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

Susceptibility-associated variation at rs11121129 disrupts an AP1 binding site associated with TNFRSF9 expression in neutrophils. (A) Top 10 binding sites ranked according to their enrichment with respect to sequences adjacent to genes co-expressed with TNFRSF9 in neutrophils. The listed binding sites include only those that are sensitive to variation at SNPs in linkage disequilibrium with rs11121129 (r2 > 0.90). The chart shows the Z statistic quantifying the degree to which each binding site is enriched among sequences adjacent to TNFRSF9-co-expressed genes. Associated p-values are listed in the left margin, where an asterisk symbol is used to denote FDR < 0.05. The right margin lists the SNP for which variation is predicted to influence binding. Blue font denotes binding sites for which the risk variant abrogates a match to the binding site, while red font denotes binding sites for which the risk variant engenders a match to the binding site. (B) Sequence logo for Fos/SWGNSNSMDG. The black arrow denotes the position for which variation at rs6687168 is predicted to influence binding (see parts D and E). (C) Sequence logo for CREL/BGGNNTTTCC/M00053. The black arrow denotes the position for which variation at rs6661746 is predicted to influence binding. (D) Top 10 binding sites matching the non-risk variant at rs6687168 (Chr 1, 8268893 – 8268933). (E) Top 10 binding sites matching the risk variant at rs6687168 (Chr 1, 8268893 – 8268933). In both (D) and (E), the right margin lists p-values quantifying the degree to which motifs are enriched among sequences adjacent to TNFRSF9-co-expressed genes in neutrophils.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Susceptibility-associated variation at rs11121129 disrupts an AP1 binding site associated with TNFRSF9 expression in neutrophils. (A) Top 10 binding sites ranked according to their enrichment with respect to sequences adjacent to genes co-expressed with TNFRSF9 in neutrophils. The listed binding sites include only those that are sensitive to variation at SNPs in linkage disequilibrium with rs11121129 (r2 > 0.90). The chart shows the Z statistic quantifying the degree to which each binding site is enriched among sequences adjacent to TNFRSF9-co-expressed genes. Associated p-values are listed in the left margin, where an asterisk symbol is used to denote FDR < 0.05. The right margin lists the SNP for which variation is predicted to influence binding. Blue font denotes binding sites for which the risk variant abrogates a match to the binding site, while red font denotes binding sites for which the risk variant engenders a match to the binding site. (B) Sequence logo for Fos/SWGNSNSMDG. The black arrow denotes the position for which variation at rs6687168 is predicted to influence binding (see parts D and E). (C) Sequence logo for CREL/BGGNNTTTCC/M00053. The black arrow denotes the position for which variation at rs6661746 is predicted to influence binding. (D) Top 10 binding sites matching the non-risk variant at rs6687168 (Chr 1, 8268893 – 8268933). (E) Top 10 binding sites matching the risk variant at rs6687168 (Chr 1, 8268893 – 8268933). In both (D) and (E), the right margin lists p-values quantifying the degree to which motifs are enriched among sequences adjacent to TNFRSF9-co-expressed genes in neutrophils.

Mentions: We assembled a dictionary of 1937 empirically-determined DNA motifs recognized by human TFs and other DNA-binding proteins (see Methods). We then assessed whether any of these motifs were enriched with respect to intergenic sequences adjacent to TNFRSF9 and those genes co-expressed with TNFRSF9 in neutrophils. We identified 91 genes co-expressed with TNFRSF9 in neutrophils, based upon a rank analysis of Spearman correlation coefficients (Figure 7B and D). The gene most strongly correlated with TNFRSF9 expression, for instance, was vav 1 guanine nucleotide exchange factor (VAV1) (rs = 0.64; Figure 7C). We next identified 595 motifs that occurred at significantly elevated frequency among intergenic regions adjacent to TNFRSF9 and its co-expression partners in neutrophils (FDR < 0.05 with Z > 0). We reasoned that binding of such motifs may be disrupted by susceptibility-associated variation near rs11121129. We identified five SNPs linked with rs11121129 (r2 > 0.90), yielding a total of 6 potentially causal SNPs, and we identified cases in which these SNPs altered sequences matching those motifs enriched with respect to genes co-expressed with TNFRSF9 in neutrophils (Figure 8A).


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)

Susceptibility-associated variation at rs11121129 disrupts an AP1 binding site associated with TNFRSF9 expression in neutrophils. (A) Top 10 binding sites ranked according to their enrichment with respect to sequences adjacent to genes co-expressed with TNFRSF9 in neutrophils. The listed binding sites include only those that are sensitive to variation at SNPs in linkage disequilibrium with rs11121129 (r2 > 0.90). The chart shows the Z statistic quantifying the degree to which each binding site is enriched among sequences adjacent to TNFRSF9-co-expressed genes. Associated p-values are listed in the left margin, where an asterisk symbol is used to denote FDR < 0.05. The right margin lists the SNP for which variation is predicted to influence binding. Blue font denotes binding sites for which the risk variant abrogates a match to the binding site, while red font denotes binding sites for which the risk variant engenders a match to the binding site. (B) Sequence logo for Fos/SWGNSNSMDG. The black arrow denotes the position for which variation at rs6687168 is predicted to influence binding (see parts D and E). (C) Sequence logo for CREL/BGGNNTTTCC/M00053. The black arrow denotes the position for which variation at rs6661746 is predicted to influence binding. (D) Top 10 binding sites matching the non-risk variant at rs6687168 (Chr 1, 8268893 – 8268933). (E) Top 10 binding sites matching the risk variant at rs6687168 (Chr 1, 8268893 – 8268933). In both (D) and (E), the right margin lists p-values quantifying the degree to which motifs are enriched among sequences adjacent to TNFRSF9-co-expressed genes in neutrophils.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Susceptibility-associated variation at rs11121129 disrupts an AP1 binding site associated with TNFRSF9 expression in neutrophils. (A) Top 10 binding sites ranked according to their enrichment with respect to sequences adjacent to genes co-expressed with TNFRSF9 in neutrophils. The listed binding sites include only those that are sensitive to variation at SNPs in linkage disequilibrium with rs11121129 (r2 > 0.90). The chart shows the Z statistic quantifying the degree to which each binding site is enriched among sequences adjacent to TNFRSF9-co-expressed genes. Associated p-values are listed in the left margin, where an asterisk symbol is used to denote FDR < 0.05. The right margin lists the SNP for which variation is predicted to influence binding. Blue font denotes binding sites for which the risk variant abrogates a match to the binding site, while red font denotes binding sites for which the risk variant engenders a match to the binding site. (B) Sequence logo for Fos/SWGNSNSMDG. The black arrow denotes the position for which variation at rs6687168 is predicted to influence binding (see parts D and E). (C) Sequence logo for CREL/BGGNNTTTCC/M00053. The black arrow denotes the position for which variation at rs6661746 is predicted to influence binding. (D) Top 10 binding sites matching the non-risk variant at rs6687168 (Chr 1, 8268893 – 8268933). (E) Top 10 binding sites matching the risk variant at rs6687168 (Chr 1, 8268893 – 8268933). In both (D) and (E), the right margin lists p-values quantifying the degree to which motifs are enriched among sequences adjacent to TNFRSF9-co-expressed genes in neutrophils.
Mentions: We assembled a dictionary of 1937 empirically-determined DNA motifs recognized by human TFs and other DNA-binding proteins (see Methods). We then assessed whether any of these motifs were enriched with respect to intergenic sequences adjacent to TNFRSF9 and those genes co-expressed with TNFRSF9 in neutrophils. We identified 91 genes co-expressed with TNFRSF9 in neutrophils, based upon a rank analysis of Spearman correlation coefficients (Figure 7B and D). The gene most strongly correlated with TNFRSF9 expression, for instance, was vav 1 guanine nucleotide exchange factor (VAV1) (rs = 0.64; Figure 7C). We next identified 595 motifs that occurred at significantly elevated frequency among intergenic regions adjacent to TNFRSF9 and its co-expression partners in neutrophils (FDR < 0.05 with Z > 0). We reasoned that binding of such motifs may be disrupted by susceptibility-associated variation near rs11121129. We identified five SNPs linked with rs11121129 (r2 > 0.90), yielding a total of 6 potentially causal SNPs, and we identified cases in which these SNPs altered sequences matching those motifs enriched with respect to genes co-expressed with TNFRSF9 in neutrophils (Figure 8A).

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