The advance from candidate gene studies to genome-wide association studies for AIDS, as for other diseases, has the notable advantage of being able to reveal previously unsuspected genetic influences. The GWAS results presented here implicate rare genetic variants in the PARD3B gene as conferring slower progression to clinical AIDS among HIV-infected EAs.
is a homolog of a C. elegans
cell polarity determinant that localizes to tight junctions in human epithelial cells 
. It may be relevant that human PARD3B
gene products interact with several members of the SMAD
(mothers against decapentaplegic homolog) family. SMAD
proteins are signal transducers and transcriptional modulators that mediate multiple signaling pathways and are involved in a range of biological activities, including cell growth, apoptosis, morphogenesis, development, and immune responses. Of particular interest are the interactions of PARD3B
encoded proteins with SMAD2
, and SMAD7
, all of which interact directly with HIV-1 [39
and 4 also interact with TGFβ to regulate Tat-mediated transcription of HIV-1 LTR. Individually, SMAD3
increases viral promoter activity, whereas SMAD4
decreases it. SMAD4
also suppresses activation by SMAD3 
. These proteins have similar effects on Tat-mediated transcription of CCL2 (formerly MCP-1; 
and 7 are involved in HIV-1 glycoprotein 120-induced tubular epithelial cell apoptosis 
. SMAD7 helps prevent apoptosis, whereas SMAD2
is involved in downstream signaling 
is a large gene (with 23 exons coding for 1205 amino acids and spanning 1.07 Mbp) located on chromosome 2. One of the exons (exon 20) is alternately spliced. Three splice variants of the PARD3B
product have been characterized and shown to have differences in their protein binding properties 
. The functional significance of these alternative forms is unknown, but they may also have different expression profiles 
. A SNP in the cluster of association, rs10185378, which introduces a missense mutation in exon 20, also eliminates a predicted splice enhancer for this exon. We tested this same SNP for transcript production using a group of 29 lymphoblastoid cell lines of alternate genotypes and observed a significant increase in messenger RNA levels of the PARD3B
isoform lacking exon 20 relative to forms with exon 20 with the rare allele (TT) at rs10185378 (). It is by no means clear that this is the causative polymorphism; additional studies into PARD3B function with respect to HIV-host interactions are indicated.
As with any association result that may produce false-positive results, replication in independent cohorts is essential. Although results here are significant for this association, several factors make independent replication particularly important. The fact that the gene identified falls in an unexpected category demands additional evidence for the association to be validated. By the same token, if confirmed, the identification of PARD3B would have the potential to reveal an entirely new avenue of HIV cellular activity, with potential new targets for therapy, and could lead to a new understanding of the process of AIDS pathogenesis. The corroborative association of PARD3B-SNP rs10185378 in the European GRIV and ACS rapid progression cohorts provides an initial replication for this association (Figure 3B). A EA seroconverter cohort with AIDS 1987 progression would be a more valuable, though unavailable, comparison, because the signal in our cohort clearly associates with this particular phenotype and is not evident when comparing rapid and slow progressors from our cohorts for CD4+ cell count <200 cells/mL and does not achieve genome-wide significance for AIDS 1993 definition (A). Therefore, it is not surprising that our SNP of highest significance did not replicate for CD4+ cell count <300 cells/mL or AIDS 1993 in a dichotomous analysis of the GRIV rapid versus slow progressors (data not shown). In addition, allele frequency and haplotype structure in African populations is quite different than in EA populations, which might account for the failure to replicate this signal in a small (n = 282) AA seroconverter replication cohort.
Figure 5. Additional analysis of the GWAS data. A, Categorical analysis of rs11884476 for different clinical outcomes. Shown here are CD4+ cell count <200 cells/mL and AIDS 1993 definition in <8 years or ≥8 years and AIDS 1987 with a cutoff (more ...)
Although this GWAS demonstrates the strength of this approach for detecting unsuspected AIDS restriction genes, it also illustrates some weaknesses. Although we observed significant unadjusted P
values for many of the previously validated ARGs [3
], none achieved genome-wide significance in the present GWAS, nor did we detect additional recently reported associations from other HIV/AIDS progression GWAS[11
] with this phenotype (Figure 5B
). Deviations in SNP choice and region coverage from platform to platform account for some of the disparity between results from similar studies (as demonstrated by our difficulty in using Illumina HapMap300 SNPs to impute Affy 6.0 SNPs with high confidence in our PARD3B
region of significance; see Methods), as do alternative choices in disease phenotype tests and genetic models. The AIDS progression end point phenotype examined here represents a proven, well-powered analysis for progression to clinical AIDS. However, it is a complex phenotype, and further exploration of PARD3B association with multiple sequelae is now clearly indicated. A more detailed exploration of genetic associations with all of the clinical data collected on these AIDS cohorts will ultimately allow a much broader view of multiple AIDS phenomena, albeit with statistical penalties for multiple test approaches (J. A. Lautenberger, J. L. Troyer, and S. J. O'Brien, unpublished data). As the interpretation of the full range of data necessarily involves subjective judgment, with a corresponding loss of statistical rigor, it seems useful to extract from the full dataset the statistically straightforward analysis presented here, which implicates a strong new AIDS progression genetic association.