An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells.

James Davies,Clive M Gray,Jonathan West,Gemma Porter,Andres F Vallejo,Sofia Sirvent,Kalum Clayton,Marta E Polak,Nyaradzo T L Chigorimbo-Murefu,Yamkela Qumbelo,Ben Macarthur,Patrick Stumpf

doi:10.3389/fimmu.2021.665312

James Davies, Clive M Gray + Show 10 more

Open Access

https://doi.org/10.3389/fimmu.2021.665312

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Abstract

Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels, coordinating both immunogenic and tolerogenic immune responses. To determine molecular switches directing induction of LC immune activation, we performed mathematical modelling of gene regulatory networks identified by single cell RNA sequencing of LCs exposed to TNF-alpha, a key pro-inflammatory signal produced by the skin. Our approach delineated three programmes of LC phenotypic activation (immunogenic, tolerogenic or ambivalent), and confirmed that TNF-alpha enhanced LC immunogenic programming. Through regulon analysis followed by mutual information modelling, we identified IRF1 as the key transcription factor for the regulation of immunogenicity in LCs. Application of a mathematical toggle switch model, coupling IRF1 with tolerance-inducing transcription factors, determined the key set of transcription factors regulating the switch between tolerance and immunogenicity, and correctly predicted LC behaviour in LCs derived from different body sites. Our findings provide a mechanistic explanation of how combinatorial interactions between different transcription factors can coordinate specific transcriptional programmes in human LCs, interpreting the microenvironmental context of the local tissue microenvironments.

Highlights

Langerhans cells (LCs), identifiable by high CD207/Langerin and CD1a expression act as immune sentinels at the epidermis and, through antigen presenting function, are responsible for maintaining tissue immune homeostasis [1]
To investigate transcriptional programmes induced by epidermal pro-inflammatory cytokines in LCs, we performed single cell analysis of human primary migrated LCs exposed to 24h stimulation with TNF-alpha vs unstimulated control
Clustering and dimensionality reduction analysis of 775 cells (UMAP, ScanPy, version=1.5.0) revealed that LC migrated from abdominal skin and cultured in the presence or absence of TNF-alpha contained a predominant large cluster, confirmed to be LCs through high expression of MHC II genes (CD74, HLADRB1, HLA-DRB5), as well as two additional populations identified to be melanocytes (TYRP1, TYR) and T cells (CD3D) (Logistic regression, ScanPy pipeline, version=1.5.0), which were removed from downstream analysis (Supplementary Figures 1A–C)

Summary

Introduction

Langerhans cells (LCs), identifiable by high CD207/Langerin and CD1a expression act as immune sentinels at the epidermis and, through antigen presenting function, are responsible for maintaining tissue immune homeostasis [1]. The plasticity of migrated LC to induce both immunogenic and tolerogenic adaptive T cell responses [4,5,6,7,8,9] has revealed the complexity in discerning the decision-making process of LCs to drive either immunogenic or tolerogenic responses and has highlighted the question as to how LCs skew T cell activation to favour responses that are preferential in different biological contexts, such as inflammation. In the context of diverse signalling from the external environment and epidermal microenvironment, LCs can promote immunogenic responses to protect against harmful pathogens, or promote tolerogenic responses to prevent unwarranted inflammation to self-antigen and innocuous agents [5, 10,11,12]. The molecular mechanisms for this decision-making process are largely unknown

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