Genetic association of the antiviral restriction factor TRIM5alpha with human immunodeficiency virus type 1 infection

Abstract

The innate antiviral factor TRIM5alpha restricts the replication of some retroviruses through its interaction with the viral capsid protein, leading to abortive infection. While overexpression of human TRIM5alpha results in modest restriction of human immunodeficiency virus type 1 (HIV-1), this inhibition is insufficient to block productive infection of human cells. We hypothesized that polymorphisms within TRIM5 may result in increased restriction of HIV-1 infection. We sequenced the TRIM5 gene (excluding exon 5) and the 4.8-kb 5' putative regulatory region in genomic DNA from 110 HIV-1-infected subjects and 96 exposed seronegative persons, along with targeted gene sequencing in a further 30 HIV-1-infected individuals. Forty-eight single nucleotide polymorphisms (SNPs), including 20 with allele frequencies of >1.0%, were identified. Among these were two synonymous and eight nonsynonymous coding polymorphisms. We observed no association between TRIM5 polymorphism in HIV-1-infected subjects and their set-point viral load after acute infection, although one TRIM5 haplotype was weakly associated with more rapid CD4(+) T-cell loss. Importantly, a TRIM5 haplotype containing the nonsynonymous SNP R136Q showed increased frequency among HIV-1-infected subjects relative to exposed seronegative persons, with an odds ratio of 5.49 (95% confidence interval = 1.83 to 16.45; P = 0.002). Nonetheless, we observed no effect of individual TRIM5alpha nonsynonymous mutations on the in vitro HIV-1 susceptibility of CD4(+) T cells. Therefore, any effect of TRIM5alpha polymorphism on HIV-1 infection in primary lymphocytes may depend on combinations of SNPs or on DNA sequences in linkage disequilibrium with the TRIM5alpha coding sequence.

FIG. 1.

TRIM5α polymorphism. (A and B) Schematic illustrating TRIM5 genetic structure (A), with boxes above the line indicating TRIM5α exons and 48 noncoding SNPs indicated by vertical lines below the line, and TRIM5α protein (B), with functional domains indicated. Ten coding SNPs are illustrated by vertical lines. The position and amino acid change are designated for 8 nonsynonymous SNPs, and asterisks denote synonymous coding SNPs.

FIG. 2.

TRIM5 SNPs demonstrate high linkage disequilibrium. Pairwise estimates of linkage disequilibrium are shown for all polymorphisms identified. D′ = 1 indicates complete disequilibrium. For a pairwise estimate in which D′ = 1, log of odds (LOD) of <2 are shown in gray and LOD of ≥2 are shown in black. For pairwise estimates in which D′ is <1, LOD of <2 are shown in white and LOD of ≥2 are denoted by hatched fields.

FIG. 3.

TRIM5 polymorphisms are not associated with altered set-point viral load in HIV-1-infected individuals. Median plasma HIV-1 RNA between 100 days and 2 years postinfection were calculated for each of 105 HIV-1-infected individuals not receiving antiretroviral therapy. Boxes demarcate interquartile range, with medians and 5th and 95th percentiles indicated. For each of nine polymorphic amino acid residues, set-point viral load data are arrayed according to dominant, heterozygous, and homozygous minor genotypes. Asterisks denote synonymous coding SNPs.

FIG. 4.

G110E polymorphism moderately associated with increased in vitro CD4⁺ T-cell HIV-1 production. Viral infectivity was measured by p24 antigen production 7 days after in vitro HIV-1_JR-CSF infection of CD4⁺ T cells from 77 seronegative individuals. Boxes demarcate interquartile range, with medians and 5th and 95th percentiles indicated. For each of six polymorphic amino acid residues, p24 production data are arrayed according to dominant, heterozygous, and homozygous minor genotypes. Asterisks indicate synonymous coding SNPs.

FIG. 5.

H43Y, G110E, V112F, R119Q, R119W, R136Q, and V140L polymorphisms do not affect HIV-1 infection in primary CD4⁺ T cells. Primary CD4⁺ lymphoblasts from exposed seronegative and HIV-1-seropositive volunteers were infected with a VSV-G-pseudotyped, GFP-expressing HIV-1 vector (HIV-1_LAIΔenvGFP). (A) Mean frequency of HIV-1 infection in three experiments comparing HIV-1 susceptibility in CD4⁺ T cells from five H43Y/H43Y (three HIV-1 infected and two ES) and 13 H43/H43 (five HIV-1-infected and eight ES) subjects. (B) Two experiments comparing six G110/G110E (two HIV-1-infected and four ES) and seven G110/G110 (three HIV-1-infected and four ES) individuals. (C) One experiment comparing three V112F/V112F (two HIV-1-infected and one ES) and six V112/V112 (four HIV-1-infected and two ES) individuals. (D) Three experiments comparing three R119/R119Q (one HIV-1-infected and two ES) and one R119/R119W ES subject to eight R119/R119 (two HIV-1-infected and six ES) individuals. (E) Two experiments comparing seven R136Q/R136Q (three HIV-1-infected and four ES) and seven R136/R136 (three HIV-1-infected and four ES) individuals. (F) One experiment comparing three V140/V140L and six V140/V140 HIV-1-infected individuals.