SurveyCytokine and cytokine receptor gene polymorphisms and their functionality
Introduction
Cytokines are a group of modulatory proteins or glycoproteins that bind their respective receptor in response to a variety of stimuli, resulting in the activation of second messenger and signal transduction pathways within a cell. The cytokine network is a highly regulated system whereby significant changes seen in cellular cytokine secretion can return to basal levels after removal of stimulus. Basal and cell-stimulated cytokine levels vary between individuals, and both genetic and environmental influences have been shown to play roles in variation. Genetic variation that results in altered structure or expression of a cytokine can have evident pathological consequences, potentially leading to a number of chronic diseases, increased risk of infection, and altered outcome of acute disorders or surgery.
A large number of polymorphisms within the coding and non-coding regions of cytokine genes have been identified, and several thousand disease-association studies have been carried out using these variants. A series of reviews by Bidwell et al. has collated many of these association studies in the form of an on-line database [1], [2], [3], [4]. This review will not focus on the many, and often conflicting, disease-association studies, but concentrate on the functionality of cytokine and cytokine receptor gene polymorphisms. It is through functional single nucleotide polymorphisms (SNPs), i.e. those that effect gene expression, mRNA stability or protein structure, that genuine disease associations are ultimately based, and this review aims to examine the often controversial findings relating to functionality. Disease associations will only be discussed where convincing, replicated data is available.
The often confusing polymorphism nomenclature can differ widely between authors. This review will refer to the commonly used name/s, but also provide a dbSNP number for clarification. As the allele frequencies of polymorphisms vary between populations, where available, minor allele frequencies (MAF) for important SNPs will be provided using data from the International HapMap Project: CEPH (Utah residents with ancestry from northern and western Europe): CEU; Yoruba in Ibadan, Nigeria: YRI; Japanese in Tokyo, Japan: JPT; Han Chinese in Beijing, China: HCB.
Section snippets
Interleukin-1 gene cluster
The complexity of the cytokine network can be epitomised by the interleukin-1 family of cytokines. This family contains the classical cytokine agonists, IL-1α and IL-1β, the receptor antagonist IL-1Ra, IL-18, IL-1F5-10 and IL-33. In addition to IL-1 agonists and antagonists, the receptors to IL-1 have also evolved in such a way that increases the potential for regulation, with IL-1R1 involved in signaling, and IL-1R2 acting as a decoy receptor with no signaling capacity. The majority of the IL1
Interleukin-2 (IL-2)
Antigen-binding to the T-cell receptor stimulates secretion of IL-2, and IL-2R. The interaction of IL-2/IL-2R results in growth, differentiation, and survival of antigen-selected cytotoxic T-cells. A study by Hoffmann et al. examined the functional consequences of IL2 −330 T>G (rs2069762 [MAF: CEU 0.23, HCB 0.24, JPT 0.27, YRI 0.0]) [23]. Upon stimulation with anti-CD3/CD28, IL-2 cytokine levels in the supernatants of peripheral blood lymphocytes were measured by ELISA. Individuals that were
Interleukin-6 (IL-6) and interleukin-6 receptor (IL-6R)
IL-6 is an important mediator of the acute phase response and the highly variable levels of acute and chronic inflammation resulting from this cytokine are thought to play a major role in disease progression and outcome. The IL-6 gene does not contain any common polymorphism within coding regions, and attention has consequently focused on promoter polymorphisms (Fig. 2).
The common polymorphism −174 G>C (rs1800795 [MAF: CEU 0.53, HCB 0.0, JPT 0.0, YRI 0.0]), the earliest to be identified in our
Interleukin-7 (IL-7) and interleukin-7 receptor α (IL-7Rα)
IL-7 is not produced by lymphocytes, but is considered a product of the stromal cells found in lymphoid tissues, skin and intestinal epithelium. The IL-7 receptor is composed of the IL-7Rα chain and the common cytokine γ chain (γc) that is also shared by receptors for IL-2, IL-4, IL-9, IL-15 and IL-21. Upon ligand binding, the two receptor chains heterodimerize, leading to activation of the JAK/STAT pathway, which has the potential to drive T-cell proliferation.
There are no reports of
Interleukin-8 (IL-8)
IL-8 acts as a potent neutrophil chemoattractant, and infected airway epithelial cells secrete high levels of this cytokine. For this reason, Hull et al. examined polymorphism within the IL8 locus in the search for variation that may predispose individuals to infection [41]. The authors identified a common promoter polymorphism, −251 T>A (rs4073 [MAF: CEU 0.40, HCB 0.39, JPT 0.27, YRI 0.83]). To examine functionality, IL-8 levels from LPS-stimulated whole blood from 50 individuals was measured.
Interleukin-10 (IL-10)
IL-10 plays a critical role in immune regulation, predominantly through the inhibition of the production of proinflammatory mediators. Elevated levels of IL-10 are believed to be associated with the pathology of a number of diseases including systemic lupus erythematosus, asthma and susceptibility to infectious diseases. A number of studies have demonstrated inter-individual variability in IL-10 production in stimulated PBMCs, leading to the hypothesis that variation in levels may be due to
Interleukin-12 (IL-12)
IL-12 is a heterodimeric cytokine composed of a p35 and p40 subunit, encoded by IL12A (chromosome 3q25.33) and IL12B (chromosome 5q33.3), respectively. The cytokine is primarily produced by antigen presenting cells, and exerts immunoregulatory effects on T and natural killer (NK) cells. Several functions are mediated by IL-12 including polarization of the T cell towards a Th1 phenotype, characterized by production of IFN-γ.
Attention to genetic variation of IL12B was increased by the proximity
Interleukin-13 (IL-13)
IL-13 is predominantly produced from Th2 cells, but is also expressed in eosinophils, mast cells and basophils. The cytokine stimulates B cells to synthesize IgE. In individuals of European ancestry, a block of SNPs in complete LD extends from −1923 C>T (intron 3) to −2749 C>T (3′-UTR). Within this block the non-synonymous, gain-of-function R130Q (rs20541, R110Q, or +2044 G>A [MAF: CEU 0.23, HCB 0.31, JPT 0.28, YRI 0.17]) is present. This SNP is also in high LD with two promoter SNPs: −1112 C>T
Interleukin-16 (IL-16)
IL-16 is a pleiotropic cytokine whose functions include chemoattraction and modulation of T cell activation. In the non-diseased state IL-16 mRNA is almost exclusively expressed in lymphatic tissue, and high levels in T cells. Under inflammation, IL-16 is synthesised in a number of other tissues.
Few variants have been described for this gene, however, a study by Burkart et al. examined the effect of the −295 T>C variant of gene expression using a luciferase reporter assay [57]. A promoter
Interleukin-18 (IL-18), interleukin-18 receptor (IL-18R), accessory protein (IL-18RAP) and binding protein (IL-18BP)
Interleukin-18, originally termed IFN-γ-inducing factor, is a member of the extended IL-1 superfamily. Examining the locus for variation, Giedraitis identified five SNPs: −656, −607, −137, +113 and +127 [58]. The authors created a luciferase construct, using each of the three common haplotypes, and found that haplotypes 1 (G-C-G-T-C) and 3 (T-A-G-T-C) resulted in increased expression in stimulated HeLa cells, compared to haplotype 2 (T-A-C-G-T; p < 0.01). Expression analysis using RT-PCR
Tumor necrosis factor-α (TNF)
The importance of TNF in inflammation has made this cytokine one of the most widely studied in relation to infectious and autoimmune diseases, and this in turn has led to TNF becoming the most widely studied gene in relation polymorphism and disease. Despite the wide attention TNF polymorphisms have attracted, controversy surrounds their functionality.
The most commonly studied TNF polymorphism is −308 G>A, also known as TNF 1/2 (rs1800629 [MAF: CEU 0.22, HCB 0.03, JPT 0.02, YRI 0.06]), and the
Interferon-γ (IFN-γ)
IFN-γ is a pleiotropic cytokine, produced by effector T and natural killer cells, and is vital for host defence. The IFN-γ gene, IFNG, is located on 12q24.1, contains 4 exons that span 5.4 kb. As with most cytokine genes, there are no common variants located within coding regions. Several polymorphisms have received attention in disease-association studies, including the intron 1 +874 A>T and CA repeat microsatellite, and the promoter SNP, −179 T>G.
The CA repeat was examined by Pravica et al.,
Transforming growth factor-β (TGF-β)
TGF-β is a multifunctional cytokine that plays key roles in normal cellular processes and disease, such as T cell activation and proliferation, tumor progression and asthma. There are a number of polymorphisms within this gene that are believed to have a role in TGF-β expression.
The −509 C>T (−1347 or rs1800469 [MAF: CEU 0.31, HCB 0.47, JPT 0.52, YRI 0.22]) is present within a proximal negative regulatory region, and the T allele has been associated with higher TGF-β1 plasma levels [85]. The
Future directions
Many cytokine and cytokine receptor genes possess functional genetic variants that either alter gene expression or the protein structure (summarized in Table 1). There remains doubt over functionality of certain polymorphisms, and increasing sample size or meta-analyses are key to resolving some of these issues. Whole genome-wide studies on global gene expression [6] and alternative splicing [93] are helping to resolve certain questions on SNP functionality, and novel methodologies such as
Andrew Smith completed his Ph.D. in the Department of Immunogenetics, University of Bristol in 2004, exploring haplotypic variation of the IL-1 gene cluster and osteoarthritis. He is currently a research fellow at the Centre for Cardiovascular Genetics, University College London, where he continues research into the functionality of polymorphism within cytokine genes and other genes involved in cardiovascular risk.
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Andrew Smith completed his Ph.D. in the Department of Immunogenetics, University of Bristol in 2004, exploring haplotypic variation of the IL-1 gene cluster and osteoarthritis. He is currently a research fellow at the Centre for Cardiovascular Genetics, University College London, where he continues research into the functionality of polymorphism within cytokine genes and other genes involved in cardiovascular risk.
Steve Humphries obtained his Ph.D. in Biochemistry in Glasgow in 1974. Following 3 years postdoctoral work in the USA, he worked in both St. Mary's and Charing Cross Hospitals in London, before moving to University College London in 1991. He is currently the British Heart Foundation Professor of Cardiovascular Genetics at UCL, and CEO of the UCL Genetics Institute.