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. 2023 Aug 3;14:1161901. doi: 10.3389/fimmu.2023.1161901

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Copyright © 2023 Medina, Murison, Smith, Kinker, Chakravarthy, Vitiello, Turpin, Shen, Yau, Sarmento, Faubion, Lupien, Silverberg, Arrowsmith and De Carvalho

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Single cell transcriptomics reveals a high proportion of cytotoxic pTh17-like cells in inflamed intestinal sites of Crohn’s disease patients. (A) UMAP plots of CD4 T cells from control and inflamed samples across 3 IBD patients, colored based on Louvain clustering (C0 – C2). (B) Bar chart showing the proportion of cells from each sample mapping to each cluster. (C) Bubble plot depicts the similarity between C0-C2 cells and reference T CD4 populations from the DICEdb. Bubble size is proportional to the significance of overlap (hypergeometric test) between gene signatures from C0-C2 and DICEdb populations. Bubbles are colored according to the average expression of DICEdb signatures by cell in C0-C2. (D) Density plots showing the expression of Th1 and Th17 gene signatures by cells in C0-C2. Shown are both classical signatures (Th1: TNF, STAT1, STAT4, CXCR3 and IFNG; Th17: CCR6, STAT3, RORA, IL17A, RORC) as well as those derived from the DICEdb populations. (E) Expression of DICEdb Th1/Th17 genes by C0-C2 cells. We only included genes with significantly increased expression in C0. Cells are ordered by their Th1/Th17 scores, as shown in the lower panel. Bar on the bottom shows the expression of the complete Th1/Th17 signature by each cell. Bars on top annotate the cluster of each cell.