HIV-1 infection causes a down-regulation of genes involved in ribosome biogenesis

Abstract

HIV-1 preferentially infects CD4+ T cells, causing fundamental changes that eventually lead to the release of new viral particles and cell death. To investigate in detail alterations in the transcriptome of the CD4+ T cells upon viral infection, we sequenced polyadenylated RNA isolated from Jurkat cells infected or not with HIV-1. We found a marked global alteration of gene expression following infection, with an overall trend toward induction of genes, indicating widespread modification of the host biology. Annotation and pathway analysis of the most deregulated genes showed that viral infection produces a down-regulation of genes associated with the nucleolus, in particular those implicated in regulating the different steps of ribosome biogenesis, such as ribosomal RNA (rRNA) transcription, pre-rRNA processing, and ribosome maturation. The impact of HIV-1 infection on genes involved in ribosome biogenesis was further validated in primary CD4+ T cells. Moreover, we provided evidence by Northern Blot experiments, that host pre-rRNA processing in Jurkat cells might be perturbed during HIV-1 infection, thus strengthening the hypothesis of a crosstalk between nucleolar functions and viral pathogenesis.

Figure 1. Viral infection globally alters gene expression profiles in CD4⁺ T cells.

(A) Hierarchical clustering by gene expression using the 50 most variant genes. The agglomeration method used was complete linkage, with Euclidean distance. (B) PCA analysis shows a clear separation between mock and infected cells.

Figure 2. Validation of RNA-Seq experiments by RT-qPCR.

RT-qPCR was used to validate the RNA sequencing data using total RNA isolated from mock-infected and HIV-1-infected Jurkat (A) and primary CD4⁺ T cells (B). Mean ± SD values obtained in three (A) or two (B) independent experiments are shown. Red, blue, and green bars depict genes that are down-regulated, up-regulated, or unaffected by HIV-1- infection, respectively, based on RNA-seq analysis.

Figure 3. HIV-1 infection affects pre-rRNA processing.

(A) Schematic representation of the pre-rRNA processing in mammals . (B) Northern Blot analysis of total RNA isolated from infected Jurkat cells and mock cells using an ITS1 rRNA specific probe. (C) Quantitation of the signals of Northern experiments reported as ratio between 30S and 21S rRNA precursors in infected Jurkat cells as compared with mock cells. The amounts of the two species were calculated after Northern blotting by phosphoimaging. This analysis was performed on both the sets of RNA analyzed by RNA-seq and standard deviation in the ratio 30S/21S is indicated.

Figure 4. Genes encoding for proteins regulating Ribosome Biogenesis are negatively affected by viral infection.

(A) and (B) Distribution of log ratios/fold-change (FC) in expression levels for all genes (blue) and genes encoding for nucleolar proteins involved in the ribosome biogenesis (orange) using Kernel density estimation; (A) samples sequenced in this study; (B) samples obtained from CHDT dataset, 24hs post infection. (C) and (D) Distribution of p-values, adjusted for multiple testing, for all genes (blue) or genes involved in the biogenesis of the nucleolus (orange); (C) this study, (D) from CHDT dataset.