The skin transcriptome in hidradenitis suppurativa uncovers an antimicrobial and sweat gland gene signature which has distinct overlap with wounded skin

Abstract

Hidradenitis suppurativa (HS) is a debilitating chronic inflammatory skin disease resulting in non-healing wounds affecting body areas of high hair follicle and sweat gland density. The pathogenesis of HS is not well understood but appears to involve dysbiosis-driven aberrant activation of the innate immune system leading to excessive inflammation. Marked dysregulation of antimicrobial peptides and proteins (AMPs) in HS is observed, which may contribute to this sustained inflammation. Here, we analyzed HS skin transcriptomes from previously published studies and integrated these findings through a comparative analysis with a published wound healing data set and with immunofluorescence and qPCR analysis from new HS patient samples. Among the top differently expressed genes between lesional and non-lesional HS skin were members of the S100 family as well as dermcidin, the latter known as a sweat gland-associated AMP and one of the most downregulated genes in HS lesions. Interestingly, many genes associated with sweat gland function, such as secretoglobins and aquaporin 5, were decreased in HS lesional skin and we discovered that these genes demonstrated opposite expression profiles in healing skin. Conversely, HS lesional and wounded skin shared a common gene signature including genes encoding for S100 proteins, defensins, and genes encoding antiviral proteins. Overall, our results suggest that the pathogenesis of HS may be driven by changes in AMP expression and altered sweat gland function, and may share a similar pathology with chronic wounds.

Fig 1. AMPs are increased in lesional HS, but DCD and other sweat-gland associated proteins are decreased.

(A) Volcano plot showing increased or decreased genes in HS. Graph shows log FC in gene expression of HS lesional skin over HS non-lesional skin samples plotted against negative log p-value of the difference in gene expression. Genes represented in red are upregulated by >2-fold in HS lesional skin (p-adj < 0.05). Genes represented in blue are downregulated by >2-fold in HS lesional skin (p-adj < 0.05). Genes represented in orange were unchanged (FC < 2, p-adj < 0.05) in HS lesional vs. HS non-lesional skin. Non-adjusted p-values were used for generation of the volcano plot to minimize points with tied y-values but significance level was set using the corresponding non-adjusted p-values. (B) Top 50 most differentially expressed probe sets between the HS lesional skin and the HS non-lesional skin. Highlighting shows DEGs. Genes highlighted in blue are downregulated genes of interest; genes highlighted in red are upregulated genes of interest. While DCD is downregulated in HS lesional skin, many other AMPs and interferon-associated molecules are enriched in lesional HS. The top 50 most differentially expressed probes were defined as genes with an adjusted p-value < 0.05 with the largest magnitude FC. Genes were z-score transformed and then the genes and samples were clustered using a correlation distance with complete linkage.

Fig 2. Enriched GO terms.

REVIGO treemap representing the most significantly enriched GO terms associated with DEGs [43]. Larger boxes indicate a smaller p-value and greater disease relevance. Colors indicate GO families in which HS DEGs fall.

Fig 3. S100 proteins are strongly upregulated in HS lesional skin.

qPCR for (A) S100A7 (log₂FC = 3.51, **p < 0.01), (B) S100A8 (log₂FC = 3.41, *p < 0.05) and (C) S100A7A (log₂FC = 6.47, **** p < 0.0001) in lesional and non-lesional HS skin. FC is expressed as average of skin samples from 3 patients. Measurements were collected in triplicate or duplicate, as allowed by RNA yield from samples. Data is shown as mean expression value compared to non-lesional skin +/- the standard error of the mean. Non-lesional and lesional samples were compared using paired t-test. (D) IF staining for S100A7 at 20X. Scale bar is 50μm. (E) IF staining for S100A8 at 20X. Scale bar is 50μm. Immunofluorescence intensity is highest in HS lesional skin, compared to non-lesional and normal skin.

Fig 4. Schematic representation eccrine sweat gland and duct cells.

Diagram of gene expression of A) eccrine sweat gland and B) duct. Genes in blue are decreased in HS lesional skin. Genes in red are increased in HS lesional skin.

Fig 5. DCD is strikingly decreased in HS lesions.

(A) qPCR for DCD (log₂FC = -3.57, *p < 0.05). FC is expressed as average of skin samples from 3 patients. Measurements were collected in triplicate or duplicate, as allowed by RNA yield from samples. Data is shown as mean FC over non-lesional skin +/- the standard error of the mean. Non-lesional and lesional samples were compared using a paired t-test. (B) Immunofluorescence for DCD (red) at 40X in normal skin, HS non-lesional skin, and HS lesional skin. Co-staining was performed with K77 (green), which is a marker of eccrine sweat glands. Scale bar is 100μm. (C) Immunofluorescence for DCD (red) and K77 (green) at 4X showing decreased number of eccrine sweat glands in HS lesional skin. Scale bar is 500μm.

Fig 6. Shared and dissimilar pathways in HS and healing skin wounds.

Venn diagram illustrating shared and dissimilar gene expression in HS lesions and wounded skin. AMP expression is increased in both HS lesional and wounded skin. DCD and other sweat-gland associated proteins show opposite expression; they are decreased in HS lesions but are increased in wounded skin.