Fig. 1: Major histocompatibility complex class II (MHCII) is strongly overexpressed during aging in whole intestinal crypts in both genders.

a Hierarchical clustering and heatmap of the Pearson correlation of the RNA-seq datasets of mouse intestinal crypts at the indicated ages. n = 4 mice per group were analyzed. b Left panels showing hierarchical clustering and heatmap of the expression level of the differentially expressed genes (DEGs) in the same datasets as in Fig. 1a. Right panels showing line-plots of DEG regulation (mean of gene base scaled count) during aging that are divided into indicated clusters of genes. c Point plot of the gender correlation (R²) of the DEGs found in each gene ontology (GO) pathways divided by the indicated main GO categories. Vertical lines indicate median. P value was calculated by Mann-Whitney two-tail test. d Stacked bar chart of −log10 enrichment p value (Fisher two-sided exact test) in the most relevant GO pathways found dysregulated in aging. GO categories were assigned by following the clustering in Fig. S1d. e Scatter plot of the log2 fold change of the DEGs during aging in the antigen-presenting pathway. r = coefficient of determination. f Venn diagram of the number of the DEGs in female and male mice in antigen-presenting pathway as in Fig. 1e. P value was calculated by hypergeometric two-sided distribution test. High P value indicating a significant gene overlap. g Representative FACS plots showing percentages of MHCII⁺ cells in the indicated conditions. h The bar chart shows the percentage of MHCII⁺ cells from EpCAM⁺ cells in the indicated groups. n = 3 mice per group were analyzed. Error bars represent SD. P value was calculated by two-sided Welch’s t test. i Representative pictures of Major Histocompatibility Complex class II (MHCII-IA) stain the H2-Aa and H2-Ab1 heterodimer of the Antigen Presentation Pathway in young and aged intestinal crypts. The dotted lines indicate the crypt structure. Scale bar, 50 µm.