BACKGROUND AND AIM: Genome-wide association studies have provided MTMR3 as a Crohn's-disease-associated gene. Pipk III, which cooperatively functions in phosphatidyl inositol 3,5-bisphosphates [PI(3,5)P2] metabolism with MTMR3, is a kinase that produces PI(3,5)P2 from phophatidyl inositol 3-bisphosphate. We generated enterocyte-specific Pipk III deficient (KO) mice which displayed diarrhea, body weight loss, and pathological findings of epithelial vacuoles, transmural inflammatory cell infiltration, increased fibrosis, and goblet cell depletion, sharing the clinical and histological findings with Crohn's diseae. In this context, we tried to elucidate the mechanisms of intestinal inflammation and fibrosis in Crohn's disease by analyzing those in our KOmice. METHODS:We examined the localization of proteins functioning at apical and basolateral membranes of enterocytes using immunofluorescence staining, and the expression of these membranous proteins in intestinal mucosa of both KO and the control mice using western blot analysis. We compared the expression of inflammationand fibrosis-related genes in intestinal mucosa using RT-PCR. In addition, we monitored the survival of Pipk III KO mice with or without antibiotics to study the relevance of intestinal bacteria in intestinal inflammation of KO mice. Furthermore, we injected fluorescent dextran per anus and observed its mucosal distribution using immunofluorescence staining to evaluate how easily intestinal microbiota can invade to mucosa of KO mice. RESULTS: Although western blot analysis did not show any differences in expression of apical and basolateral membranous proteins between KO and the control mice, immunofluorescence staining revealed mislocalization of these proteins in KO enterocytes, suggesting impaired intracellular vesicle transport and cellular polarity. We found the increased genes expression of proinflammatory cytokines including TNF-alpha, IL-1beta, and IL-6. Meanwhile, the expression of fibrosis-promoting genes such as TGF-beta1 and CTGF, and Snail1, which is a transcription factor that promotes epithelial mesenchymal transition (EMT), was increased in KO mice compared to the control mice. Consistent with this result, immunofluorescence staining revealed that KO enterocytes expressed Vimentin protein more intensely than the control. Furthermore, the survival of KO mice treated with antibiotics was prolonged and fluorescent dextran injected per anus was distributed more scattered in KO mice with antibiotics than those without antibiotics. CONCLUSION: Facilitating entry of intestinal bacteria to mucoca based on impaired intracellular vesicle transport and cellular polarity in enterocytes seems to bring about intestinal inflammation in KO mice. Meanwhile, there is a possibility that EMT in KO enterocytes induces intestinal fibrosis.