BATF DRIVES A TARGETABLE CONVERGENT GENE PROGRAM IN CROHN’S DISEASE ASSOCIATED CD4+ T CELLS

Abstract INTRODUCTION Dysfunction of T helper cells promotes uncontrolled inflammation in Crohn’s Disease (CD). Chromatin accessible domains can be hijacked by transcription factors (TFs) to drive pathogenic programs in disease. BATF is a pioneering TF that is essential in T cell differentiation, especially in the proinflammatory TH17 cells. BATF was recently reported to regulate 3D chromatin structure in mouse CD4+ T cells. The aim of this study is to identify an actionable target to sustain T cell identity and function. METHODS We used single cell RNA sequencing from gut resident CD4+ T cells to compare the transcriptional profiles of the CD4+ T helper cells in healthy individuals and CD patients. To discover upstream regulators of T cell identities in CD, we used a multiomic approach including RNA-seq and assay for transposase-accessible chromatin (ATAC-seq) in different T cell subtypes (TH1, TH17, and T regulatory cells). We used motif analysis pipelines to identify unique and distinct TFs in chromatin regions specific to each T cell subtype. To target BATF driven genes, we used CRISPR-mediated deletion. Given the reported role of BATF in 3D chromatin, we performed HiChIP to identify long-range interacting regions in the context of BATF activation by TNFa. RESULTS We found that gut resident CD4+ T cells in healthy individuals have distinct transcriptional profiles. In contrast, identities of T helper cells converge in CD patients, adopting a shared pathogenic transcriptional identity. Interestingly, BATF was significantly upregulated in all gut-resident T helper cells of CD patients compared to healthy controls. We also found that the inflammatory signal, TNFa, induces BATF gene programs in CD4+ T cells. We identified the upstream epigenetic activator, BRD4, as a major regulator of BATF induced genes. Knockout of BRD4 in T cells significantly downregulated these gene programs. We found that inflammation promotes reprogramming of the 3D chromatin landscape of T cells, increasing the number of interactions of activator DNA elements to BATF and BRD4 driven genes and disrupting T cell function. CONCLUSIONS This study identifies a new mechanism of T cell dysfunction in CD. BATF and BRD4 promote expression of a shared pathogenic transcriptional program in all gut-resident T helper cells of CD patients. These factors alter the 3D chromatin landscape of T helper cells, leading to aberrant activation of pathogenic genes. In this study, we uncover BRD4 as an actionable target to sustain function of T helper cells with the goal of controlling inflammation in CD patients.