Genomic programming of IRF4-expressing human Langerhans cells

Abstract

Langerhans cells (LC) can prime tolerogenic as well as immunogenic responses in skin, but the genomic states and transcription factors (TF) regulating these context-specific responses are unclear. Bulk and single-cell transcriptional profiling demonstrates that human migratory LCs are robustly programmed for MHC-I and MHC-II antigen presentation. Chromatin analysis reveals enrichment of ETS-IRF and AP1-IRF composite regulatory elements in antigen-presentation genes, coinciding with expression of the TFs, PU.1, IRF4 and BATF3 but not IRF8. Migration of LCs from the epidermis is accompanied by upregulation of IRF4, antigen processing components and co-stimulatory molecules. TNF stimulation augments LC cross-presentation while attenuating IRF4 expression. CRISPR-mediated editing reveals IRF4 to positively regulate the LC activation programme, but repress NF2EL2 and NF-kB pathway genes that promote responsiveness to oxidative stress and inflammatory cytokines. Thus, IRF4-dependent genomic programming of human migratory LCs appears to enable LC maturation while attenuating excessive inflammatory and immunogenic responses in the epidermis.

Langerhans cells immunocompetency is critical for IDO1-dependent ability to induce tolerogenic T cells

“…Supporting the association between immunocompetence and ability to induce tolerance, LC migration out of the epidermis resulted in an even greater ability to induce Tregs than immunocompetent (S2) steadystate LCs. Analysis of single LC transcriptomes confirmed that migratory LCs are mature and characterised by upregulation of MHC II molecules, co-stimulatory molecules (CD80 and CD86) and chemokine receptors (CCR7), indicating readiness for migration to local lymph nodes, mediating interaction with T cells to promote adaptive immune responses 39,40,41,19,27,28 .…”

“…This is in concordance with the current understanding of gene transcription regulation, and highlights the importance of tolerance for LCs. While IRF4 51,52 , KLF6 53 RELB 54,55 , and ELK1 56 have been previously implicated in regulation of immunity or tolerance, HMGN3 binds to nucleosomes and regultes chromatin organisation 57 . Implication of its function in LCs are certainly intriguing, and warrant further detailed investigations.…”

“…To explore further the link between LC activation status and tolerance induction, we sought to investigate the effect of in vitro migration from epidermal sheets on LCs tolerogenic characteristics and their molecular profile. We and others have previously shown that LCs, which have migrated out of the epidermis are more immune activated and primed to mediating T cell responses 6,27,28 . Therefore, we sought to compare the capability of both steady-state LC and migrated LC to prime naïve CD4 T cells towards a tolerogenic phenotype.…”

“…However, when compared to dexamethasone and vitamin D3 stimulated model tolerogenic dendritic cells (TolMoDC), trypsinised steady-state LC display unique upregulated biological pathways with no crossover of differentially expressed genes (DEGs) when compared to unstimulated TolMoDC (FigureS1A, Figure S1B, Supplementary table 1A). To explore the gene expression profiles underlying healthy LC tolerogenic function and to evaluate population heterogeneity in situ we performed single cell RNAseq on "steady-state LC" dissociated from healthy skin using the dispase/liberase protocol, as published previously 27,28 . UMAP dimensionality reduction analysis of 607 steady-state LCs revealed heterogeneity was present amongst the population, with LCs transitioning from one state to another ( Figure 1A).…”

“…Figure S4A). Upregulated genes in migrated LC included CD83 and HLA-DRA as well as CCR7 and IRF4, which have been highlighted as key regulators of LC migration and activation 27,28 . Upregulation of CD86 was also seen in migrated LC compared to both steady-state LC clusters ( Figure 4C), validating their highly immunocompetent status.…”