Abstract A024: Harnessing repressive β-catenin-LEF1 complexes in chronic lymphocytic leukemia and Richter’s transformation

Abstract

Chronic lymphocytic leukemia (CLL) and Richter’s transformation (RT) are characterized by high expression of LEF1, a key partner of β-catenin. Despite elevated LEF1 levels, β-catenin protein remains low in CLL and RT compared to solid tumors, due to continuous phosphorylation by GSK3β and subsequent proteasomal degradation (Cosgun et al., Nature Cancer, 2026). To identify mechanisms driving this constitutive β-catenin turnover, we performed genome-wide CRISPR knockout screens in β-catenin reporter cell lines. In addition to known negative regulators such as APC, CSNK1A1, and AXIN1, multiple components of the neddylation pathway emerged as top hits, including the NEDD8-activating enzyme subunits (NAE1, UBA3), the E3 ligase FBXW11, and NEDD8 itself. Deletion of these genes increased β-catenin levels while reducing cell viability and colony formation, indicating a critical role for NAE1-mediated neddylation in β-catenin degradation. Using the Eμ-Tcl1 transgenic CLL model, we found that loss of β-catenin did not affect expansion of CD5+CD19+ leukemic cells or leukemia-free survival. In contrast, stabilization of β-catenin selectively depleted CD5+CD19+ cells and prevented disease development. Consistently, primary samples from CLL (n=10) and RT (n=3) patients were highly sensitive to pharmacological β-catenin stabilization using the GSK3β inhibitor LY2090314 (IC50 = 3.5 nM). Analysis of public drug-screening datasets revealed a strong correlation between LEF1 expression and sensitivity to GSK3β inhibition (P = 0.0004). CRISPR screens performed under GSK3β inhibitor treatment (LY2090314, AZD1080, CHIR99021) further identified formation of β-catenin-LEF1 complexes as the central mechanism of toxicity in B cells. In this context, β-catenin/LEF1 activation induced canonical target genes but, unlike in epithelial cells, repressed MYC and BCL2. Deletion of LEF1 impaired β-catenin nuclear localization, reversed transcriptional changes, and rescued cell viability. Co-immunoprecipitation and CUT&RUN analyses showed that LEF1 recruits β-catenin to Ikaros factors and NuRD complexes, reducing H3K27ac at MYC and BCL2 enhancers and leading to gene repression and cell death. Because β-catenin phosphorylation by GSK3β precedes neddylation, we tested whether dual inhibition of GSK3β and NAE1 would enhance therapeutic effects. NAE1 inhibitors (pevonedistat and TAS4464) showed strong synergy with LY2090314 in patient-derived CLL and RT samples. While each agent alone demonstrated activity in preclinical RT models, the combination significantly reduced leukemia burden and prolonged survival (P = 2.3 × 10-6). Importantly, clinical trials for patients with solid tumors, neurological disorders and autoimmune diseases demonstrated favorable safety and PK/PD profiles of GSK3B- and NAE1-inhibitors. Together, these findings identify repressive β-catenin/LEF1 complexes as a previously unrecognized therapeutic vulnerability and support a rationale to repurpose existing GSK3β- and NAE1-inhibitors for the treatment of advanced CLL and RT.