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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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Cell type assignments for 105 psoriasis GWAS candidate genes. The left margin lists each individual gene, the assigned cell type, and the gene’s detection frequency with respect to that cell type (KC = keratinocytes; FB = fibroblasts; CD4 = CD4+ T-cells; NK = NK Cells; CD8 = CD8+ T-cells; B = B-cells; MP = macrophage; MC = monocyte; DC = dendritic cells; NP = neutrophils). Genes are ranked by the degree to which they showed specific expression in the assigned cell type. To obtain the p-value shown for each gene, expression in the assigned cell type was compared to expression in each of the other nine cell types, respectively (n = 50 samples per cell type; Wilcoxon rank sum test). The p-value shown for each gene corresponds to the largest p-value obtained from each of the 9 comparisons to other cell types (asterisk, FDR < 0.05).
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Figure 6: Cell type assignments for 105 psoriasis GWAS candidate genes. The left margin lists each individual gene, the assigned cell type, and the gene’s detection frequency with respect to that cell type (KC = keratinocytes; FB = fibroblasts; CD4 = CD4+ T-cells; NK = NK Cells; CD8 = CD8+ T-cells; B = B-cells; MP = macrophage; MC = monocyte; DC = dendritic cells; NP = neutrophils). Genes are ranked by the degree to which they showed specific expression in the assigned cell type. To obtain the p-value shown for each gene, expression in the assigned cell type was compared to expression in each of the other nine cell types, respectively (n = 50 samples per cell type; Wilcoxon rank sum test). The p-value shown for each gene corresponds to the largest p-value obtained from each of the 9 comparisons to other cell types (asterisk, FDR < 0.05).

Mentions: Further inspection of the 117 psoriasis GWAS candidates revealed that, for many, expression was significantly altered in psoriasis lesions, although in most cases estimated fold-changes did not meet DEG criteria (Figure 5). Overall, 13 candidate genes were also PP-increased DEGs, while 2 others were PP-decreased DEGs (Figure 5). Candidate genes varied in the degree to which expression was specific to a given cell type, and this influenced the confidence with which candidate cell types could be assigned (Figure 6). With respect to LCE3D, for instance, KCs were assigned as the candidate cell type with high confidence, since expression was distinguishably greater in KCs as compared to any other cell type (Figures 5 and 6). Among the candidate genes for which cell type assignment confidence was greatest, most were assigned to KCs or neutrophils, although some were also assigned to fibroblasts (e.g., PTRF and FNDC1; see Figure 6).


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)

Cell type assignments for 105 psoriasis GWAS candidate genes. The left margin lists each individual gene, the assigned cell type, and the gene’s detection frequency with respect to that cell type (KC = keratinocytes; FB = fibroblasts; CD4 = CD4+ T-cells; NK = NK Cells; CD8 = CD8+ T-cells; B = B-cells; MP = macrophage; MC = monocyte; DC = dendritic cells; NP = neutrophils). Genes are ranked by the degree to which they showed specific expression in the assigned cell type. To obtain the p-value shown for each gene, expression in the assigned cell type was compared to expression in each of the other nine cell types, respectively (n = 50 samples per cell type; Wilcoxon rank sum test). The p-value shown for each gene corresponds to the largest p-value obtained from each of the 9 comparisons to other cell types (asterisk, FDR < 0.05).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Cell type assignments for 105 psoriasis GWAS candidate genes. The left margin lists each individual gene, the assigned cell type, and the gene’s detection frequency with respect to that cell type (KC = keratinocytes; FB = fibroblasts; CD4 = CD4+ T-cells; NK = NK Cells; CD8 = CD8+ T-cells; B = B-cells; MP = macrophage; MC = monocyte; DC = dendritic cells; NP = neutrophils). Genes are ranked by the degree to which they showed specific expression in the assigned cell type. To obtain the p-value shown for each gene, expression in the assigned cell type was compared to expression in each of the other nine cell types, respectively (n = 50 samples per cell type; Wilcoxon rank sum test). The p-value shown for each gene corresponds to the largest p-value obtained from each of the 9 comparisons to other cell types (asterisk, FDR < 0.05).
Mentions: Further inspection of the 117 psoriasis GWAS candidates revealed that, for many, expression was significantly altered in psoriasis lesions, although in most cases estimated fold-changes did not meet DEG criteria (Figure 5). Overall, 13 candidate genes were also PP-increased DEGs, while 2 others were PP-decreased DEGs (Figure 5). Candidate genes varied in the degree to which expression was specific to a given cell type, and this influenced the confidence with which candidate cell types could be assigned (Figure 6). With respect to LCE3D, for instance, KCs were assigned as the candidate cell type with high confidence, since expression was distinguishably greater in KCs as compared to any other cell type (Figures 5 and 6). Among the candidate genes for which cell type assignment confidence was greatest, most were assigned to KCs or neutrophils, although some were also assigned to fibroblasts (e.g., PTRF and FNDC1; see Figure 6).

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