Limits...
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.

Show MeSH

Related in: MedlinePlus

Common SNP markers in LEP are associated with IL-6 and leptin expression. (A) Single marker allelic association results for LEP gene locus with IL-6 or leptin expression plotted as −log10(P) values by genomic coordinate. With reference to rs4731427, SNPs with MAF greater than 5% and r2 < 0.2 are shown as white squares, 0.2–0.5 (yellow) and 0.5–0.8 (orange). LEP gene structure and genotyped SNPs are shown below. Estimated recombination rates are shown from HapMap (using Build 35 coordinates). Gene structure, vertebrate multiz alignment and conservation track (17 species) (49) and genotyped SNP locations adapted from screenshot of the UCSC Genome Browser (Human March 2006 Assembly). (B) Manhattan plot showing strength of association from PLINK analysis plotted as −log10(P) values by chromosome for leptin expression.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DDP530F2: Common SNP markers in LEP are associated with IL-6 and leptin expression. (A) Single marker allelic association results for LEP gene locus with IL-6 or leptin expression plotted as −log10(P) values by genomic coordinate. With reference to rs4731427, SNPs with MAF greater than 5% and r2 < 0.2 are shown as white squares, 0.2–0.5 (yellow) and 0.5–0.8 (orange). LEP gene structure and genotyped SNPs are shown below. Estimated recombination rates are shown from HapMap (using Build 35 coordinates). Gene structure, vertebrate multiz alignment and conservation track (17 species) (49) and genotyped SNP locations adapted from screenshot of the UCSC Genome Browser (Human March 2006 Assembly). (B) Manhattan plot showing strength of association from PLINK analysis plotted as −log10(P) values by chromosome for leptin expression.

Mentions: The observed association of IL-6 expression with common SNP markers at or near the LEP gene is of particular biological interest given the evidence that leptin can play an important immunomodulatory role, and specifically published data showing that leptin can both directly activate and augment IL-6 production by PBMCs induced with LPS (19–22). We successfully genotyped 52 SNPs within a 25 kb region spanning LEP of which 16 SNPs were informative with a minor allele frequency (MAF) of greater than 5%. Several common SNP markers showed association with basal and induced IL-6 expression phenotypes at this locus, notably rs4731427 (c.29+3030T>C) (Fig. 2). Individuals possessing a copy of the minor C allele had a 7-fold higher level of basal IL6 expression compared with those without (Fig. 3) (Mann–Whitney test two-tailed P= 0.003), while following LPS induction (2 ng/ml) a 2.3-fold increase in IL6 expression was seen at the RNA level. This was reproduced at the protein level with a 1.7- or 2.0-fold higher level of IL-6 expression (2 or 20 ng/ml LPS, respectively) (P< 0.0001 on unpaired t-test, two-tailed, for either phenotype) (Fig. 3).


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)

Common SNP markers in LEP are associated with IL-6 and leptin expression. (A) Single marker allelic association results for LEP gene locus with IL-6 or leptin expression plotted as −log10(P) values by genomic coordinate. With reference to rs4731427, SNPs with MAF greater than 5% and r2 < 0.2 are shown as white squares, 0.2–0.5 (yellow) and 0.5–0.8 (orange). LEP gene structure and genotyped SNPs are shown below. Estimated recombination rates are shown from HapMap (using Build 35 coordinates). Gene structure, vertebrate multiz alignment and conservation track (17 species) (49) and genotyped SNP locations adapted from screenshot of the UCSC Genome Browser (Human March 2006 Assembly). (B) Manhattan plot showing strength of association from PLINK analysis plotted as −log10(P) values by chromosome for leptin expression.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DDP530F2: Common SNP markers in LEP are associated with IL-6 and leptin expression. (A) Single marker allelic association results for LEP gene locus with IL-6 or leptin expression plotted as −log10(P) values by genomic coordinate. With reference to rs4731427, SNPs with MAF greater than 5% and r2 < 0.2 are shown as white squares, 0.2–0.5 (yellow) and 0.5–0.8 (orange). LEP gene structure and genotyped SNPs are shown below. Estimated recombination rates are shown from HapMap (using Build 35 coordinates). Gene structure, vertebrate multiz alignment and conservation track (17 species) (49) and genotyped SNP locations adapted from screenshot of the UCSC Genome Browser (Human March 2006 Assembly). (B) Manhattan plot showing strength of association from PLINK analysis plotted as −log10(P) values by chromosome for leptin expression.
Mentions: The observed association of IL-6 expression with common SNP markers at or near the LEP gene is of particular biological interest given the evidence that leptin can play an important immunomodulatory role, and specifically published data showing that leptin can both directly activate and augment IL-6 production by PBMCs induced with LPS (19–22). We successfully genotyped 52 SNPs within a 25 kb region spanning LEP of which 16 SNPs were informative with a minor allele frequency (MAF) of greater than 5%. Several common SNP markers showed association with basal and induced IL-6 expression phenotypes at this locus, notably rs4731427 (c.29+3030T>C) (Fig. 2). Individuals possessing a copy of the minor C allele had a 7-fold higher level of basal IL6 expression compared with those without (Fig. 3) (Mann–Whitney test two-tailed P= 0.003), while following LPS induction (2 ng/ml) a 2.3-fold increase in IL6 expression was seen at the RNA level. This was reproduced at the protein level with a 1.7- or 2.0-fold higher level of IL-6 expression (2 or 20 ng/ml LPS, respectively) (P< 0.0001 on unpaired t-test, two-tailed, for either phenotype) (Fig. 3).

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