Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages

Abstract

Background: HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART), macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages.

Methodology/principal findings: Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96) or high (n = 96) p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.16 × 10(-5)). While the association was not genome-wide significant (p<1 × 10(-7)), we could replicate this association using monocyte-derived macrophages from an independent group of 31 individuals (p = 0.0034). Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.84 × 10(-6)). In addition, we found this SNP to be associated with HIV-1 disease progression in vivo in two independent cohort studies (p = 0.035 and p = 0.0048).

Conclusions/significance: These findings suggest that the kinase DYRK1A is involved in the replication of HIV-1, in vitro in macrophages as well as in vivo.

Figure 1. Association between HIV-1 replication in monocyte-derived macrophages (MDM) and the genotypes for the SNPs rs12483205 in DYRK1A, rs2304418 in PDE8A, rs2905 in UBR7, rs1046099 and rs1270629 in MOAP1, and rs17519417 in SPOCK3.

Only donors with MDM with low (n = 95) or high (n = 96) HIV-1 replication in vitro were included in the genome-wide SNP analysis. This selection of donors with a more extreme phenotype explains the absence of circles in the middle section of the graphs. MAJ, homozygous for the major allele; HZ, heterozygote; MIN, homozygous for the minor allele.

Figure 2. Significant association between rs12483205 and in vitro replication of HIV-1 in macrophages derived from an independent group of 31 healthy blood donors.

The negative association between the rs12483205 minor allele and Gag p24 levels in MDM culture supernatant 14 days after inoculation with HIV-1, was found to match with the results from the genome-wide association study. Open circles represent results from donors with the CCR5 Δ32 wild-type genotype, filled circles from donors with the CCR5 wt/Δ32 heterozygous genotype. MAJ, homozygous for the major allele; HZ, heterozygote; MIN, homozygous for the minor allele.

Figure 3. Schematic representation of the DYRK1A gene region, depicting all four transcript variants (1, 2, 3 and 5) and the localization of SNP rs12483205.

Untranslated regions (UTR) are shown as open blocks, whereas exons are shown as filled blocks. SNP rs12483205 lies in close proximity to a part of the 5′ UTR unique for splice variant 3.

Figure 4. Detection of different DYRK1A transcript variants in macrophages.

Amplicons were generated by PCR on cDNA from U87 cells, used as a positive control for the PCR, and from monocyte-derived macrophages (MDM) obtained from three individuals, using DYRK1A transcript variant specific primers. DYRK1A transcript variants 1, 2 and 3 were detected in MDM and U87 cells (panel A, B and C respectively). Transcript variant 5, however, was only convincingly detected in U87 cells, and not in MDM. Numbers on the left side of each picture indicate the size (in base pairs, bp) for the corresponding DNA fragment of the DNA ladder or PCR amplicons. 1 kb, 1 kb DNA ladder; 100 bp, 100 bp DNA ladder.