Hepatic leukemia factor directs tissue residency of proinflammatory CD4+ T cells [bulk]
CD4+ tissue-resident memory T cells (TRM) contribute to both host defense and pathogenesis of chronic inflammatory diseases.  However, the molecular mechanisms that direct tissue residency and functional heterogeneity of CD4+ TRM remain unknown.  We herein show that the transcription factor, hepatic leukemia factor (HLF), directs the tissue residency program and functionality of CD4+ TRM. HLF simultaneously upregulates tissue retention receptors and downregulates tissue egress receptors via changes in chromatin accessibility, and drives proinflammatory CD4+ TRM by inducing Bhlhe40.  Genetic deletion of Hlf inhibits CD4+ TRM generation, consequently ameliorating airway tissue inflammation in vivo.  In humans, HLF-positive CD4+ TRM from inflamed airway tissue have a tissue residency signature and express inflammatory cytokines.  HLF is therefore a central regulator of proinflammatory CD4+ TRM development and function. Overall design: This study employed RNA-seq, ChIP-seq, and ATAC-seq to investigate the transcriptional and epigenetic roles of Hlf in T cell populations. RNA-seq was used to compare gene expression profiles between circulating and tissue-resident memory T cells with or without Hlf expression. Total RNA was extracted using TRIzol, libraries were prepared with the TruSeq RNA Sample Prep Kit v2, and sequencing was performed on an Illumina NextSeq500. Reads were aligned to the mouse genome (GRCm38) using Bowtie 2 and TopHat, and expression levels were quantified with Cufflinks. ChIP-seq was conducted to identify genome-wide Hlf binding sites in Th2 and Th17 cells using anti-Flag antibodies, followed by library preparation with the NEBNext Ultra II DNA Library Prep Kit and sequencing on a NextSeq500. ATAC-seq was performed to assess chromatin accessibility in Hlf-positive and Hlf-negative cells. Cells were lysed and tagmented with Tn5 transposase, and the resulting libraries were sequenced on a NextSeq500. These approaches provided a comprehensive view of Hlf-mediated transcriptional regulation and chromatin dynamics in T cell subsets.