Integrated single-cell and spatial transcriptomics reveals heterogeneity of fibroblast and pivotal genes in psoriasis

Abstract

Psoriasis, which is one of the most common skin diseases, involves an array of complex immune constituents including T cells, dendritic cells and monocytes. Particularly, the cytokine IL17A, primarily generated by TH17 cells, assumes a crucial function in the etiology of psoriasis. In this study, a comprehensive investigation utilizing bulk RNA analysis, single-cell RNA sequencing, and spatial transcriptomics was employed to elucidate the underlying mechanisms of psoriasis. Our study revealed that there is an overlap between the genes that are differentially expressed in psoriasis patients receiving three anti-IL17A monoclonal antibody drugs and the genes that are differentially expressed in lesion versus non-lesion samples in these patients. Further analysis using single-cell and spatial data from psoriasis samples confirmed the expression of hub genes that had low expressions in psoriasis tissue but were up-regulated after anti-IL17A treatments. These genes were found to be associated with the treatment effects of brodalumab and methotrexate, but not adalimumab, etanercept, and ustekinumab. Additionally, these genes were predominantly expressed in fibroblasts. In our study, fibroblasts were categorized into five clusters. Notably, hub genes exhibited predominant expression in cluster 3 fibroblasts, which were primarily engaged in the regulation of the extracellular matrix and were predominantly located in the reticular dermis. Subsequent analysis unveiled that cluster 3 fibroblasts also established communication with epithelial cells and monocytes via the ANGPTL-SDC4 ligand-receptor configuration, and their regulation was governed by the transcription factor TWIST1. Conversely, cluster 4 fibroblasts, responsible for vascular endothelial regulation, were predominantly distributed in the papillary dermis. Cluster 4 predominantly engaged in interactions with endothelial cells via MDK signals and was governed by the distinctive transcription factor, ERG. By means of an integrated analysis encompassing bulk transcriptomics, single-cell RNA sequencing, and spatial transcriptomics, we have discerned genes and clusters of fibroblasts that potentially contribute to the pathogenesis of psoriasis.

Figure 1

Single cell data of psoriasis (A) cells were divided to 10 clusters via umap dimensionality reduction algorithm in healthy and psoriasis tissues (B) expression of marker genes in each cluster (C) protein–protein network of hub genes low expressed in psoriasis tissue and up-regulated after ANTI-IL17A treatments (D) expression of hub genes in each cluster (E) subclusters of fibroblasts (F) expression of hub genes in fibroblasts (G) biological process of each cluster of fibroblast involved.

Figure 2

Heterogeneous of fibroblasts in psoriasis (A, B) pseudotime trajectory of fibroblasts in normal skin and psoriasis skin. (C) Branched expression analysis modeling (beam) analysis of genes regulating cell fates, there were two fates of fibroblasts in psoriasis at the first bifurcation. Functions of those genes showed in the left (D) expression of PRELP,FBLN1,MFAP5 and IGFBP5 in psoriasis tissue (E) expression of hub genes in different clusters in spatial tissue (f) distribution of fibroblasts in psoriasis tissue (G, H) expression model of cluster 3 and 4 fibroblasts identified in single-cell data in spatial.

Figure 3

Cell and cell communications in psoriasis (A) increased expression of ligand-receptor pair in psoriasis compared with normal tissue (B) top 20 ligands in fibroblasts identified by the method of NICHENETR (C) top20 receptors on endothelial cells and fibroblasts (D) interaction strengths of different clusters of fibroblasts to other cells (E) significant ligand-receptor pair of fibroblasts to other cells (F) expression of genes in MK, TGFb, IL6 and ANGPTL signals. g. expression of ligands and receptors on spatial transcriptome.

Figure 4

Transcription factors in different fibroblasts clusters (A) transcription factor regulons enriched in fibroblasts. “Extended” means the regulons include motifs that have been linked to the TF using motif similarity from SCENIC pipeline, number of genes contained in regulons showed at end (B) activity of regulons (TWIST, ERG) in fibroblast (C) correlation of genes expressed in fibroblasts (D) expression of TWIST1 and ERG in spatial dimension.