Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection

Abstract

Untreated HIV-1 infection progresses through acute and asymptomatic stages to AIDS. Although each of the three stages has well-known clinical, virologic, and immunologic characteristics, much less is known of the molecular mechanisms underlying each stage. In this study, we report lymphatic tissue microarray analyses, revealing for the first time stage-specific patterns of gene expression during HIV-1 infection. We show that although there is a common set of key genes with altered expression throughout all stages, each stage has a unique gene expression signature. The acute stage is most notably characterized by increased expression of hundreds of genes involved in immune activation, innate immune defenses (e.g., RIG-1, MDA-5, TLR7 and TLR8, PKR, APOBEC3B, 3F, 3G), adaptive immunity, and in the proapoptotic Fas-Fas ligand pathway. Yet, quite strikingly, the expression of nearly all acute stage genes return to baseline levels in the asymptomatic stage, accompanying partial control of infection. This transition from acute to asymptomatic stage is tied to increased expression of a diverse array of immunosuppressive genes (e.g., CLEC12B, ILT4, galectin-3, CD160, BCMA, FGL2, LAG3, GPNMB). In the AIDS stage, decreased expression of numerous genes involved in T cell signaling identifies genes contributing to T cell dysfunction. These common and stage-specific gene expression signatures identify potential molecular mechanisms underlying the host response and the slow, natural course of HIV-1 infection.

FIGURE 1

Classification of altered genes in LT from HIV-1-infected patients into disease stages and representative hierarchical clustering reveals stage-specific gene signatures. Genes with altered expression (≥1.7 times the level at uninfected baseline, p < 0.05) at the three stages of HIV-1 infection were characterized as the following: unique to the acute stage (S1), asymptomatic stage (S2), or AIDS stage (S3); C1, common to all stages; C2, common to acute and asymptomatic stages; C3, common to asymptomatic and AIDS stages; and C4, common to acute and AIDS stages. A, Hierarchical cluster analysis of altered genes from HIV-1-infected subjects (stage indicated at the bottom). Green, red, and black areas indicate, respectively, decreased, increased, and no significant change in expression compared with uninfected controls. B, Venn diagram depicting the number of genes with altered expression. The size of each region is proportional to the number of altered genes. Green and red numbers indicate, respectively, decreased and increased expression.

FIGURE 2

In human LT of HIV-1-infected subjects, the general functional categories of genes with altered expression (≥1.7 times the level at baseline, p < 0.05). A, Common to all stages (C1); B, unique to the acute stage (S1); C, unique to the asymptomatic stage (S2); and D, unique to the AIDS stage (S3). Green and red letters indicate, respectively, decreased and increased expression. The size of each sector in a pie diagram is proportional to the number of genes in its category (in parentheses). All genes and their names derived from abbreviations can be found in supplemental Table I.

FIGURE 3

Illustration of altered genes in the acute stage related to canonical apoptotic signaling pathways reveals activation of the Fas-Fas ligand pathway. Ingenuity Pathways Analysis software was used to identify altered genes related to canonical apoptotic pathways; red indicates genes significantly increased in expression and black indicates no significant change in gene expression.