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An integrated expression phenotype mapping approach defines common variants in LEP, ALOX15 and CAPNS1 associated with induction of IL-6.

Fairfax BP, Vannberg FO, Radhakrishnan J, Hakonarson H, Keating BJ, Hill AV, Knight JC - Hum. Mol. Genet. (2009)

Bottom Line: Interleukin-6 (IL-6) is an important modulator of inflammation and immunity whose dysregulation is associated with a number of disease states.We find that variation involving two other genomic regions, CAPNS1 (encoding calpain small subunit 1) and ALOX15 (encoding arachidonate 15-lipoxygenase), show significant association with IL-6 expression.It also provides proof of concept for use of an integrated expression phenotype mapping approach.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

ABSTRACT
Interleukin-6 (IL-6) is an important modulator of inflammation and immunity whose dysregulation is associated with a number of disease states. There is evidence of significant heritability in inter-individual variation in IL6 gene expression but the genetic variants responsible for this remain to be defined. We adopted a combined approach of mapping protein and expression quantitative trait loci in peripheral blood mononuclear cells using high-density single-nucleotide polymorphism (SNP) typing for approximately 2000 loci implicated in cardiovascular, metabolic and inflammatory syndromes to show that common SNP markers and haplotypes of LEP (encoding leptin) associate with a 1.7- to 2-fold higher level of lipopolysaccharide (LPS)-induced IL-6 expression. We subsequently demonstrate that basal leptin expression significantly correlates with LPS-induced IL-6 expression and that the same variants at LEP which associate with IL-6 expression are also major determinants of leptin expression in these cells. We find that variation involving two other genomic regions, CAPNS1 (encoding calpain small subunit 1) and ALOX15 (encoding arachidonate 15-lipoxygenase), show significant association with IL-6 expression. Although this may be a subset of all such trans-acting effects, we find that the same ALOX15 variants are associated with induced expression of tumour necrosis factor and IL-1beta consistent with a broader role in acute inflammation for ALOX15. This study provides evidence of novel genetic determinants of IL-6 production with implications for understanding susceptibility to inflammatory disease processes and insight into cross talk between metabolic and inflammatory pathways. It also provides proof of concept for use of an integrated expression phenotype mapping approach.

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Association with IL-6 and SNP markers at ALOX15 and CAPNS1. Single marker allelic association results for IL-6 eQTL and pQTLs are shown plotted as −log10(P) versus genomic coordinate for (A) ALOX15 gene region and (B) CAPNS1 gene region. For each of the top associated SNPs in the two gene loci (plotted with blue squares), SNPs with MAF greater than 5% and r2 < 0.2 are shown as white squares, 0.2–0.5 (yellow) and >0.8 (red). In total, 45 SNPs over a 20 kb region spanning ALOX15 and 47 SNPs over a 50 kb region at CAPNS1 were genotyped.
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DDP530F5: Association with IL-6 and SNP markers at ALOX15 and CAPNS1. Single marker allelic association results for IL-6 eQTL and pQTLs are shown plotted as −log10(P) versus genomic coordinate for (A) ALOX15 gene region and (B) CAPNS1 gene region. For each of the top associated SNPs in the two gene loci (plotted with blue squares), SNPs with MAF greater than 5% and r2 < 0.2 are shown as white squares, 0.2–0.5 (yellow) and >0.8 (red). In total, 45 SNPs over a 20 kb region spanning ALOX15 and 47 SNPs over a 50 kb region at CAPNS1 were genotyped.

Mentions: We found two SNP markers in complete LD (rs11568131 and rs11078527) (c.*287C>T and c.808-94C>T) located in the 3′-UTR and sixth intron of ALOX15 which showed a robust signal of association with IL-6 expression at both the RNA and protein level, and with different doses of LPS (Fig. 5, Supplementary Material, Figs S1 and S3). LD was relatively low and haplotypic analysis was not more informative than single SNP association for IL-6 expression. In our population sample, possession of one or more copies of the haplotype carried by the T alleles of rs11568131 and rs11078527 was associated with a 3-fold higher level of IL6 RNA expression following 2 ng/ml LPS induction for 6 h (Mann–Whitney test two-tailed P= 0.0002) and a 1.5- or 1.7-fold higher level of IL-6 protein expression (following 2 or 20 ng/ml LPS induction, respectively) (unpaired t-test two-tailed P= 0.0007 and P= 0.0008) (Supplementary Material, Fig. S3). The SNPs are present in non-conserved regions of DNA not associated with regulatory potential based on seven species alignments (27) or any predicted transcription factor binding site (28). We note that the associated SNPs occur twice as frequently among individuals of Caucasian geographic ancestry (MAF in CEU 0.183) compared with individuals of African or Asian ancestry (29).


An integrated expression phenotype mapping approach defines common variants in LEP, ALOX15 and CAPNS1 associated with induction of IL-6.

Fairfax BP, Vannberg FO, Radhakrishnan J, Hakonarson H, Keating BJ, Hill AV, Knight JC - Hum. Mol. Genet. (2009)

Association with IL-6 and SNP markers at ALOX15 and CAPNS1. Single marker allelic association results for IL-6 eQTL and pQTLs are shown plotted as −log10(P) versus genomic coordinate for (A) ALOX15 gene region and (B) CAPNS1 gene region. For each of the top associated SNPs in the two gene loci (plotted with blue squares), SNPs with MAF greater than 5% and r2 < 0.2 are shown as white squares, 0.2–0.5 (yellow) and >0.8 (red). In total, 45 SNPs over a 20 kb region spanning ALOX15 and 47 SNPs over a 50 kb region at CAPNS1 were genotyped.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2807371&req=5

DDP530F5: Association with IL-6 and SNP markers at ALOX15 and CAPNS1. Single marker allelic association results for IL-6 eQTL and pQTLs are shown plotted as −log10(P) versus genomic coordinate for (A) ALOX15 gene region and (B) CAPNS1 gene region. For each of the top associated SNPs in the two gene loci (plotted with blue squares), SNPs with MAF greater than 5% and r2 < 0.2 are shown as white squares, 0.2–0.5 (yellow) and >0.8 (red). In total, 45 SNPs over a 20 kb region spanning ALOX15 and 47 SNPs over a 50 kb region at CAPNS1 were genotyped.
Mentions: We found two SNP markers in complete LD (rs11568131 and rs11078527) (c.*287C>T and c.808-94C>T) located in the 3′-UTR and sixth intron of ALOX15 which showed a robust signal of association with IL-6 expression at both the RNA and protein level, and with different doses of LPS (Fig. 5, Supplementary Material, Figs S1 and S3). LD was relatively low and haplotypic analysis was not more informative than single SNP association for IL-6 expression. In our population sample, possession of one or more copies of the haplotype carried by the T alleles of rs11568131 and rs11078527 was associated with a 3-fold higher level of IL6 RNA expression following 2 ng/ml LPS induction for 6 h (Mann–Whitney test two-tailed P= 0.0002) and a 1.5- or 1.7-fold higher level of IL-6 protein expression (following 2 or 20 ng/ml LPS induction, respectively) (unpaired t-test two-tailed P= 0.0007 and P= 0.0008) (Supplementary Material, Fig. S3). The SNPs are present in non-conserved regions of DNA not associated with regulatory potential based on seven species alignments (27) or any predicted transcription factor binding site (28). We note that the associated SNPs occur twice as frequently among individuals of Caucasian geographic ancestry (MAF in CEU 0.183) compared with individuals of African or Asian ancestry (29).

Bottom Line: Interleukin-6 (IL-6) is an important modulator of inflammation and immunity whose dysregulation is associated with a number of disease states.We find that variation involving two other genomic regions, CAPNS1 (encoding calpain small subunit 1) and ALOX15 (encoding arachidonate 15-lipoxygenase), show significant association with IL-6 expression.It also provides proof of concept for use of an integrated expression phenotype mapping approach.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

ABSTRACT
Interleukin-6 (IL-6) is an important modulator of inflammation and immunity whose dysregulation is associated with a number of disease states. There is evidence of significant heritability in inter-individual variation in IL6 gene expression but the genetic variants responsible for this remain to be defined. We adopted a combined approach of mapping protein and expression quantitative trait loci in peripheral blood mononuclear cells using high-density single-nucleotide polymorphism (SNP) typing for approximately 2000 loci implicated in cardiovascular, metabolic and inflammatory syndromes to show that common SNP markers and haplotypes of LEP (encoding leptin) associate with a 1.7- to 2-fold higher level of lipopolysaccharide (LPS)-induced IL-6 expression. We subsequently demonstrate that basal leptin expression significantly correlates with LPS-induced IL-6 expression and that the same variants at LEP which associate with IL-6 expression are also major determinants of leptin expression in these cells. We find that variation involving two other genomic regions, CAPNS1 (encoding calpain small subunit 1) and ALOX15 (encoding arachidonate 15-lipoxygenase), show significant association with IL-6 expression. Although this may be a subset of all such trans-acting effects, we find that the same ALOX15 variants are associated with induced expression of tumour necrosis factor and IL-1beta consistent with a broader role in acute inflammation for ALOX15. This study provides evidence of novel genetic determinants of IL-6 production with implications for understanding susceptibility to inflammatory disease processes and insight into cross talk between metabolic and inflammatory pathways. It also provides proof of concept for use of an integrated expression phenotype mapping approach.

Show MeSH
Related in: MedlinePlus