoform of SAT1 (SAT1sp) on polyamine metabolism. The results showed a significant increase in N1-acetylspermidine levels in SAT1sp-overexpressing MEC-1 cells. Additionally, untargeted metabolomic analysis revealed a concomitant enrichment of glutamine metabolism and oxidative phosphorylation, forming a specific metabolic pattern that supports cell survival and proliferation. Functionally, SAT1sp overexpression enhanced cell proliferation and clonogenic potential in CLL cell lines (MEC-1 and JVM-3) and primary CLL cells, while SAT1 knockdown induced apoptosis in these cells. To assess whether CLL-associated SAT1sp expression disrupts T-cell function ex vivo, activated CD8 T cells from healthy donors were co-cultured with MEC-1 cells for 72 hours, and IFNγ production was measured by ELISA. The data demonstrated that SAT1sp overexpression in MEC-1 cells reduced IFNγ secretion and decreased the percentage of GZMB+ and TNFα+ CD8 T cells following co-culture. In line with this, SAT1sp inhibited T-cell-induced cell lysis, as shown by a reduced proportion of CD19+PI+ CLL cells. To investigate the impact of SAT1 on CLL progression in vivo, MEC-1 cells with overexpressed SAT1sp were injected into NSG mice. Mice injected with SAT1sp-overexpressing MEC-1 cells exhibited more pronounced splenomegaly and increased leukemia infiltration, as indicated by CD19 positive staining. To explore the effect of CLL-derived SAT1sp on T-cell function in vivo, a MEC-1 xenograft mouse model was established, followed by two rounds of CD8 T cell injections in NSG mice. The leukemic burden was significantly reduced, with smaller spleens and reduced infiltration in the spleen and liver, while SAT1sp overexpression largely abrogated these effects. These findings highlight the novel role of SAT1 in dampening T-cell functions and facilitating immune evasion in CLL. Mechanistic studies using RNA-seq revealed differentially expressed genes (DEGs) in MEC-1 cells upon SAT1sp overexpression, which were enriched in gene ontology (GO) terms related to “histone modifying activity” and “histone binding.” Consistently, SAT1sp increased the level of H3 acetylation in MEC-1 cells. ChIP-seq further identified Ac-H3 enrichment at the promoter region of IL18BP, a well-known immune checkpoint. Consequently, SAT1sp induced transcription and secretion of IL18BP in both MEC-1 and primary CLL cells. Notably, SAT1 was recently shown to non-canonically acetylate H3K27 domains in mitosis-regulating genes in ovarian cancer (Zheng et al., Nature Communications 2025), suggesting that SAT1-mediated acetylation could serve as a conserved oncogenic mechanism supporting multiple cancer traits. Furthermore, conditioned medium from SAT1sp-overexpressing MEC-1 cells or primary CLL cells significantly decreased the percentage of activated GZMB+ and TNFα+ T cells. Encouragingly, IL18BP knockdown or blockade rescued this effect, indicating that SAT1 suppresses T-cell activation in an IL18BP-dependent manner.
ConclusionThis study provides evidence for a dual mechanism by which SAT1 regulates polyamine metabolism and immune response in SF3B1-mutated CLL. SAT1 enhances polyamine catabolism, supporting leukemia survival through metabolic rewiring. Simultaneously, SAT1 regulates Ac-H3 at the IL18BP promoter, promoting IL18BP expression, inhibiting the IL18/IL18RAP axis, and suppressing CD8 T cell activation, which leads to immune evasion. These findings suggest that targeting SAT1 could be a therapeutic strategy to enhance T-cell-mediated immunity and improve outcomes in SF3B1-mutated CLL.
