Single-cell response to Wnt signaling activation reveals uncoupling of Wnt target gene expression

Wnt signaling drives nuclear translocation of beta-catenin and its subsequent association with the DNA-bound TCF/LEF transcription factors, which dictate target gene specificity by recognizing Wnt responsive elements across the genome. beta-Catenin target genes are therefore thought to be collectively activated upon Wnt pathway stimulation. However, this appears in contrast with the non-overlapping patterns of Wnt target gene expression in several contexts, including early mammalian embryogenesis. Here we followed Wnt target gene expression in human embryonic stem cells after Wnt pathway stimulation at a single-cell resolution. Cells changed gene expression program over time consistent with three key developmental events: i) loss of pluripotency, ii) induction of Wnt target genes, and iii) mesoderm specification. Contrary to our expectation, not all cells displayed equal amplitude of Wnt target gene activation; rather, they distributed in a continuum from strong to weak responders when ranked based on the expression of the target AXIN2. Moreover, high AXIN2 did not always correspond to elevated expression of other Wnt targets, which were activated in different proportions in individual cells. The uncoupling of Wnt target gene expression was also identified in single cell transcriptomics profiling of other Wnt-responding cell types, including HEK293T, murine developing forelimbs, and human colorectal cancer. Our finding underlines the necessity to identify additional mechanisms that explain the heterogeneity of the Wnt/beta-catenin-mediated transcriptional outputs in single cells.

Automated summary

Wnt signaling activates the nuclear translocation of beta-catenin, which interacts with DNA-bound TCF/LEF transcription factors to regulate target gene specificity. However, the expression patterns of Wnt target genes do not always overlap. In this study, single-cell analysis revealed heterogeneity in the activation of Wnt target genes in human embryonic stem cells and other Wnt-responding cell types. The uncoupling of Wnt target gene expression suggests the presence of additional mechanisms that contribute to the diverse transcriptional outputs mediated by Wnt/beta-catenin signaling in single cells.