KD of RUNX2 and BHLHE40 in colonic CD4 ⁺ T cells in CD patients leads to a loss of functionality in T _RM _2. (A) Overview of the experimental steps. (B) qPCR analysis of RUNX2 and BHLHE40 KD in colonic CD4⁺ T cells from CD patients. Statistical significance for the comparisons was determined using RM one-way ANOVA, Dunnett’s multiple comparison test. n = 11–15 per group. *P < 0.05, **P < 0.01, ***P < 0.001. (C) Heatmap showing the expression levels of selected genes across the following groups: control (NC), RUNX2 KD (RUNX2i), and BHLHE40 KD (BHLHE40i). Each row represents an individual gene, and each column represents a sample. Color intensity indicates the relative expression level. (D) Pathway analysis of downregulated genes from RUNX2 KD (left) and BHLHE40 KD (right).