Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cells
- Gladstone Institutes, United States
- University of California San Francisco, United States
- Buck Institute for Research on Aging, United States
- Blood Systems Research Institute, United States
- The Wistar Institute, United States
- Karolinska Institutet, Sweden
- The Rockefeller University, United States
- International Research Center, Brazil
Figures
Figure 1 with 1 supplement
Second generation of dual-fluorescence HIV-1 reporter, HIVGKO to quantify stable latency.
(A) Schematic representation of first (top: HIVDuoFluoI) and second generation (bottom: HIVGKO) of dual-labeled HIV-1 reporters. (B) Representative experiment of HIVGKO virus titration in activated …
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Figure 1—source data 1
Taqman RT-qPCR analysis of unspliced (US), singly spliced (SS), and multiply spliced (MS) HIV-1 mRNAs in the uninfected, double negative, latent and productive populations.
The experiment is detailed in the main text and Figure 1 legend.
- https://doi.org/10.7554/eLife.34655.004
Figure 1—figure supplement 1
Comparison of HIVGKO and HIVDuoFluoI.
Titration of HIVGKO input revealed that latently and productively infected cells increased proportionately as viral input increased (Figure 1—figure supplement 1A and B), as reflected by steady …
Figure 2
LRAs efficacy in patient samples is predicted by activity in HIVGKO latently infected cells.
(A) Intracellular HIV-1 mRNA levels in rCD4s, obtained from infected individuals and treated ex vivo with a single LRA or a combination of two LRAs for 24 hr in presence of raltegravir, presented as …
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Figure 2—source data 1
Intracellular HIV-1 mRNA levels in rCD4s, obtained from infected individuals, or in HIVGKO latently infected CD4+ T-cells.
The experiment is detailed in the main text and Figure 2 legend.
- https://doi.org/10.7554/eLife.34655.006
Figure 3
Few HIVGKO latently infected primary CD4+ T cells are reactivated.
(A) Schematic of experimental procedure with primary CD4+ T cells. Briefly, CD4+ T cells were purified from blood of healthy donors and activated for 72 hr with αCD3/CD28 beads and 100 U/ml IL-2 …
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Figure 3—source data 1
Percentage of GFP+ cells is shown after stimulation of latently infected CD4+ T-cells with LRAs as well as percent live cells for each drug treatment.
The experiment is detailed in the main text and Figure 3 legend.
- https://doi.org/10.7554/eLife.34655.008
Figure 4 with 1 supplement
Low-level latency reactivation is not explained by low cellular responses to activation signals.
T-cell activation patterns between double negative, reactivated (RLIC) and non-reactivated (NRLIC) latently infected cells. Briefly, CD4+ T-cells were purified from blood of four healthy donors and …
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Figure 4—source data 1
CD25, CD69, and HLA-DR activation markers patterns between double negative, reactivated (RLIC) and non-reactivated (NRLIC) latently infected cells.
The experiment is detailed in the main text and Figure 4 legend.
- https://doi.org/10.7554/eLife.34655.012
Figure 4—figure supplement 1
24 hr treatment effectively activate primary CD4+ T cells.
Quantification of T-cell activation-associated surface markers after 24 hr stimulation. Briefly, CD4+ T-cells were purified from blood of two healthy donors and activated for 72 hr with αCD3/CD28 …
Figure 5
Relative expression of HIV-1 integration targeted genes for each population, before or after TCR activation.
(A) Scatter chart showing primary CD4+ T-cell gene expression changes after 48 hr of stimulation with αCD3/CD28 beads. Integration sites displayed outside of the two solid gray lines were targeted …
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Figure 5—source data 1
Fraction of integration sites from the different populations PIC, RLIC or NRLIC, integrated within genes whose expression is at least ± twofold differentially expressed after 48 hr of αCD3/CD28 stimulation.
The experiment is detailed in the main text and Figure 5 legend.
- https://doi.org/10.7554/eLife.34655.014
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Figure 5—source data 2
Relative expression of genes targeted by HIV-1 integration in PIC, RLIC or NRLIC before TCR stimulation and after 48 hr αCD3/CD28 stimulation.
The experiment is detailed in the main text and Figure 6 legend.
- https://doi.org/10.7554/eLife.34655.015
Figure 6
Insertion landscapes of HIV-1.
(A) Proportion of mapped insertions that are in genic or intergenic regions. (Figure 6—source data 1). (B) Proportion of integration sites in transcribed regions with high (top 1/8), medium (top …
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Figure 6—source data 1
Proportion of mapped insertions that are in genic or intergenic regions; of integration sites in transcribed regions with high, medium, low expression, trace or silent expression; of unique genic integration sites located in introns, exons, UTR or promoters; and transcriptional orientation of integrated HIV-1 relative to host gene.
The experiment is detailed in the main text and Figure 6 legend.
- https://doi.org/10.7554/eLife.34655.017
Figure 7
Epigenetics marks and nuclear localization of HIV-1 integration sites.
(A) 500 bp centered on HIV-1 integration sites for each population were analyzed for the presence of H3K4me1 (active enhancers), H3K36m3 (active transcribed regions), H3K9m3 and H3K27m3 (repressive …
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Figure 7—source data 1
HIV-1 integration sites for each population were analyzed for the presence of H3K4me1, H3K36m3, H3K9m3, H3K27m3, DNA accessibility, as well as their nuclear localization.
The experiment is detailed in the main text and Figure 7 legend.
- https://doi.org/10.7554/eLife.34655.019
Author response image 1
Time-course plot of percent of GFP+ cells (bars) and live cells (lines) after sort of latently infected CD4+ T-cells (n = 2, mean + SEM).
https://doi.org/10.7554/eLife.34655.023
Author response image 2
(1)Intracellular HIV-1 mRNA levels in rCD4s, obtained from infected individuals and treated ex vivo with a single LRA or a combination of two LRAs for 24 hours, presented as fold induction relative to DMSO control.
(n = 4, mean + SEM).
Author response image 3
Percentage of GFP+ cells are shown after stimulation of latently infected CD4+ T-cells with LRAs for 24-, 36- or 48 hours (n = 2 (different donors), mean + SEM, paired t-test).
https://doi.org/10.7554/eLife.34655.025
Author response image 4
T-cell activation patterns between double negative, reactivated (RLIC) and non-reactivated (NRLIC) latently infected cells.
Briefly, CD4+ T-cells were purified from blood of four healthy donors and activated for 72 hours with αCD3/CD28 beads and 20 U/ml IL-2 before infection with HIVGKO. At 4 days post-infection, csGFP- …
Tables
Table 1
Characteristics of HIV-1-infected study participants
ABC, abacavir; DRV, darunavir; FTC, emtricitabine; RPV, rilpivirine; RTV, ritonavir; TCV, tivicay; TDF, tenofovir; 3TC, lamivudine; VL, viral load.
| Scope ID | Age | Sex | Ethnicity | CD4 Count | Duration of infection (years) | ART regimen | Duration of ART (years) | Peak reporter VL (copies/ml−1) |
|---|---|---|---|---|---|---|---|---|
| 1597 | 56 | M | Mixed | 469 | 19 | RPV/TDF/FTC | 5 | 45734 |
| 2147 | 59 | M | Asian | 597 | 28 | RPV/TDF/FTC | 23 | 374000 |
| 2461 | 62 | M | White | 664 | 32 | RPV/TCV | 19 | 20000 |
| 3162 | 54 | M | White | 734 | 29 | RTV, DRV, ABC/TCV/3TC | 20 | 171000 |
Additional files
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Source data 1
Integration Sites - Source Data: List of integration sites for each donor and each population.
- https://doi.org/10.7554/eLife.34655.020
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Transparent reporting form
- https://doi.org/10.7554/eLife.34655.021
