Cytokine typing: SNP allele frequencies in the Iranian population

Multiplex genotyping of cytokine gene SNPs using fluorescence bead array

Single nucleotide polymorphisms (SNPs) of genes that affect cytokine production and function are known to influence the susceptibility and progression of immune-related conditions such as infection, autoimmune diseases, transplantation, and cancer. We established a multiplex genotyping method to analyze the SNPs of cytokine genes by combining the multiplex PCR and bead array platform. Thirteen cytokine gene regions, including 20 SNPs, were amplified, and allele-specific primer extension was performed in a single tube. High-quality allele-specific primers were selected for signals greater than 1000 median fluorescence intensity (MFI) for positive alleles, and less than 500 MFI for negative alleles. To select and improve the extension primers, modifications for the reverse direction, length or refractory were performed. 24 primers in the forward or reverse direction step and 12 primers in length or refractory modifications were selected and showed high concordance with results by nucleotide sequencing. Among the 13 candidate cytokine genes, the SNPs of 12 cytokine genes, including IL-1α, IL-1R, IL-1RA, IL-1β, IL-2, IL-4, IL-4Rα, IL-6, IL-10, IL-12, TGF-β1, and TNF-α, were successfully defined with the selected allele-specific primers in healthy Korean subjects. Our genotyping system provides a fast and accurate detection for SNPs of multiple cytokine genes to investigate their association with immune-related diseases and transplantation outcomes.

Distribution of cytokine gene polymorphisms in the general Lebanese population: the first report

CONTEXT

Cytokines are polypeptide regulatory molecules that play a significant role in inflammatory and regulatory responses of the immune system. Several cytokine gene polymorphisms have been studied to date and have been found to be associated with distorted cytokine production or activity by affecting transcriptional regulation and with vulnerability to a variety of infectious and autoimmune diseases as well as to transplant rejection.

RESULTS

We studied 106 healthy Lebanese individuals using polymerase chain reaction/sequence-specific priming technique to detect 22 single-nucleotide polymorphisms within 13 cytokine genes: IL1alpha 889-T/C, IL1beta 511-T/C, IL1beta +3962-T/C, IL1R pst1 1970-T/C, IL1RA mspa1 11100-T/C, IL4Ralpha 1902-G/A, IL12 1188-C/A, IFNgamma 874-A/T, TGFbeta codon 10-C/T, TGF-beta codon 25-G/C, TNFalpha 308-A/G, TNFalpha 238-A/G, IL2 166-G/T, IL2 330-T/G, IL4 1098-T/G, IL4 590-T/C, IL4 33-T/C, IL6 174-C/G, IL6 nt565-G/A, IL10 1082-G/A, IL10 819-C/T, and IL10 592-A/C. We compared our results to those reported in other populations with similarities observed between the Lebanese and the Italian populations.

CONCLUSION

The study of different cytokine polymorphisms will aid in understanding the susceptibility of populations to various diseases, and this is the first report from the Lebanese community.

Single nucleotide polymorphisms of cytokine genes in the healthy Slovak population

Cytokines are molecules that control and modulate the activities of numerous target cells via binding to specific receptors. The observed differences in the cytokine production among individuals can be, at least partially, explained by gene polymorphisms. Several cytokine gene polymorphisms have been identified to play a role in susceptibility to various diseases, including autoimmune, infectious, allergic or cardiovascular diseases. The aim of the current study was to determine allele and genotype frequencies of 22 polymorphisms in 13 cytokine genes in the healthy Slovak population and to compare them with data available from six populations from Central and Southern Europe. A polymerase chain reaction with sequence-specific primers was used to genotype polymorphisms within genes encoding IL-1alpha, IL-1beta, IL-1R, IL-1RA, IL-4Ralpha, IL-12, IFN-gamma, TGF-beta, TNF-alpha, IL-2, IL-4, IL-6 and IL-10 in a sample of 140 unrelated Slovak subjects. The allelic distribution of all polymorphisms in the Slovak population was very close to that in the geographically and historically closest populations in Central Europe--the Czech and the Polish. However, several differences were found between the Slovak and four populations from Southern Europe. The obtained data represent a basis for further studies on association of cytokine gene polymorphisms with some diseases.