A NOVEL TRUNCATING EP300 MUTATION IMPAIRS INTESTINAL EPITHELIAL DIFFERENTIATION IN PATIENT TISSUE AND ORGANOIDS AND CAN BE RESCUED BY CHEMICAL HDAC INHIBITION

Abstract BACKGROUND EP300 encodes p300, a histone acetyltransferase and essential regulator of chromatin accessibility and transcription. We describe a novel human mutation in EP300 causing very early onset IBD (VEOIBD)-like disease, and employ patient-derived organoids to characterize its effects on the intestinal epithelium and validate a precision therapy. RESULTS A 20-month-old female presented with secretory diarrhea and hypovolemic shock, necessitating prolonged intensive care and parenteral nutrition use. Intestinal histology exhibited striking abnormalities, with severe chronic mucosal injury in the colon, and foveolar metaplasia, with abnormal mucosal architecture in the duodenum, implicating defects in epithelial cell differentiation and identity. Whole genome sequencing revealed a novel, heterozygous truncating variant in EP300, which in combination with hallmark syndromic features, confirmed Rubinstein-Taybi syndrome (RTS). Gastrointestinal inflammation or metaplasia have not previously been described in RTS, but two additional subsequently identified cases displayed similar features. We therefore hypothesized that partial loss of p300 function induces decreased chromatin acetylation, leading to impaired cellular differentiation and abnormal epithelial maturation. Analysis of patient duodenoids from the index EP300 variant showed severely impaired viability, abnormal morphology, and reduced growth. Western blot revealed reduced histone H3 acetylation, consistent with defective p300 activity. Transcriptional analysis showed aberrant upregulation of Pepsinogen and reduced Epcam, Alpi, and Neurog3, suggestive of abnormal ectopic lineage differentiation. We hypothesized that treatment with the histone deacetylase inhibitor (HDACi) valproic acid (VPA) would compensate for reduced EP300 function by favoring a state of histone acetylation. VPA-treated EP300 variant duodenoids exhibited increased viability and H3 acetylation and normalization of morphology. VPA also modulated cell differentiation with reduction in pepsinogen expression. CONCLUSION We identified EP300 as a novel monogenic cause of VEOIBD/congenital enteropathy. p300 loss of function leads to significant epithelial disorganization, gastrointestinal metaplasia/dysplasia and altered cell identity in intestinal tissue and enteroids. In vitro application of VPA resulted in significant improvement in epithelial viability and a reduction in ectopic lineage differentiation, supporting its use as precision therapy for our EP300 patient. These results suggest that EP300 function is critical for defining intestinal epithelial differentiation programs and cellular identity. Our work supports a precision approach for epigenetic therapies in genetically defined GI disease and highlights the translational utility of organoids to guide individualized clinical care.