Hepatic leukemia factor directs tissue residency of proinflammatory CD4+ T cells

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. Freshly isolated or thawed single-cell suspensions from human nasal polyps and peripheral blood as well as CD4(iv)-negative tissue-resident and CD4(iv)-positive circulating CD4⁺ T cells from murine lungs, were processed for scRNA-seq using Chromium Single Cell 3’ v3.1 (10x Genomics), and for scATAC-seq using Chromium ATAC v1.1 kits, with all libraries sequenced on a NovaSeq 6000 system (Illumina) using paired-end dual indexing and protocol-specific cycle numbers, at a depth of ≥20,000 read pairs per cell for scRNA-seq and ≥25,000 read pairs per nucleus for scATAC-seq.