Novel Single Nucleotide Polymorphisms in the Distal IL-10 Promoter Affect IL-10 Production and Enhance the Risk of Systemic Lupus Erythematosus

Abstract

Family studies of first-degree relatives and analysis of twins indicate that as much as 75% of the differences in quantitative IL-10 production in man derive from heritable genetic factors. Studies of single nucleotide polymorphisms (SNP) in the proximal 1.0 kb of the IL-10 promoter have yielded inconsistent association with IL-10 production and variable results in promoter-reporter studies. However, in normal donors, an association of quantitative production with certain alleles of the IL-10.R short tandem repeat polymorphism at −4.0 kb suggested that SNPs in the more distal promoter might be informative. We have identified seven novel SNP sites in the genomic sequence of the first 4 kb of the IL-10 promoter region 5′ to the ATG start site from Caucasian individuals with either a high or a low IL-10 production phenotype. We have also identified eight SNP haplotypes in the distal promoter that segregate with significant differences in quantitative IL-10 production in normal donors. These SNPs are significantly associated with systemic lupus erythematosus in African-Americans and may define one component of the genetic susceptibility to systemic lupus erythematosus in this group.

Association tests with systemic lupus erythematosus (SLE) of IL10 markers indicate a direct involvement of a CA repeat in the 5′ regulatory region

“…We thus exclude that 13 of the tested markers confer a risk higher than IL10.G-140bp (OR ¼ 1.57; Table 5). Our results are in agreement with previous studies in different populations failing to detect an association with SLE susceptibility of five SNPs located at positions À3533, À2828, À1082, À819 and À592 19,[26][27][28]34 although a role in the clinical phenotype was suggested. 26,27,35 Conversely, the SNP at position À2726 (named À2763 in Ref.…”

“…Direct sequencing of the heteroduplex samples and one homoduplex as a reference for each fragment led to the identification of 16 sequence variations (Table 1). Most of them had been previously, identified in other studies 14,[17][18][19][20][21] with the exception of four SNPs located at positions À1270, +3814, +4123 and +4230 (Table 1).…”

“…They correspond to the previously described most frequent haplotypes in the Dutch and Italian populations. [17][18][19] The overall distribution of the haplotype frequencies was not significantly different in patients and controls (P ¼ 0.076). The frequency of the single haplotype TAGGAGA was higher in controls, but the difference was not significant (overlapped when considering frequencies of the 7 2 standard deviations).…”

“…This distance does not exclude the IL10 gene since peaks of linkage in complex diseases only define a confidence interval for the location of a gene and, therefore, susceptibility genes may map near peaks of linkage rather than directly under them. 13 Different polymorphisms were identified both in the 5' flanking region [14][15][16][17][18][19][20] and, more recently, in the transcribed region 21 of the IL10 gene including two microsatellites at position À4000 (IL10 15 ) and À1100 (IL10 16 ). One of the two microsatellites, IL10.G, has been shown to be associated to SLE by three independent studies, including ours [22][23][24] although this was not supported by a fourth work.…”

“…Previously, only five of these SNPs had been tested. 19,[26][27][28] The markers covered the 5' flanking and the transcribed region of the gene. Basically, the study was performed by the DNA pool method [29][30][31][32] on an extended panel of patients and controls.…”