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Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era.

Swindell WR, Stuart PE, Sarkar MK, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE - BMC Med Genomics (2014)

Bottom Line: Susceptibility-associated variation at intergenic (non-coding) loci was evaluated to identify sites of allele-specific transcription factor binding.Half of DEGs showed highest expression in skin cells, although the dominant cell type differed between psoriasis-increased DEGs (keratinocytes, 35%) and psoriasis-decreased DEGs (fibroblasts, 33%).Assignment of candidate cell types to genes emerging from GWAS studies provides a first step towards functional analysis, and we have proposed an approach for generating hypotheses to explain GWAS hits at intergenic loci.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA. wswindel@umich.edu.

ABSTRACT

Background: Genome-scale studies of psoriasis have been used to identify genes of potential relevance to disease mechanisms. For many identified genes, however, the cell type mediating disease activity is uncertain, which has limited our ability to design gene functional studies based on genomic findings.

Methods: We identified differentially expressed genes (DEGs) with altered expression in psoriasis lesions (n = 216 patients), as well as candidate genes near susceptibility loci from psoriasis GWAS studies. These gene sets were characterized based upon their expression across 10 cell types present in psoriasis lesions. Susceptibility-associated variation at intergenic (non-coding) loci was evaluated to identify sites of allele-specific transcription factor binding.

Results: Half of DEGs showed highest expression in skin cells, although the dominant cell type differed between psoriasis-increased DEGs (keratinocytes, 35%) and psoriasis-decreased DEGs (fibroblasts, 33%). In contrast, psoriasis GWAS candidates tended to have highest expression in immune cells (71%), with a significant fraction showing maximal expression in neutrophils (24%, P < 0.001). By identifying candidate cell types for genes near susceptibility loci, we could identify and prioritize SNPs at which susceptibility variants are predicted to influence transcription factor binding. This led to the identification of potentially causal (non-coding) SNPs for which susceptibility variants influence binding of AP-1, NF-κB, IRF1, STAT3 and STAT4.

Conclusions: These findings underscore the role of innate immunity in psoriasis and highlight neutrophils as a cell type linked with pathogenetic mechanisms. Assignment of candidate cell types to genes emerging from GWAS studies provides a first step towards functional analysis, and we have proposed an approach for generating hypotheses to explain GWAS hits at intergenic loci.

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Cluster analysis of 885 genes decreased in psoriasis lesions and their expression across 10 cell types. We identified 885 PP-decreased DEGs with PP/PN fold-change less than 0.67 and FDR less than 0.05 (n = 216 patients; Wilcoxon rank sum test). These genes were clustered based upon their expression pattern across 10 cell types (Spearman correlation distance metric and average linkage). The red-blue heatmap shows the expression of each gene in each cell type, with red colors indicating relatively high expression (compared to normal human skin) and blue colors indicating relatively low expression (compared to normal human skin). The yellow-black heatmap shows the cell type assigned to each gene (highest median expression with detection frequency greater than 10%). The chart on the far right shows the estimated median fold-change (PP/PN) for each gene (n = 216 patients).
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Figure 4: Cluster analysis of 885 genes decreased in psoriasis lesions and their expression across 10 cell types. We identified 885 PP-decreased DEGs with PP/PN fold-change less than 0.67 and FDR less than 0.05 (n = 216 patients; Wilcoxon rank sum test). These genes were clustered based upon their expression pattern across 10 cell types (Spearman correlation distance metric and average linkage). The red-blue heatmap shows the expression of each gene in each cell type, with red colors indicating relatively high expression (compared to normal human skin) and blue colors indicating relatively low expression (compared to normal human skin). The yellow-black heatmap shows the cell type assigned to each gene (highest median expression with detection frequency greater than 10%). The chart on the far right shows the estimated median fold-change (PP/PN) for each gene (n = 216 patients).

Mentions: PP-decreased DEGs included a disproportionate number of genes assigned to fibroblasts (P < 0.05; Fisher’s Exact Test; Figures 2 and 4). This trend was reinforced by a rank-based analysis, which showed that fibroblast-associated genes tended to have decreased expression in PP versus PN skin (P = 1.2 × 10−97; GSEA; Additional file 6, Part B). Additionally, whereas PP-decreased DEGs usually had lower-than-expected detection frequency and expression in most cell types, this wasn’t the case for fibroblasts; in contrast, PP-decreased DEGs had higher-than-expected detection frequency in fibroblasts on average (P = 0.048; Additional file 10). Moreover, for nearly all patients (84%), fibroblast signature scores were significantly low (P < 0.05), indicating that genes specifically expressed by fibroblasts tend to decline in PP skin (Additional file 9). Consistent with these results, PP-decreased genes were enriched with respect to genes showing elevated expression in LCM-dissected reticular dermis in comparison to normal human skin (P = 1.2 × 10−46; GSEA; data not shown). 33% of PP-decreased DEGs (291/885) were expressed more highly in fibroblasts than any other cell type (Figure 2), of which TSPAN8 and PAMR1 were among the most strongly repressed in psoriasis lesions (Additional file 11). PP-decreased DEGs assigned to fibroblasts were associated with functions involving development, morphogenesis and cell adhesion (data not shown).


Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era.

Swindell WR, Stuart PE, Sarkar MK, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE - BMC Med Genomics (2014)

Cluster analysis of 885 genes decreased in psoriasis lesions and their expression across 10 cell types. We identified 885 PP-decreased DEGs with PP/PN fold-change less than 0.67 and FDR less than 0.05 (n = 216 patients; Wilcoxon rank sum test). These genes were clustered based upon their expression pattern across 10 cell types (Spearman correlation distance metric and average linkage). The red-blue heatmap shows the expression of each gene in each cell type, with red colors indicating relatively high expression (compared to normal human skin) and blue colors indicating relatively low expression (compared to normal human skin). The yellow-black heatmap shows the cell type assigned to each gene (highest median expression with detection frequency greater than 10%). The chart on the far right shows the estimated median fold-change (PP/PN) for each gene (n = 216 patients).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4060870&req=5

Figure 4: Cluster analysis of 885 genes decreased in psoriasis lesions and their expression across 10 cell types. We identified 885 PP-decreased DEGs with PP/PN fold-change less than 0.67 and FDR less than 0.05 (n = 216 patients; Wilcoxon rank sum test). These genes were clustered based upon their expression pattern across 10 cell types (Spearman correlation distance metric and average linkage). The red-blue heatmap shows the expression of each gene in each cell type, with red colors indicating relatively high expression (compared to normal human skin) and blue colors indicating relatively low expression (compared to normal human skin). The yellow-black heatmap shows the cell type assigned to each gene (highest median expression with detection frequency greater than 10%). The chart on the far right shows the estimated median fold-change (PP/PN) for each gene (n = 216 patients).
Mentions: PP-decreased DEGs included a disproportionate number of genes assigned to fibroblasts (P < 0.05; Fisher’s Exact Test; Figures 2 and 4). This trend was reinforced by a rank-based analysis, which showed that fibroblast-associated genes tended to have decreased expression in PP versus PN skin (P = 1.2 × 10−97; GSEA; Additional file 6, Part B). Additionally, whereas PP-decreased DEGs usually had lower-than-expected detection frequency and expression in most cell types, this wasn’t the case for fibroblasts; in contrast, PP-decreased DEGs had higher-than-expected detection frequency in fibroblasts on average (P = 0.048; Additional file 10). Moreover, for nearly all patients (84%), fibroblast signature scores were significantly low (P < 0.05), indicating that genes specifically expressed by fibroblasts tend to decline in PP skin (Additional file 9). Consistent with these results, PP-decreased genes were enriched with respect to genes showing elevated expression in LCM-dissected reticular dermis in comparison to normal human skin (P = 1.2 × 10−46; GSEA; data not shown). 33% of PP-decreased DEGs (291/885) were expressed more highly in fibroblasts than any other cell type (Figure 2), of which TSPAN8 and PAMR1 were among the most strongly repressed in psoriasis lesions (Additional file 11). PP-decreased DEGs assigned to fibroblasts were associated with functions involving development, morphogenesis and cell adhesion (data not shown).

Bottom Line: Susceptibility-associated variation at intergenic (non-coding) loci was evaluated to identify sites of allele-specific transcription factor binding.Half of DEGs showed highest expression in skin cells, although the dominant cell type differed between psoriasis-increased DEGs (keratinocytes, 35%) and psoriasis-decreased DEGs (fibroblasts, 33%).Assignment of candidate cell types to genes emerging from GWAS studies provides a first step towards functional analysis, and we have proposed an approach for generating hypotheses to explain GWAS hits at intergenic loci.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, MI 48109-2200, USA. wswindel@umich.edu.

ABSTRACT

Background: Genome-scale studies of psoriasis have been used to identify genes of potential relevance to disease mechanisms. For many identified genes, however, the cell type mediating disease activity is uncertain, which has limited our ability to design gene functional studies based on genomic findings.

Methods: We identified differentially expressed genes (DEGs) with altered expression in psoriasis lesions (n = 216 patients), as well as candidate genes near susceptibility loci from psoriasis GWAS studies. These gene sets were characterized based upon their expression across 10 cell types present in psoriasis lesions. Susceptibility-associated variation at intergenic (non-coding) loci was evaluated to identify sites of allele-specific transcription factor binding.

Results: Half of DEGs showed highest expression in skin cells, although the dominant cell type differed between psoriasis-increased DEGs (keratinocytes, 35%) and psoriasis-decreased DEGs (fibroblasts, 33%). In contrast, psoriasis GWAS candidates tended to have highest expression in immune cells (71%), with a significant fraction showing maximal expression in neutrophils (24%, P < 0.001). By identifying candidate cell types for genes near susceptibility loci, we could identify and prioritize SNPs at which susceptibility variants are predicted to influence transcription factor binding. This led to the identification of potentially causal (non-coding) SNPs for which susceptibility variants influence binding of AP-1, NF-κB, IRF1, STAT3 and STAT4.

Conclusions: These findings underscore the role of innate immunity in psoriasis and highlight neutrophils as a cell type linked with pathogenetic mechanisms. Assignment of candidate cell types to genes emerging from GWAS studies provides a first step towards functional analysis, and we have proposed an approach for generating hypotheses to explain GWAS hits at intergenic loci.

Show MeSH
Related in: MedlinePlus