Progression of acute-to-chronic atopic dermatitis is associated with quantitative rather than qualitative changes in cytokine responses

Abstract

Background: Although multiple studies have assessed molecular changes in chronic atopic dermatitis (AD) lesions, little is known about the transition from acute to chronic disease stages, and the factors and mechanisms that shape chronic inflammatory activity.

Objectives: We sought to assess the global transcriptome changes that characterize the progression from acute to chronic stages of AD.

Methods: We analyzed transcriptome changes in paired nonlesional skin, acute and chronic AD lesions from 11 patients and 38 healthy controls by RNA-sequencing, and conducted in vivo and histological assays to evaluate findings.

Results: Our data demonstrate that approximately 74% of the genes dysregulated in acute lesions remain or are further dysregulated in chronic lesions, whereas only 34% of the genes dysregulated in chronic lesions are altered already in the acute stage. Nonlesional AD skin exhibited enrichment of TNF, T_H1, T_H2, and T_H17 response genes. Acute lesions showed marked dendritic-cell signatures and a prominent enrichment of T_H1, T_H2, and T_H17 responses, along with increased IL-36 and thymic stromal lymphopoietin expression, which were further heightened in chronic lesions. In addition, genes involved in skin barrier repair, keratinocyte proliferation, wound healing, and negative regulation of T-cell activation showed a significant dysregulation in the chronic versus acute comparison. Furthermore, our data show progressive changes in vasculature and maturation of dendritic-cell subsets with chronicity, with FOXK1 acting as immune regulator.

Conclusions: Our results show that the changes accompanying the transition from nonlesional to acute to chronic inflammation in AD are quantitative rather than qualitative, with chronic AD having heightened T_H2, T_H1, T_H17, and IL36 responses and skin barrier repair mechanisms. These findings provide novel insights and highlight underappreciated pathways in AD pathogenesis that may be amenable to therapeutic targeting.

Keywords: Atopic dermatitis; RNA-sequencing; acute AD; chronic AD; nonlesional.

Figure 1.. Transcriptomic landscape and progressive profiles in AD disease stages.

a) the top three principal components computed using the whole transcriptomic data; b) heatmap illustrating the expression profiles for genes with progressive pattern of up-regulation from non-lesional to acute to chronic AD.

Figure 2. Molecular profiling for AD progression from acute to chronic.

a) effect size in the acute vs chronic AD comparison for genes dysregulated in non-lesional vs. acute AD; b) effect size comparison between non-lesional vs. acute AD (x-axis) against acute AD vs. chronic AD (y-axis). Genes are colored if they are dysregulated in the first (blue), second (red) or both comparisons (purple); c-d) boxplots to illustrate the expression profiles for 2 genes dysregulated in the acute vs. chronic comparison but not in the non-lesional vs. acute comparison.

Figure 3. Heatmap to indicate the presence of cell type signature comparing control vs different AD disease stages.

The color in the heatmap correlates with the presence of the cell type specific signature. The bars on the left indicate the significance level for the difference in cell type signatures when comparing control with different AD skin types.

Figure 4. Cytokine expression and effect in AD.

a) heatmap shows the expression profiles for different cytokines in healthy skin, non-lesional, acute and chronic AD subtypes; b) distributions of the cytokine stimulated “burden” in healthy skin, non-lesional, acute and chronic stages of AD. The values are normalized referencing the control samples.

Figure 5. Changes in gene expression from control to different types of AD skin.

*FDR ≤0.1; **FDR≤0.01; ***FDR≤1×10⁻⁵

Figure 6. Expression of FOXK1 in AD and its modulating effect upon cytokine stimulation.

a) immunostaining for FOXK1 in normal, acute, and chronic AD lesional skin; b) RNA expression (from RT-PCR) of FOXK1, IL4R, CCL5, and IL32 upon the indicated cytokine stimulation in keratinocytes under control (NC) or FOXK1 knockdown (siFOXK1). *p<0.05; **p<0.01; ***p<0.001.