Loss of BAP1 expression is a very rare event in gastrointestinal stromal tumors

Gastrointestinal stromal tumors (GISTs), the most common mesenchymal tumors affecting the gastrointestinal tract, are primarily driven by activating KIT and platelet-derived growth factor receptor alpha (PDGRFA) mutations and respond to targeted tyrosine kinase therapy. However, GISTs exhibit various clinical behaviors, regardless of the proposed risk classification. Here, we investigated the expression of BRCA1-associated protein-1 (BAP1) in GIST and analyzed its prognostic significance and utility as a marker in the context of differential diagnosis. Among a total of 226 GIST, only one (0.44%, 1/226 cases) GIST exhibited a loss of BAP1 expression. In the univariate analysis, small intestinal and colorectal GISTs, GISTs with necrosis, recurrence/metastasis, or a higher risk of malignancy were associated with poor overall survival. In the multivariate analysis, GISTs with a higher risk of malignancy or recurrence/metastasis were identified as independent prognostic factors. We conclude that a loss of BAP1 expression is a very rare event, then BAP1 would not play a major role in pathogenesis of GIST.