Using publicly available databases, we have shown that the major alleles of two correlated IRF5
3′ SNPs, rs13242262 and rs2280714 (SNPs 10 and 14), are associated with increased IRF5 expression in unstimulated LCLs from unrelated individuals from three ethnic groups. Results from recent publications showed increased IRF5 expression in CEU LCLs containing the risk allele of SNP 14,12
and in CEU, CHB and JPT LCLs containing the risk allele of rs10954213,11,14,44
for which SNP 10 is a proxy. In our study, SNPs spanning IRF5
were associated with increased IRF5 transcripts in the CEU and CHB+JPT samples, but only SNPs tagging for the 3′ block () were associated with increased mRNA in the YRI sample. One SNP from the 3′ region (rs10488631) in the CEU sample showed increased IFNα levels by multiple testing criteria; this was not seen in the other populations. IRF5
studies of SLE in East Asians indicate that the 3′ region may be less important to SLE susceptibility than in individuals of European descent.14,46
Whether one region of IRF5
is more important in the regulation of gene expression to certain ethnic groups awaits further testing in larger samples.
We report that the minor allele of rs10488631 (SNP 13) was associated with increased IRF5, total IFNα and IFN-inducible chemokine transcripts in unstimulated CEU LCLs. Along with a CGGGG promoter indel, rs10488631 has accounted for the strongest association signals observed with IRF5
in Swedish SLE studies.45
rs10488631 can be considered a marker for an SLE risk haplotype, as described in two large-scale studies of diverse European ancestries, which contains the three other functional IRF5
risk alleles: rs2004640, rs10954213 and the exon 6 indel.9,44
SLE risk haplotype has been associated with increased IFNα pathway activation in European and Hispanic Americans with SLE;29
the same has not been reported in healthy individuals. In our study, a CEU haplotype defined by the risk alleles of rs13242262, rs10488631 and rs2280714 was associated with increased IRF5, total IFNα and IFN-inducible chemokine transcripts. The CGGGG indel is in LD with the risk allele of rs10488631 (r2
=0.61), which has been associated with SLE in European and African American cohorts11,15
and is present in our risk haplotype. This SNP was not associated with increased IRF5 expression in the YRI sample but, as the YRI sample does not reflect the genetic admixture seen in African Americans, this again shows that different IRF5
variations may impact on the IFNα pathway among ethnic groups.
The representation of SNPs across IRF5
in our haplotypes allowed for a straightforward comparison with previously reported SLE risk haplotypes. In 555 families of diverse European descent, SNPs from three groups (rs2004640, the exon 6 indel and rs10954213) are contained in a risk haplotype for SLE.44
Risk alleles of SNPs representing rs2004640 and rs10954213 (as described in the Results section) are present in our CEU risk haplotype. In another report, two over-transmitted haplotypes made up of six SNPs were found by transmission disequilibrium test analysis of UK SLE trios.11
Of these, SNPs 2, 3, 13 and 14 overlapped with our analysis and the alleles present in our CEU risk haplotype were the same as in the SLE study. Finally, a large combined study from eight European countries identified the minor allele of rs10488631 as defining a susceptibility haplotype in European patients with SLE.9
As we reported, the minor allele of this SNP is contained in our CEU risk haplotype. Although IRF5
polymorphisms, including rs2004640, have been associated with SLE in East Asians,14,46,47
the results in these populations do not report identical SLE risk haplotypes as those in individuals of European descent. Specifically, haplotypes containing the three European risk alleles of rs2004640, the exon 6 indel and rs10954213 are not associated with an increased risk of SLE in Japanese and Korean samples.14,46
Our study did not identify an association between IRF5
variants and IFNα pathway activation in CHB+JPT or YRI individuals. It remains to be seen whether other variants not included in this study may be responsible for pathway activation in non-European populations, or whether other genes involved in IFNα regulation may play a more important role.
Given the heterogeneity and incomplete penetrance of SLE, and given the relatively small role that B cells play in the IFN response, it is remarkable to observe an association of IRF5
variants with unstimulated mRNA levels of IFNα and IFN-inducible chemokines, however small, in LCLs from Hapmap individuals. The lack of association of IRF5
variants with IFN-inducible genes in these individuals may be explained by a number of factors. It is plausible that other transcription factors such as IRF7, IRF3, OPN
may be involved in activation of the IFNα pathway,48
or that this association may only be present after stimulation by autoantibodies or IFNα. A recent study showed that some patients with SLE had raised levels of IFN-inducible genes and chemokines whereas others only had raised levels of IFN-inducible chemokines,41
suggesting a non-linear pattern of modulation of IFN-inducible genes and downstream chemokines. Based on the results from our computer simulated study, we are investigating whether genetic variants of the IFNα signalling pathway regulate its threshold of activation, potentially contributing to the development of SLE and other autoimmune diseases in unaffected individuals of different populations.