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KMID : 0381120230450070957
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Genes and Genomics
2023 Volume.45 No. 7 p.957 ~ p.967
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Identification of ulcerative colitis-specific immune cell signatures from public single-cell RNA-seq data
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Kim Han-Byeol
Kim Hyo-Keun
Hong Da-Won
Kim Min-Su
Jang Se-In
Yang Chul-Su
Yoon Seok-Hyun
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Abstract
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Background : Single-cell RNA-seq enabled microscopic studies on tissue microenvironment of many diseases. Inflammatory bowel disease, an autoimmune disease, is involved with various dysfunction of immune cells, for which single-cell RNA-seq may provide us a deeper insight into the causes and mechanism of this complex disease.
Objective : In this work, we used public single-cell RNA-seq data to study tissue microenvironment around ulcerative colitis, an inflammatory bowel disease causing chronic inflammation and ulcers in large intestine.
Methods : Since not all the datasets provide cell-type annotations, we first identified cell identities to select cell populations of our interest. Differentially expressed genes and gene set enrichment analysis was then performed to infer the polarization/activation state of macrophages and T cells. Cell-to-cell interaction analysis was also performed to discover distinct interactions in ulcerative colitis.
Results : Differentially expressed genes analysis of the two datasets confirmed the regulation of CTLA4, IL2RA, and CCL5 genes in the T cell subset and regulation of S100A8/A9, CLEC10A genes in macrophages. Cell-to-cell interaction analysis showed CD4+ T cells and macrophages interact actively to each other. We also identified IL-18 pathway activation in inflammatory macrophages, evidence that CD4+ T cells induce Th1 and Th2 differentiation, and also found that macrophages regulate T cell activation through different ligand-receptor pairs, viz. CD86-CTL4, LGALS9-CD47, SIRPA-CD47, and GRN-TNFRSF1B.
Conclusion : Analysis of these immune cell subsets may suggest novel strategies for the treatment of inflammatory bowel disease.
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KEYWORD
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Ulcerative colitis, Inflammatory bowel disease, Single-cell RNA-seq, Immune cell signature
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