RUNX2 and BHLHE40 KD, and RUNX1 and RUNX3 KO by the lentiviral CRISPR system. (A) qPCR analysis of RUNX2 and BHLHE40 KD in CD patient–derived CD4⁺ T cells. n = 11–15 per group; statistical significance was determined using a paired t test, ****P < 0.0001. (B) Gating strategy of mScarlet3-positive infected cells indicating successful transfection. (C) qPCR analysis of RUNX2 and BHLHE40 KD T cells from control patient–derived CD4⁺ T cells. n = 4 per group; statistical significance was determined using a paired t test, *P < 0.05. (D) Validation of RUNX1 and RUNX3 KO by western blot. KO efficiency of RUNX1 and RUNX3 using three independent RNAs for RUNX1 (KO1–3), and two for RUNX3 (KO 1 and 2). KO2 for both RUNX1 and RUNX3 KO was used for the analysis. (E) qPCR analysis of RUNX1 and RUNX3 KO 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 = 8 per group. *P < 0.05, **P < 0.01, ****P < 0.0001. Source data are available for this figure: SourceData FS5.