Abstract Background Previous studies have shown anti-saccharomyces cerevisiae antibody (ASCA) positivity in inflammatory bowel disease (IBD) patients is associated with increased risk of developing IBD and poor prognosis. However, no comprehensive study has elucidated the ASCA positive-related immunological phenotype in non-inflamed and inflamed colonic mucosa and its clinical implications. Methods We collected endoscopic biopsies from 43 ulcerative colitis [28 non-inflamed sites and 43 inflamed sites] and 20 Crohn’s disease at Seoul National University Hospital. Single-cell RNA sequencing (scRNA-seq) was performed on these samples according to the ASCA positivity. First, we compared ASCA-positive and -negative samples obtained from non-lesion sites of UC patients. Second, we investigated immunologic phenotypes in inflamed mucosa based on the disease activity (remission vs active). Results We conducted scRNA-seq analysis of over 130,000 single cells from 28 biopsies obtained from non-inflamed tissues of UC patients. Substantial reduction in the frequency of type 3 innate lymphoid cells (ILC3) and expression of IL18 and IL22 in ILC3s, along with a significant decrease in tight junction-associated genes (TJP1, CLDN3, CLDN4) within epithelial cells were observed in the positive group[P <0.05]. In addition, data from positive group exhibited decreased levels of CSF2 in ILC3s, which is likely contributing to reduced M2 macrophage polarization. We performed scRNA-seq analysis of over 123,673 single cells from 63 biopsies obtained from inflamed tissues. In active inflamed status, the expression of IL-17A - a cytokine that helps maintain tight-junction barrier in the intestinal epithelium during inflammation was decreased in tissue-resident memory T cells (Tc17 TRM) [P 0.026]. In addition, ASCA positive resulted in decreased CD4 central memory T cells (CD4 TCM) [P 0.046], suggesting impaired gut barrier function and subsequent rapid response to reencountered antigens. Cytotoxic gene expression, including granzyme and perforin 1, was increased in CD8 T effector memory cells (CD8 TEM) [P<0.05] during remission, suggesting that ongoing subclinical inflammation may develop and contribute to tissue damage. Conclusion These findings suggest that Saccharomyces cerevisiae infection induces immunological changes characterized by gut barrier dysfunction, rapid responses to commensal antigens, and increased cytotoxic gene expression. Based on these findings, we believe that Saccharomyces cerevisiae may serve as a potential target for preventing disease progression in patients with IBD.
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