Limits...
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.

Show MeSH

Related in: MedlinePlus

Cluster analysis of 1019 genes elevated in psoriasis lesions and their expression across 10 cell types. We identified 1019 PP-increased DEGs with PP/PN fold-change greater than 1.50 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 and average linkage). The red-blue heatmap shows expression of genes 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 (i.e., the cell type for which the gene’s median expression was highest, 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
getmorefigures.php?uid=PMC4060870&req=5

Figure 3: Cluster analysis of 1019 genes elevated in psoriasis lesions and their expression across 10 cell types. We identified 1019 PP-increased DEGs with PP/PN fold-change greater than 1.50 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 and average linkage). The red-blue heatmap shows expression of genes 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 (i.e., the cell type for which the gene’s median expression was highest, 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: Approximately 50% of PP-increased DEGs were assigned to KCs or fibroblasts, while the remaining 50% were assigned to immune cell types. PP-increased DEGs were enriched with respect to the number of genes assigned to KCs and macrophages (P < 0.05; Fisher’s Exact Test; Figures 2 and 3). These trends were further supported by rank-based analyses, which showed that KC- and macrophage-assigned genes tended to have elevated expression in PP versus PN skin (P ≤ 2.2 × 10−20; GSEA; Additional file 6, Part A). A non-parametric bootstrap analysis also indicated that PP-increased DEGs, on average, had higher-than-expected expression and detection frequency only for KCs and macrophages, but not for other cell types (Additional file 7). 35% of PP-increased DEGs (358/1019) were expressed more highly in KCs than any other cell type (Figure 2). Examples of KC-assigned genes strongly elevated in psoriasis lesions included SERPINB4, SPRR2C and SERPINB3 (Additional file 8). Consistent with heightened KC proliferation, KC-assigned PP-increased DEGs were frequently associated with organelle fission, cell division and the cell cycle (data not shown). Approximately 8% of PP-increased DEGs (82/1019) were assigned to macrophages (Figure 2), the strongest examples of which included KYNU, ADAMDEC1 and CXCL13 (Additional file 8). These and other macrophage DEGs were commonly associated with response to biotic stimulus, immune response and programmed cell death (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 1019 genes elevated in psoriasis lesions and their expression across 10 cell types. We identified 1019 PP-increased DEGs with PP/PN fold-change greater than 1.50 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 and average linkage). The red-blue heatmap shows expression of genes 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 (i.e., the cell type for which the gene’s median expression was highest, 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 3: Cluster analysis of 1019 genes elevated in psoriasis lesions and their expression across 10 cell types. We identified 1019 PP-increased DEGs with PP/PN fold-change greater than 1.50 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 and average linkage). The red-blue heatmap shows expression of genes 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 (i.e., the cell type for which the gene’s median expression was highest, 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: Approximately 50% of PP-increased DEGs were assigned to KCs or fibroblasts, while the remaining 50% were assigned to immune cell types. PP-increased DEGs were enriched with respect to the number of genes assigned to KCs and macrophages (P < 0.05; Fisher’s Exact Test; Figures 2 and 3). These trends were further supported by rank-based analyses, which showed that KC- and macrophage-assigned genes tended to have elevated expression in PP versus PN skin (P ≤ 2.2 × 10−20; GSEA; Additional file 6, Part A). A non-parametric bootstrap analysis also indicated that PP-increased DEGs, on average, had higher-than-expected expression and detection frequency only for KCs and macrophages, but not for other cell types (Additional file 7). 35% of PP-increased DEGs (358/1019) were expressed more highly in KCs than any other cell type (Figure 2). Examples of KC-assigned genes strongly elevated in psoriasis lesions included SERPINB4, SPRR2C and SERPINB3 (Additional file 8). Consistent with heightened KC proliferation, KC-assigned PP-increased DEGs were frequently associated with organelle fission, cell division and the cell cycle (data not shown). Approximately 8% of PP-increased DEGs (82/1019) were assigned to macrophages (Figure 2), the strongest examples of which included KYNU, ADAMDEC1 and CXCL13 (Additional file 8). These and other macrophage DEGs were commonly associated with response to biotic stimulus, immune response and programmed cell death (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