The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (RNA-seq, CD4+ T cell, part1)

Tissue-resident T-cells (TRM) are deeply involved in immune memory at the site of inflammation. Here, we identified two key transcription factors, RUNX2 and BHLHE40 as regulators of pathologically relevant CD4-positive TRM in the inflamed gut mucosa of Crohn’s disease patients. CD4+ T cells were sorted from mononuclear cells isolated from surgically resected fresh gut specimens by flow cytometry. RUNX2 and BHLHE40 were then knocked down using lentiviral transduction. Infected cells were subsequently re-sorted by flow cytometry, total RNA was extracted using TRIzol reagent, and samples were subjected to bulk RNA sequencing.