Research ArticleGENETICS

Allele-specific long-distance regulation dictates IL-32 isoform switching and mediates susceptibility to HIV-1

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Science Advances  21 Feb 2018:
Vol. 4, no. 2, e1701729
DOI: 10.1126/sciadv.1701729

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Abstract

We integrated data obtained from HIV-1 genome-wide association studies with T cell–derived epigenome data and found that the noncoding intergenic variant rs4349147, which is statistically associated with HIV-1 acquisition, is located in a CD4+ T cell–specific deoxyribonuclease I hypersensitive region, suggesting regulatory potential for this variant. Deletion of the rs4349147 element in Jurkat cells strongly reduced expression of interleukin-32 (IL-32), approximately 10-kb upstream, and chromosome conformation capture assays identified a chromatin loop between rs4349147 and the IL-32 promoter validating its function as a long-distance enhancer. We generated single rs4349147-A or rs4349147-G allele clones and demonstrated that IL-32 enhancer activity and interaction with the IL-32 promoter are strongly allele dependent; rs4349147 −/A cells display reduced IL-32 expression and altered chromatin conformation as compared to rs4349147 G/− cells. Moreover, RNA sequencing demonstrated that rs4349147 G/− cells express a lower relative ratio of IL-32α to non-α isoforms than rs4349147 −/A cells and display increased expression of lymphocyte activation factors rendering them more prone to infection with HIV-1. In agreement, in primary CD4+ T cells, both treatment with recombinant IL-32γ (rIL-32γ) but not rIL-32α, and exogenous lentiviral overexpression of IL-32γ or IL-32β but not IL-32α resulted in a proinflammatory T cell cytokine environment concomitant with increased susceptibility to HIV infection. Our data demonstrate that rs4349147-G promotes transcription of non–IL-32α isoforms, generating a proinflammatory environment more conducive to HIV infection. This study provides a mechanistic link between a HIV-associated noncoding DNA variant and the expression of different IL-32 isoforms that display discrete anti-HIV properties.

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