Genomic programming of antigen cross-presentation in IRF4-expressing human Langerhans cells

Abstract

Langerhans cells (LCs) in the epidermis present MHC I and MHC II-restricted antigens thereby priming either CD8 or CD4 T cell immune responses. The genomic programs and transcription factors regulating antigen presentation in LCs remain to be elucidated. We show human LCs are highly efficient in MHC I-antigen cross-presentation but lack the transcription factor IRF8 that is critical in dendritic cells. LC migration from the epidermis enhances their ability to cross-present antigens and is accompanied by the induction of the transcription factor IRF4, whose expression is correlated by scRNA-seq with genes involved in ubiquitin-dependent protein degradation. Chromatin profiling reveals enrichment of EICE and AICE composite DNA binding motifs in regulatory regions of antigen-presentation genes, which can be recognized by IRF4 in conjunction with PU.1 or BATF3 expressed in LCs. Thus, the genomic programming of human LCs including inducible expression of IRF4 with enhanced cross-presentation distinguishes them from conventional dendritic cells.

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 .…”

“…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.…”