Rs4804803

The SNP rs4804803 is a variant (-336A>G) in the promoter region for the CD209 gene that results in altered CD209 transcription. It is associated with modified resistance to several infectious diseases, including viruses (Hepatitis C, HIV, dengue, SARS), and bacteria (Mycobacterium tuberculosis), as well as other disorders of varying etiology (ulcerative colitis). The CD209 gene encodes a transmembrane receptor found on the surface of dendritic cells and macrophages. The protein product of CD209, DC-SIGN, plays an important role within both the innate and adaptive immune systems.

DC-SIGN's role differs depending on which cell type it resides. On macrophages, DC-SIGN is responsible for recognizing and binding to mannose-type carbohydrates, which are found in almost all pathogenic organisms (viruses, bacteria, fungi, etc.) but not human cells; this binding induces phagocytosis of the offending pathogen by the macrophage. On dendritic cells, DC-SIGN binds the ICAM-3 molecule on naive T-cells with high affinity, mediating the initial interaction of T-cells with dendritic cells that is responsible for initiating the adaptive immune response. However, pathogens can also exploit this T-cell adhesion for their own purposes (see sections on HIV and Hepatitis C virus).

Mechanism of Action
The rs4804803 SNP is located in the promoter region of CD209, 212 base pairs from the major transcription start site toward the 5' end of the gene. Variants at this location affect transcription factor binding sites for Sp1/GATA1/CACCC and Sp1/GATA1/CACAC-binding transcription factors of the type GGGTGGG; the G allele at position 5 (GGGTGGG) is associated with transcription factor binding, and the A allele (GGGTAGG) with its absence. The rs4804803 SNP is empirically known to affect the binding of nuclear extract proteins to the promoter region of CD209. Both electrophoretic mobility shift assays (EMSA) and promoter activity assays have revealed that the presence of the A allele results in higher rates of CD209 transcription and the production of more DC-SIGN gene product.

Associations with Disease
Hepatitis C Virus

In one study of 131 Irish women who had received HCV-contaminated anti-D-immunoglobulin (resulting in chronic HCV infection) and 79 healthy controls, Ryan et al found no association between rs4804803 genotype and the risk of HCV chronicity. However, of those women with chronic HCV infection, presence of at least one G-allele at position 366 was associated with more advanced liver disease. Specifically, patients with the AG or GG genotype had significantly worse liver fibrosis scores (p<0.05, Mann-Whitney U-test) and higher alanine aminotransferase (biomarker for hepatocellular injury) levels (p<0.01, Mann-Whitney U-test) than those with the AA genotype. This study tested only the rs4804803 SNP, so p<0.05 was considered significant.

The exact mechanism behind the HCV/DC-SIGN association is still unknown. However, DC-SIGN binds proteins on the surface of Hepatitis C virions (HCV), specifically the E1 and E2 viral glycoproteins. Capture of circulating Hepatitis C viral particles by DC-SIGN on cells within the liver may facilitate viral infection of nearby hepatocytes and lymphocyte subpopulations, which can lead to the establishment of chronic HCV infection and hepatocellular damage.

Human T-cell Lymphotropic Virus Type 1

A study of HTLV-1 occurrence in four different Brazilian ethnic groups revealed that the -336A variant was more frequently-observed in HTLV-1-infected patients than in controls (OR = 2.511, p = 0.0197). The study tested four CD209 variants (336A/G, 332A/G, 201T/G and 139A/G; significance threshold approximately p<0.0125); the protective effect of the rs4804803 G-allele for HTLV-1 infection (the reverse of what is observed for HCV) should therefore be considered weak. These authors also observed that the -336G allele occurred with higher frequency among Afro-Brazilians (42.0%) and Caucasians (26.7%) than in Asians (5.4%), and was not observed at all in the Amerindian group.

Dengue Fever Virus

The G allele of the rs4804803 SNP was associated with strong protection against dengue fever in three independent Thai cohorts. This study investigated the effects of 40 separate CD209 polymorphisms on dengue susceptibility (significance threshold approximately p=0.00125), and rs4804803 was the only polymorphism that displayed a significant association. The carrier frequency of the G allele among individuals with dengue fever was 4.7%, compared to 22.4% in individuals with dengue hemorrhagic fever, and 19.5% in controls. This seems to indicate that the presence of the G allele at rs4804803 provides dominant protection against dengue fever (OR for protection = 4.90, p = 2e-6), but not against dengue hemorrhagic fever. Among individuals with dengue, genotypes GG and GA increased the risk of contracting dengue hemorrhagic fever instead of dengue fever (OR = 5.84, p = 1.4e-7).

In another study that investigated only the rs4804803 SNP (significance threshold p=0.05), investigators found that GG/AG genotypes at SNP rs4804803 occurred at a significantly higher rate in dengue patients than in patients with non-dengue febrile illnesses (OR = 3.23, p = 0.002), and population controls (OR = 2.36, p = 0.020). A strong association between GG/AG genotypes of rs4804803 and the risk of dengue hemorrhagic fever was found when compared to dengue fever, non-dengue febrile illness, and control patients (p = 0.004, 3e-5, 0.001 respectively). The AA genotype was associated with protection against dengue infection compared with non-dengue febrile illnesses and controls (p = 0.002 and 0.020 respectively). In addition, dendritic cells from individuals from individuals with the AG genotype displayed higher levels of DC-SIGN expression and significantly higher expression of several important cytokines compared to those from AA individuals in response to dengue infection, but the viral replication in dendritic cells with the AG genotype was lower than those with the AA genotype. This study seemed to contradict the result from that the G allele was protective against dengue; however, the authors mentioned that the definitions of dengue fever and dengue hemorrhagic fever used in the two studies were different; in addition, the latter study was conducted in Taiwan while the former was conducted in Thailand, and the frequency of the G allele differed significantly between the two study populations (3.8% in populations of Chinese descent; 9.5-10.4% in Thailand).

Mycobacterium Tuberculosis

One study that investigated the role of the rs4804803 SNP (significance threshold p=0.05) on tuberculosis in a large cohort of individuals from sub-Saharan Africa found that the -336G allele provided significant overall protection against pulmonary tuberculosis (OR = 0.86, p = 0.006), and patients homozygous for the G allele had a decreased risk of tuberculosis-induced lung cavitation, a more severe form of TB (OR = 0.42, p = 0.00003).

In a previous study of a South African cohort (8 SNPs investigated; significance threshold approximately p=0.00625), Barreiro and colleagues found that rs4804803 genotypes GG and GA were more frequently observed in tuberculosis cases (70.6%) than controls (61.9%, p = 0.01). The presence of the G allele was therefore associated with an increased risk of developing TB. Because the A allele was mainly confined to Eurasian populations, the authors speculated that this variant may have increased in frequency in non-African populations as a result of host genetic adaptation to a longer history of exposure to tuberculosis.

Human Immunodeficiency Virus (HIV)

Using samples obtained from 1,611 European-American participants at risk for parenteral or mucosal HIV infection (5 SNPs investigated; significance threshold approximately p=0.01), Martin et al found that individuals at risk for parenterally-acquired infection who had the -336G polymorphism were more susceptible to infection than individuals with the -336A allele (odds ratio = 1.87, p = 0.001).

The mechanism by which this variant may lead to differential HIV infection risk is unknown; however, it is known that the HIV virus attaches to dendritic cells via the binding of viral protein gp120 to DC-SIGN. By binding to DC-SIGN, the virus is engulfed into a mildly-acidic endosomal compartment within the cell, which protects it as the dendritic cell makes its way to lymphoid tissue and promotes trans-infection of T-cells.

SARS Coronavirus

DC-SIGN shares 77% amino acid similarity with CLEC4M, the usual binding receptor for the SARS coronavirus (SARS-CoV). It was found to interact with the spike protein of the virus, facilitating viral transmission to susceptible cells.

SARS patients with a -336G-positive genotype (either AG or GG) have a 2.5-fold greater chance of having lower lactate dehydrogenase (LDH) levels compared with -336AA patients (one SNP tested; significance threshold = 0.05; p = 0.014). High LDH levels are known to be an independent predictor for poor SARS clinical outcome, possibly because of the increased tissue destruction that is the result of immune hyperactivity. Thus, SARS patients with the AA genotype have a 60% greater chance of a poor prognosis than GG or AG patients.

Inflammatory Bowel Diseases

The CD209 gene is located in a region previously linked to inflammatory bowel diseases (IBD), including ulcerative colitis and Crohn's disease. One group found no initial association between the rs4804803 SNP and IBD, but upon stratification of ulcerative colitis patients by HLA-DR3 status (a strong protective allele), showed that carriage of the -366G allele increased susceptibility in the HLA-DR3-positive individuals (one SNP tested; significance threshold = 0.05; OR = 1.77, p = 0.03) relative to controls.

Summary of Effects
Overall, the empirically-observed effects between the rs4804803 SNP and risk for various diseases have been contradictory, even among studies of the same disease. For HCV, the presence of the G allele appears to cause a worse clinical outcome than the A allele, while for HTLV-1, the G allele is protective. For dengue, two separate studies yielded two different results: in a Thai cohort, the G allele was strongly protective, while for a Taiwanese cohort the A allele was protective. A similar contradiction was observed for tuberculosis, where one study observed that the G allele was protective and another observed that it was destructive. So far, the G allele appears protective for SARS, but the A allele is protective for both HIV and inflammatory bowel diseases.

Perhaps these contradictory results are due to the conflicting effects of DC-SIGN expression when an organism is confronted with different infectious organisms. The A allele at position 336 in CD209 is correlated with increased DC-SIGN expression in vitro, but it is unclear how this would manifest itself clinically. For example, increased DC-SIGN expression on dendritic cells could lead to a faster and stronger immune response to certain infections, but it could cause others (for example, viruses that can use DC-SIGN as an entry portal to host cells) to increase in severity. It is clear, however, that differences in expression of the CD209 gene product do lead to differential host response to infection; much of the variability among studies could be due to geographic/ethnic differences in study population, or different mechanisms of pathogenesis for the organisms involved. Clearly, further work is needed to firmly establish the clinical effects of this important SNP.

Tuberculosis Susceptibility