Expression profiling of chromatin-modifying enzymes and global DNA methylation in CD4+ T cells from patients with chronic HIV infection at different HIV control and progression states

Abstract

Background: Integration of human immunodeficiency virus type 1 (HIV-1) into the host genome causes global disruption of the chromatin environment. The abundance level of various chromatin-modifying enzymes produces these alterations and affects both the provirus and cellular gene expression. Here, we investigated potential changes in enzyme expression and global DNA methylation in chronically infected individuals with HIV-1 and compared these changes with non-HIV infected individuals. We also evaluated the effect of viral replication and degree of disease progression over these changes.

Results: Individuals with HIV-1 had a significant surge in the expression of DNA and histone methyltransferases (DNMT3A and DNMT3B, SETDB1, SUV39H1) compared with non-infected individuals, with the exception of PRMT6, which was downregulated. Some histone deacetylases (HDAC2 and HDAC3) were also upregulated in patients with HIV. Among individuals with HIV-1 with various degrees of progression and HIV control, the group of treated patients with undetectable viremia showed greater differences with the other two groups (untreated HIV-1 controllers and non-controllers). These latter two groups exhibited a similar behavior between them. Of interest, the overexpression of genes that associate with viral protein Tat (such as SETDB1 along with DNMT3A and HDAC1, and SIRT-1) was more prevalent in treated patients. We also observed elevated levels of global DNA methylation in individuals with HIV-1 in an inverse correlation with the CD4/CD8 ratio.

Conclusions: The current study shows an increase in chromatin-modifying enzymes and remodelers and in global DNA methylation in patients with chronic HIV-1 infection, modulated by various levels of viral control and progression.

Keywords: Chromatin-modifying enzymes; DNA methylation; Epigenetics; HDAC; HIV; Methyltransferases; Progression.

Fig. 1

Chromatin-modifying enzyme expression profiling in individuals with chronic immunodeficiency virus type 1 infection-matched HIV-negative controls. a Histone methyltransferases (HMTs); (b) histone deacetylases (HDACs) Class I, II, and III; (c) DNA methyltransferases 1 and 3a and methyl binding protein; (d) DNA methyltransferase 3b; and (e) histone acetyltransferase 1. Y-exe values represent relative levels of mRNA obtained by the ΔΔCt method. Horizontal bars indicate median values, boxes indicate interquartile range (IQR), and p values for each gene are indicated

Fig. 2

Expression of mRNA levels of SETDB1, DNMT3a, and HDAC1 in patients positive for HIV. a Correlation between pairs (SETDB1-DNMT3a, SETDB1-HDAC1, and DNMT3a-HDAC1); (b) Differences in SETDB1, DNMT3a, and HDAC1 expression observed in each group of patients positive for HIV. Y-exe values represent relative levels of mRNA obtained by the ΔΔCt method. Horizontal bars indicate median values; p values indicate differences for each gene between noncontrollers versus cART recipients and controllers versus cART recipients

Fig. 3

Western blot analysis. a Cropped gels/blots obtained by each protein evaluation. b, c Quantification of the expression of tested proteins and differences between HIV and non-HIV infected individuals: b DNMT3a and c DNMT1. The optical density of each sample was measured and normalized using an Actin run on the same gel. The data are expressed as relative expression (ratio DNMT/actin). Horizontal bars indicate median values, boxes indicate interquartile range (IQR), and p values for each protein are indicated

Fig. 4

CpG methylation analysis. a Percentage of 5′-methylcytosine content in genomic DNA in patients with HIV versus non-HIV infected individuals. Horizontal bars represent mean values and boxes IQR; (b) correlation plot between global DNA methylation and CD4+/CD8+ T cell ratio (Pearson correlation test); and (c) correlation plot between global DNA methylation and DNMT1 expression in the group of HIV-1 controllers (due to the nature of variables, the nonparametric Spearman correlation test was used)