de Kleine, R. H. | bioRxiv Science

bioRxiv2025

Differential Wnt/β-Catenin Signaling via TCF7L2/LEF1 Binding Specificity Shapes Cellular and Tumor Phenotypes

The mechanisms by which Wnt/{beta}-catenin signaling regulates gene expression in a tissue- and context-specific manner remain poorly understood, limiting our ability to target the aberrant cell growth typical of many Wnt-driven cancers. Here we focus on malignant liver tumors driven by activating CTNNB1 ({beta}-catenin) mutations that nevertheless display distinct phenotypic states and Wnt outputs. By profiling patient-derived organoids via single-cell transcriptomics and chromatin dynamics, we identify subtype-specific transcriptional and epigenetic profiles. Using CUT&RUN, we show that {beta}-catenin engages distinct genomic regions, dictated by differential association with TCF/LEF family transcription factors. Specifically, we define a novel sequence-specific regulatory element engaged by {beta}-catenin only upon interaction with TCF7L2, revealing that partner choice, independent of CTNNB1 mutational status, ultimately determines cell fate. Our findings, validated across multiple tumor models and patient tissues, offer a framework for understanding how differential {beta}-catenin-TCF/LEF interaction orchestrates context-specific Wnt signaling outcomes. SignificanceWnt/{beta}-catenin signaling is crucial for development and cancer, yet how it drives different gene programs across tissues is unclear. Using patient-derived liver tumor organoids, we show that {beta}-catenins transcriptional output depends on its binding partner: LEF1 or TCF7L2. These factors guide {beta}-catenin to distinct genomic regions, activating either stemness or differentiation genes. We identify a novel helper motif that directs {beta}-catenin-TCF7L2 binding and target selection. By linking partner choice and motif specificity to context-dependent gene regulation, our work provides a unifying mechanism explaining how Wnt/{beta}-catenin signaling produces diverse cellular outcomes.

cancer biology↗

bioRxiv2023

Multi-dimensional profiling of hepatoblastomas and patient-derived tumor organoids uncovers tumor subpopulations with divergent WNT activation profiles and identifies pan-hepatoblastoma drug sensitivities

Hepatoblastoma, the most prevalent pediatric liver cancer, almost always carries a WNT-activating CTNNB1 mutation, yet exhibits notable molecular heterogeneity. To characterize this heterogeneity and identify novel targeted therapies, we performed comprehensive analysis of hepatoblastomas and tumor-derived organoids using single-cell RNA-seq, spatial transcriptomics, single-cell ATAC-seq and high throughput drug profiling. We identified two distinct tumor epithelial signatures: hepatic fetal-like and WNT-high embryonal-like signatures, displaying divergent WNT signaling patterns. The liver-specific WNT targets were enriched in the fetal-like group, while the embryonal-like group was enriched in canonical WNT target genes. Gene regulatory network analysis revealed enrichment of regulons related to hepatic function such as bile acid, lipid and xenobiotic metabolism in the fetal-like subgroup but not in the embryonal-like subgroup. In addition, the dichotomous expression pattern of the transcription factors HNF4A and LEF1 allowed for a clear distinction between the fetal- and embryonal-like tumors. We also performed high-throughput drug screening using patient-derived tumor organoids and identified sensitivity to multiple inhibitor classes, most notably HDAC inhibitors. Intriguingly, embryonal-like tumor organoids, but not fetal-like tumor organoids, were sensitive to FGFR inhibitor treatments, suggesting a dependency on FGFR signaling. In summary, our data uncover the molecular and drug sensitivity landscapes of hepatoblastoma and pave the way for the development of targeted therapies.

cancer biology↗