Table 1.
Properties of the primary cell models of HIV-1 latency used in this study.
Fig 1.
HIV genome and the targets for HIV transcription profiling assays.
This schematic shows the genetic organization of proviral HIV DNA and the HIV “transcription profiling” assays targeting specific HIV RNA sequence regions that provide insight into blocks to transcription.
Fig 2.
The Wild-type model: HIV latency is regulated by blocks to initiation, multiple splicing, and possibly elongation.
(A) Diagram of the model, (B) total HIV DNA, (C) level of HIV transcripts per million cells, (D) level of HIV transcripts per provirus, (E) progression through HIV transcription stages. Individual values per donor (dots), and median and range (bars) are shown. Unstimulated cells (days 10 and 12 post-infection) are shown in light colors and stimulated cells (day 12) in dark color.
Fig 3.
The Resting-cell model: HIV latency is regulated mostly by a block to multiple splicing.
(A) Diagram of the model, (B) total HIV DNA, (C) level of HIV transcripts per million cells, (D) level of HIV transcripts per provirus, (E) progression through HIV transcription stages. Individual values per donor (dots), and median and range (bars) are shown. Unstimulated cells (days 5 and 7 post-infection) are shown in light colors and stimulated cells (day 7) in dark color.
Fig 4.
The Dual-reporter model: HIV latency is regulated by blocks to initiation and multiple splicing.
(A) Diagram of the model, (B) total HIV DNA, (C) level of HIV transcripts per million cells, (D) level of HIV transcripts per provirus, (E) progression through HIV transcription stages. Individual values per donor (dots), and median and range (bars) are shown. Double negative and latent cells are shown in light colors and productive cells in dark color.
Fig 5.
Primary cell HIV latency models recapitulate the block to multiple splicing observed in CD4+ T cells from ART-suppressed individuals.
Comparison of (A) Level of HIV transcripts per provirus, and (B) progression through HIV transcription stages in cells from the Dual-reporter (orange), the Resting-cell (green) and the Wild-type (purple) primary cell models, and cells from ART-suppressed individuals (blue), in latently- (light color) and productively-infected or stimulated cells (dark color). Median and range (bars) are shown. (C) Comparison of HIV transcriptional initiation, elongation, completion, and multiple splicing in the latent (unstimulated) and productive (stimulated) populations in all donors from the three main models shown in Figs 2–4. Bars indicate the median; P-values were calculated using the Wilcoxon signed rank test.
Fig 6.
Transcriptome analysis of the Resting-cell model, Wild-type model, and cells from ART-suppressed individuals.
Venn diagram showing the number of differentially expressed genes between unstimulated and stimulated peripheral CD4+ T cells from the Resting-cell model, the Wild-type model (infection using wtNL4.3 HIV and no raltegravir), and ART-treated individuals (2 donors/model). Up-regulated genes are shown in red, down-regulated in blue, and discordant genes in orange.