HIV-1 Disease-Influencing Effects Associated with ZNRD1 , HCP5 and HLA-C Alleles Are Attributable Mainly to Either HLA-A10 or HLA-B*57 Alleles Gabriel Catano1,2., Hemant Kulkarni1,2., Weijing He1,2., Vincent C. Marconi3,4, Brian K. Agan3,4,5, Michael Landrum3,4,5, Stephanie Anderson3,5, Judith Delmar3,4, Vanessa Telles1,2, Li Song1,2, John Castiblanco1,2, Robert A. Clark1,2, Matthew J. Dolan3,4,5*, Sunil K. Ahuja1,2,6,7* 1 Veterans Administration Research Center for AIDS and HIV-1 Infection, South Texas Veterans Health Care System, San Antonio, Texas, United States of America, 2 Department of Medicine, University of Texas Health Science Center, San Antonio, Texas, United States of America, 3 Infectious Disease Clinical Research Program (IDCRP), Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America, 4 Infectious Disease Service, San Antonio Military Medical Center (SAMMC), Ft. Sam Houston, Texas, United States of America, 5 Henry M. Jackson Foundation, Wilford Hall United States Air Force Medical Center, Lackland AFB, Texas, United States of America, 6 Department of Microbiology and Immunology, University of Texas Health Science Center, San Antonio, Texas, United States of America, 7 Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas, United States of America Abstract A recent genome-wide association study (GWAS) suggested that polymorphisms in or around the genes HCP5, HLA-C and ZNRD1 confer restriction against HIV-1 viral replication or disease progression. Here, we also find that these alleles are associated with different aspects of HIV disease, albeit mainly in European Americans. Additionally, we offer that because the GWAS cohort was a subset of HIV-positive individuals, selected based in part on having a low viral load, the observed associations for viral load are magnified compared with those we detect in a large well-characterized prospective natural history cohort of HIV-1-infected persons. We also find that because of linkage disequilibrium (LD) patterns, the dominant viral load- and disease-influencing associations for the ZNRD1 or HLA-C and HCP5 alleles are apparent mainly when these alleles are present in HLA-A10- or HLA-B*57-containing haplotypes, respectively. ZNRD1 alleles lacking HLA-A10 did not confer disease protection whereas ZNRD1-A10 haplotypes did. When examined in isolation, the HCP5-G allele associates with a slow disease course and lower viral loads. However, in multivariate models, after partitioning out the protective effects of B*57, the HCP5-G allele associates with disease-acceleration and enhanced viral replication; these associations for HCP5-G are otherwise obscured because of the very strong LD between this allele and a subset of protective B*57 alleles. Furthermore, HCP5 and HLA-C alleles stratify B*57-containing genotypes into those that associate with either striking disease retardation or progressive disease, providing one explanation for the long-standing conundrum of why some HLA-B*57-carrying individuals are long-term non-progressors, whereas others exhibit progressive disease. Collectively, these data generally underscore the strong dependence of genotype-phenotype relationships upon cohort design, phenotype selection, LD patterns and populations studied. They specifically demonstrate that the influence of ZNRD1 alleles on disease progression rates are attributable to HLA-A10, help clarify the relationship between the HCP5, HLA-C and HLA-B*57 alleles, and reaffirm a critical role of HLA-B*57 alleles in HIV disease. Furthermore, as the protective B*57-containing genotypes convey striking salutary effects independent of their strong impact on viral control, it is conceivable that T cell-based therapeutic vaccine strategies aimed at reducing viral loads may be inadequate for limiting AIDS progression, raising the potential need for complementary strategies that target viral load-independent determinants of pathogenesis. Citation: Catano G, Kulkarni H, He W, Marconi VC, Agan BK, et al. (2008) HIV-1 Disease-Influencing Effects Associated with ZNRD1, HCP5 and HLA-C Alleles Are Attributable Mainly to Either HLA-A10 or HLA-B*57 Alleles. PLoS ONE 3(11): e3636. doi:10.1371/journal.pone.0003636 Editor: Esper Georges Kallas, Federal University of Sao Paulo, Brazil Received August 25, 2008; Accepted October 1, 2008; Published November 4, 2008 Copyright: 2008 Catano et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the Veterans Administration Center on AIDS and HIV Infection of the South Texas Veterans Health Care System, and by a MERIT award (R37046326) and other awards (AI043279 and MH069270) from the NIH (to S.K.A.). S.K.A. is a recipient of the Elizabeth Glaser Scientist Award and the Burroughs Wellcome Clinical Scientist Award in Translational Research. Support for the WHMC cohort was provided by the Infectious Disease Clinical Research Program (IDCRP) of the Uniformed Services University of the Health Sciences (USUHS), of which the Tri-Service AIDS Clinical Consortium (TACC) is a component. The IDCRP is a Department of Defense tri-service program executed through USUHS and the Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF), in collaboration with HHS/NIH/NIAID/DCR through Interagency Agreement HU0001-05-2-0011. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: mdolan@hjf.org (MJD); ahujas@uthscsa.edu (SKA) . These authors contributed equally to this work. Introduction An important goal of HIV-1 vaccine research is to identify vaccine-induced immune responses that will predict protection from HIV infection or disease. However, this is proving to be an immensely complex task because it is difficult to predict which immunological response(s) in candidate vaccine-challenged ani- mals or in vitro studies will convey a protective effect in humans [1,2,3]. This is exemplified by the results of the recent STEP trial, which showed that a HIV-1 vaccine that conferred protection in PLoS ONE | www.plosone.org 1 November 2008 | Volume 3 | Issue 11 | e3636