β-Catenin in desmoid-type fibromatosis: deep insights into the role of T41A and S45F mutations on protein structure and gene expression

Desmoid-type fibromatosis (DF) is a rare mesenchymal lesion with high risk of local recurrence. Specific beta-catenin mutations (S45F) appeared to be related to this higher risk compared to T41A-mutated or wild-type (WT). We explored the influence of both mutations and WT on structure stability and affinity of beta-catenin for alpha-catenin and the pattern of gene expression that may influence DF behavior. Using 33 surgically resected primary DFs harboring T41A (n = 14), S45F (n = 10), or WT (n = 9), we performed a comparative molecular analysis by protein/protein interaction modeling, gene expression by DASL microarrays, human inflammation gene panel, and assessment of immune system-based biomarkers by immunohistochemistry. Mutated proteins were more stable than WT and formed a weaker complex with alpha-catenin. Consensus unsupervised gene clustering revealed the presence of two DF group-mutated (T41A + S45F) and WT (P = 0.0047). The gene sets 'Inflammatory-Defense-Humoral Immune Response' and 'Antigen Binding' were significantly enriched in T41A. The deregulation of 16 inflammation-related genes was confirmed. Low numbers of T cells and tumor-associated macrophages (TAM) infiltrating the tumors and low/absent PD-1/PD-L1 expression were also identified. We demonstrated that mutated DFs (T41A or S45F) and WT are two distinct molecular subgroups with regard to beta-catenin stability, alpha-catenin affinity, and gene expression profiling. A different inflammation signature characterized the two mutated groups, suggesting mediation either by T41A or by S45F. Finally, all mutated cases showed a low number of TIL and TAM cells and a low or absent expression of PD-1 and PD-L1 consistent with beta-catenin activation insensitive to checkpoint blockade.