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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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Assignment of psoriasis DEGs and GWAS candidates to cell types present in lesional skin. Human genes were assigned to one of 10 cell types present in psoriasis lesions. Genes were assigned to the cell type for which median expression was highest, provided that the gene’s expression was detected in at least 10% of microarray samples for that cell type (P < 0.05, Wilcoxon signed-rank test). If a gene’s expression was not detected with respect to at least 10% of microarray samples for any cell type, no assignment was made (i.e., unassigned). Pie charts show the percentage of PP-increased DEGs (top), PP-decreased DEGs (middle) and GWAS candidates (bottom) that were either unassigned or allocated to one of the 10 cell types. Magenta labels denote those cell types for which the number of assigned genes was significantly large in comparison to all skin-expressed genes (PP-increased and PP-decreased DEGs) or in comparison to all genes represented on the Affymetrix Human Genome U133 Plus 2.0 array platform (GWAS candidates) (one asterisk, P < 0.05; two asterisks, FDR < 0.05; Fisher’s Exact Test).
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Figure 2: Assignment of psoriasis DEGs and GWAS candidates to cell types present in lesional skin. Human genes were assigned to one of 10 cell types present in psoriasis lesions. Genes were assigned to the cell type for which median expression was highest, provided that the gene’s expression was detected in at least 10% of microarray samples for that cell type (P < 0.05, Wilcoxon signed-rank test). If a gene’s expression was not detected with respect to at least 10% of microarray samples for any cell type, no assignment was made (i.e., unassigned). Pie charts show the percentage of PP-increased DEGs (top), PP-decreased DEGs (middle) and GWAS candidates (bottom) that were either unassigned or allocated to one of the 10 cell types. Magenta labels denote those cell types for which the number of assigned genes was significantly large in comparison to all skin-expressed genes (PP-increased and PP-decreased DEGs) or in comparison to all genes represented on the Affymetrix Human Genome U133 Plus 2.0 array platform (GWAS candidates) (one asterisk, P < 0.05; two asterisks, FDR < 0.05; Fisher’s Exact Test).

Mentions: The database was used to assign a candidate cell type to each human gene based upon the gene’s expression level across the 10 cell types. For each gene, we identified the cell type for which the gene’s median expression was highest, provided that expression was detected in at least 10% of microarray samples (P < 0.05, Wilcoxon signed rank test) [38]. No assignment was made if a gene’s expression was not detected in at least 10% of microarray samples for any cell type (P < 0.05). After assignments were made, we assessed trends among PP-increased and PP-decreased DEGs, as well as among candidate genes identified from psoriasis GWAS studies (Figure 2).


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)

Assignment of psoriasis DEGs and GWAS candidates to cell types present in lesional skin. Human genes were assigned to one of 10 cell types present in psoriasis lesions. Genes were assigned to the cell type for which median expression was highest, provided that the gene’s expression was detected in at least 10% of microarray samples for that cell type (P < 0.05, Wilcoxon signed-rank test). If a gene’s expression was not detected with respect to at least 10% of microarray samples for any cell type, no assignment was made (i.e., unassigned). Pie charts show the percentage of PP-increased DEGs (top), PP-decreased DEGs (middle) and GWAS candidates (bottom) that were either unassigned or allocated to one of the 10 cell types. Magenta labels denote those cell types for which the number of assigned genes was significantly large in comparison to all skin-expressed genes (PP-increased and PP-decreased DEGs) or in comparison to all genes represented on the Affymetrix Human Genome U133 Plus 2.0 array platform (GWAS candidates) (one asterisk, P < 0.05; two asterisks, FDR < 0.05; Fisher’s Exact Test).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Assignment of psoriasis DEGs and GWAS candidates to cell types present in lesional skin. Human genes were assigned to one of 10 cell types present in psoriasis lesions. Genes were assigned to the cell type for which median expression was highest, provided that the gene’s expression was detected in at least 10% of microarray samples for that cell type (P < 0.05, Wilcoxon signed-rank test). If a gene’s expression was not detected with respect to at least 10% of microarray samples for any cell type, no assignment was made (i.e., unassigned). Pie charts show the percentage of PP-increased DEGs (top), PP-decreased DEGs (middle) and GWAS candidates (bottom) that were either unassigned or allocated to one of the 10 cell types. Magenta labels denote those cell types for which the number of assigned genes was significantly large in comparison to all skin-expressed genes (PP-increased and PP-decreased DEGs) or in comparison to all genes represented on the Affymetrix Human Genome U133 Plus 2.0 array platform (GWAS candidates) (one asterisk, P < 0.05; two asterisks, FDR < 0.05; Fisher’s Exact Test).
Mentions: The database was used to assign a candidate cell type to each human gene based upon the gene’s expression level across the 10 cell types. For each gene, we identified the cell type for which the gene’s median expression was highest, provided that expression was detected in at least 10% of microarray samples (P < 0.05, Wilcoxon signed rank test) [38]. No assignment was made if a gene’s expression was not detected in at least 10% of microarray samples for any cell type (P < 0.05). After assignments were made, we assessed trends among PP-increased and PP-decreased DEGs, as well as among candidate genes identified from psoriasis GWAS studies (Figure 2).

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