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. 2023 Sep 30;14:6109. doi: 10.1038/s41467-023-41683-y

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© The Author(s) 2023, corrected publication 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 7 — a Gene set A: DEGs using young CD74⁻ intestinal stem cell versus old CD74⁺ intestinal stem cell in crypts, Gene set B: DEGs using control CD74⁻ intestinal stem cell versus IFNγ treated CD74⁺ intestinal stem cell in organoids, Gene set C: IPA-predicted upstream regulators for secretory lineage. b, c Box plot of Stat1 expression in the indicated groups. P value was calculated by two-tail Wilcoxon rank sum test. d Transcription factor and binding motif prediction on the promoters of the gene markers of the secretory cells in intestine. Top5 significant predicted motifs (q value < 0.001) are shown, indicating STAT6 and STAT1 were significantly enriched to bind secretory lineage gene promoters. P values was calculated by two-tail binomial distribution. Q value was Benjamini-adjusted p value. e, f ChIP-qRT-PCR analysis of the ChIP of Stat1 on H2-Ab1 and Wars promoters in e organoids treated or untreated with IFNγ (2 ng/ml) for 24 h or f intestinal crypts of young or old mice. Each dot represents one mouse. n = 4 mice per group were analyzed. Error bars represent the SD. P value was calculated by paired two-tail t test. g qRT-PCR analysis of Stat1, H2-Ab1, and Wars gene expression level in the indicated conditions. n = 7 mice per group were analyzed. Error bars represent the SD. P value was calculated by two-sided Welch’s t test. h The bar chart shows the percentage of MHCII⁺ cells in the indicated conditions. Organoids treated with IFNγ (2 ng/ml) with or without Ruxolitinib (Rux) for 3 days. n = 4 mice per group were analyzed. Error bars represent the SD. P value was calculated by two-sided Welch’s t test. i The bar chart shows the percentage of Lgr5⁺ cells and cKit⁺ cells in the indicated conditions. n = 4 mice per group were analyzed. Error bars represent the SD. P value was calculated by two-sided Welch’s t test. j Graphical abstract modeling aging-induced alteration in intestinal tissue.