Doubling dolutegravir dosage reduces the viral reservoir in ART-treated people with HIV
- Laboratory of Immunology and Infectious Diseases, GIGA-Institute, University of Liège, Belgium
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Netherlands
- Antiviral Pharmacology Laboratory, University of Nebraska Medical Center, United States
- Department of Biostatistics and Medico-Economic Information, University Hospital of Liège, Belgium
- Department of General Internal Medicine and Infectious Diseases, University Hospital of Liège, Belgium
- GIGA Flow Cytometry Platform, University of Liège, Belgium
- Department of Clinical Chemistry, University Hospital of Liège, Belgium
- Laboratory of Clinical Microbiology, University Hospital of Liège, Belgium
- Department of Gastroenterology, University Hospital of Liège, Belgium
Figures
Figure 1
Study design.
(A) Inclusion criteria, study groups, and sampling time points. (B) Time points where markers were measured.
Figure 2 with 1 supplement
Antiretroviral drug concentrations in plasma and rectal tissue.
Plasma (A) and tissue (B) concentrations of DTG, as well as plasma (C) and tissue (D) concentrations of 3TC, were compared between days 0 (D0) and 84 (D84) in intensified and control groups. Wilcoxon tests were used to calculate statistical significance.
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Figure 2—source data 1
Numerical data corresponding to Figure 2A.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig2-data1-v1.xlsx
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Figure 2—source data 2
Numerical data corresponding to Figure 2B.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig2-data2-v1.xlsx
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Figure 2—source data 3
Numerical data corresponding to Figure 2C.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig2-data3-v1.xlsx
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Figure 2—source data 4
Numerical data corresponding to Figure 2D.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig2-data4-v1.xlsx
Figure 2—figure supplement 1
Plasma concentrations of DTG and 3TC in intensified (blue) and control (red) groups.
Median values and interquartile ranges are shown. Participant numbers: intensified group, n=10; control group, n=10.
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Figure 2—figure supplement 1—source data 1
Numerical data corresponding to Figure 2—figure supplement 1.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig2-figsupp1-data1-v1.xlsx
Figure 3 with 3 supplements
Longitudinal dynamics of HIV reservoir markers.
Fold change of total HIV DNA in PBMCs (A), US HIV RNA in PBMCs (B), and US RNA/total DNA ratios (C) from baseline on days 1, 28, 56, and 84 of the study in the intensified (blue) and control (red) groups. Median values and interquartile ranges (IQRs) are shown. Linear mixed-effects modelling on log10-transformed values was used to calculate statistical significance. p values at the bottom of the graphs show the significance of between-group comparisons and those on top of the graphs show the significance of comparisons of the changes from baseline with zero in each group separately (intercept-only analysis). An upward or downward facing arrow next to a p value indicates a statistically significant increase or decrease from baseline, respectively. Participant numbers in both groups per time point are indicated below the graphs. Comparisons of intact HIV DNA in PBMCs (D) and of total HIV DNA in rectal tissue (E) between days 0 (D0) and 84 (D84) in the intensified and control groups. Open circles depict undetectable values, assigned the values corresponding to 50% of the assay detection limits. Wilcoxon tests were used to calculate statistical significance. All p values are marked red if significant (<0.05).
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Figure 3—source data 1
Numerical data corresponding to Figure 3A.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-data1-v1.xlsx
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Figure 3—source data 2
Numerical data corresponding to Figure 3B.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-data2-v1.xlsx
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Figure 3—source data 3
Numerical data corresponding to Figure 3C.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-data3-v1.xlsx
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Figure 3—source data 4
Numerical data corresponding to Figure 3D.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-data4-v1.xlsx
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Figure 3—source data 5
Numerical data corresponding to Figure 3E.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-data5-v1.xlsx
Figure 3—figure supplement 1
Longitudinal dynamics of total HIV DNA in PBMCs.
(A) Levels of total HIV DNA in intensified (blue) and control (red) groups. Median values and interquartile ranges are shown. Participant numbers: intensified group, n=10; control group, n=10. (B) Total HIV DNA was compared between days 0 (D0) and 84 (D84) in intensified and control groups. Open circles depict undetectable values, assigned the values corresponding to 50% of the assay detection limits. Wilcoxon tests were used to calculate statistical significance. (C) Time-weighted changes of total HIV DNA from baseline were compared between intensified and control groups and compared with 0 in each group separately. (D) Day 1/day 0, day 28/day 0, day 56/day 0, and day 84/day 0 ratios of total HIV DNA were compared between intensified and control groups and compared with 1 in each group separately. Panels C and D: Mann–Whitney tests and one-sample Wilcoxon tests were used to calculate between- and within-group statistical significance, respectively. If a within-group p value is <0.2, an upward or downward facing arrow is depicted next to this p value, indicating a trend to increase or decrease from baseline, respectively. p values are marked red if significant (<0.05). All statistical analysis was performed on log10-transformed values of total HIV DNA. (E) Individual trajectories of total HIV DNA (fold change from baseline) in intensified (blue) and control (red) groups.
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Figure 3—figure supplement 1—source data 1
Numerical data corresponding to Figure 3—figure supplement 1A.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp1-data1-v1.xlsx
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Figure 3—figure supplement 1—source data 2
Numerical data corresponding to Figure 3—figure supplement 1B.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp1-data2-v1.xlsx
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Figure 3—figure supplement 1—source data 3
Numerical data corresponding to Figure 3—figure supplement 1C.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp1-data3-v1.xlsx
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Figure 3—figure supplement 1—source data 4
Numerical data corresponding to Figure 3—figure supplement 1D.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp1-data4-v1.xlsx
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Figure 3—figure supplement 1—source data 5
Numerical data corresponding to Figure 3—figure supplement 1E.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp1-data5-v1.xlsx
Figure 3—figure supplement 2
Longitudinal dynamics of US HIV RNA in PBMCs.
(A) Levels of US HIV RNA in intensified (blue) and control (red) groups. Median values and interquartile ranges are shown. Participant numbers: intensified group, n=10; control group, n=10. (B) US HIV RNA was compared between days 0 (D0) and 84 (D84) in intensified and control groups. Open circles depict undetectable values, assigned the values corresponding to 50% of the assay detection limits. Wilcoxon tests were used to calculate statistical significance. (C) Time-weighted changes of US HIV RNA from baseline were compared between intensified and control groups and compared with 0 in each group separately. (D) Day 1/day 0, day 28/day 0, day 56/day 0, and day 84/day 0 ratios of US HIV RNA were compared between intensified and control groups and compared with 1 in each group separately. Panels C and D: Mann–Whitney tests and one-sample Wilcoxon tests were used to calculate between- and within-group statistical significance, respectively. If a within-group p value is <0.2, an upward or downward facing arrow is depicted next to this p value, indicating a trend to increase or decrease from baseline, respectively. p values are marked red if significant (<0.05). All statistical analysis was performed on log10-transformed values of US HIV RNA. (E) Individual trajectories of US HIV RNA (fold change from baseline) in intensified (blue) and control (red) groups.
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Figure 3—figure supplement 2—source data 1
Numerical data corresponding to Figure 3—figure supplement 2A.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp2-data1-v1.xlsx
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Figure 3—figure supplement 2—source data 2
Numerical data corresponding to Figure 3—figure supplement 2B.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp2-data2-v1.xlsx
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Figure 3—figure supplement 2—source data 3
Numerical data corresponding to Figure 3—figure supplement 2C.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp2-data3-v1.xlsx
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Figure 3—figure supplement 2—source data 4
Numerical data corresponding to Figure 3—figure supplement 2D.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp2-data4-v1.xlsx
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Figure 3—figure supplement 2—source data 5
Numerical data corresponding to Figure 3—figure supplement 2E.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp2-data5-v1.xlsx
Figure 3—figure supplement 3
Longitudinal dynamics of US RNA/total DNA ratio in PBMCs.
(A) Levels of US RNA/total DNA ratio in intensified (blue) and control (red) groups. Median values and interquartile ranges are shown. Participant numbers: intensified group, n=10; control group, n=10. (B) US RNA/total DNA ratios were compared between days 0 (D0) and 84 (D84) in intensified and control groups. Open circles depict undetectable values. Wilcoxon tests were used to calculate statistical significance. (C) Time-weighted changes of US RNA/total DNA ratio from baseline were compared between intensified and control groups and compared with 0 in each group separately. (D) Day 1/day 0, day 28/day 0, day 56/day 0, and day 84/day 0 ratios of US RNA/total DNA ratio were compared between intensified and control groups and compared with 1 in each group separately. Panels C and D: Mann–Whitney tests and one-sample Wilcoxon tests were used to calculate between- and within-group statistical significance, respectively. If a within-group p value is <0.2, an upward or downward facing arrow is depicted next to this p value, indicating a trend to increase or decrease from baseline, respectively. p values are marked red if significant (<0.05). All statistical analysis was performed on log10-transformed values of US RNA/total DNA ratios. (E) Individual trajectories of US RNA/total DNA ratio (fold change from baseline) in intensified (blue) and control (red) groups.
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Figure 3—figure supplement 3—source data 1
Numerical data corresponding to Figure 3—figure supplement 3A.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp3-data1-v1.xlsx
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Figure 3—figure supplement 3—source data 2
Numerical data corresponding to Figure 3—figure supplement 3B.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp3-data2-v1.xlsx
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Figure 3—figure supplement 3—source data 3
Numerical data corresponding to Figure 3—figure supplement 3C.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp3-data3-v1.xlsx
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Figure 3—figure supplement 3—source data 4
Numerical data corresponding to Figure 3—figure supplement 3D.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp3-data4-v1.xlsx
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Figure 3—figure supplement 3—source data 5
Numerical data corresponding to Figure 3—figure supplement 3E.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig3-figsupp3-data5-v1.xlsx
Figure 4 with 1 supplement
Longitudinal dynamics of cellular markers of immune activation and exhaustion.
Graphs show changes of (A) CD4+ cell markers and (B) CD8+ cell markers from baseline on days 1, 28, 56, and 84 of the study in the intensified (blue) and control (red) groups. Median values and interquartile ranges (IQRs) are shown. Participant numbers: intensified group, n=10; control group, n=10. Linear mixed-effects modelling was used to calculate statistical significance. p values at the bottom of the graphs show the significance of between-group comparisons and those on top of the graphs show the significance of comparisons of the changes from baseline with zero in each group separately (intercept-only analysis). An upward or downward facing arrow next to a p value indicates a statistically significant increase or decrease from baseline, respectively. p values are marked red if significant (<0.05).
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Figure 4—source data 1
Numerical data corresponding to Figure 4A.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig4-data1-v1.xlsx
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Figure 4—source data 2
Numerical data corresponding to Figure 4B.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig4-data2-v1.xlsx
Figure 4—figure supplement 1
Levels of cellular markers of immune activation and exhaustion.
Levels of cellular markers of immune activation and exhaustion on CD4+ (A) and CD8+ (B) T cells in intensified (blue) and control (red) groups. Median values and interquartile ranges are shown. Participant numbers: intensified group, n=10; control group, n=10.
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Figure 4—figure supplement 1—source data 1
Numerical data corresponding to Figure 4—figure supplement 1A.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig4-figsupp1-data1-v1.xlsx
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Figure 4—figure supplement 1—source data 2
Numerical data corresponding to Figure 4—figure supplement 1B.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig4-figsupp1-data2-v1.xlsx
Figure 5 with 1 supplement
Longitudinal dynamics of inflammation markers in plasma and tissue.
(A) Plasma inflammation markers. Graphs show changes of markers from baseline on days 1, 28, 56, and 84 of the study in the intensified (blue) and control (red) groups. Median values and interquartile ranges (IQRs) are shown. Participant numbers: intensified group, n=10; control group, n=10. Linear mixed-effects modelling was used to calculate statistical significance. p values at the bottom of the graphs show the significance of between-group comparisons and those on top of the graphs show the significance of comparisons of the changes from baseline with zero in each group separately (intercept-only analysis). An upward or downward facing arrow next to a p value indicates a statistically significant increase or decrease from baseline, respectively. p values are marked red if significant (<0.05). (B) Tissue inflammation markers. Markers were compared between days 0 (D0) and 84 (D84) in the intensified and control groups. Open circles depict undetectable values, assigned the values corresponding to 50% of the assay detection limits. Wilcoxon tests were used to calculate statistical significance.
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Figure 5—source data 1
Numerical data corresponding to Figure 5A.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig5-data1-v1.xlsx
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Figure 5—source data 2
Numerical data corresponding to Figure 5B.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig5-data2-v1.xlsx
Figure 5—figure supplement 1
Levels of inflammation markers in plasma in intensified (blue) and control (red) groups.
Median values and interquartile ranges are shown. Participant numbers: intensified group, n=10; control group, n=10.
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Figure 5—figure supplement 1—source data 1
Numerical data corresponding to Figure 5—figure supplement 1.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig5-figsupp1-data1-v1.xlsx
Figure 6 with 1 supplement
Longitudinal dynamics of clinical markers.
Graphs show changes of markers from baseline on days 1, 28, 56, and 84 of the study in the intensified (blue) and control (red) groups. Median values and interquartile ranges (IQRs) are shown. Participant numbers: intensified group, n=10; control group, n=10. Linear mixed-effects modelling was used to calculate statistical significance. p values at the bottom of the graphs show the significance of between-group comparisons and those on top of the graphs show the significance of comparisons of the changes from baseline with zero in each group separately (intercept-only analysis). An upward or downward facing arrow next to a p value indicates a statistically significant increase or decrease from baseline, respectively. p values are marked red if significant (<0.05).
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Figure 6—source data 1
Numerical data corresponding to Figure 6.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig6-data1-v1.xlsx
Figure 6—figure supplement 1
Levels of clinical markers in intensified (blue) and control (red) groups.
Median values and interquartile ranges are shown. Participant numbers: intensified group, n=10; control group, n=10.
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Figure 6—figure supplement 1—source data 1
Numerical data corresponding to Figure 6—figure supplement 1.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig6-figsupp1-data1-v1.xlsx
Figure 7 with 2 supplements
Spearman correlogram of baseline parameters.
A heat map is used to indicate the strengths of associations between parameters. Red indicates a negative correlation, and blue indicates a positive correlation.
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Figure 7—source data 1
Numerical data corresponding to Figure 7.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig7-data1-v1.xlsx
Figure 7—figure supplement 1
Spearman correlogram of time-weighted changes from baseline.
A heat map is used to indicate the strengths of associations between parameters. Red indicates a negative correlation, and blue indicates a positive correlation.
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Figure 7—figure supplement 1—source data 1
Numerical data corresponding to Figure 7—figure supplement 1.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig7-figsupp1-data1-v1.xlsx
Figure 7—figure supplement 2
Spearman correlogram of changes between days 0 and 84.
A heat map is used to indicate the strengths of associations between parameters. Red indicates a negative correlation, and blue indicates a positive correlation.
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Figure 7—figure supplement 2—source data 1
Numerical data corresponding to Figure 7—figure supplement 2.
- https://cdn.elifesciences.org/articles/106931/elife-106931-fig7-figsupp2-data1-v1.xlsx
Appendix 3—figure 1
Gating strategy of the flow cytometry measurements.
Tables
Table 1
Clinical characteristics of participants at baseline.
| All(n = 20) | Control group (n = 10) | DTG group(n = 10) | p* | |
|---|---|---|---|---|
| Sex, male | 19 (95.0)† | 9 (90.0) | 10 (100.0) | 1.00 |
| Age, years | 52 (43–60; 25–73) | 52 (40–62; 25–73) | 51 (46–59; 36–66) | 0.94 |
| BMI, kg/m2 | 24 (22–26; 18–36) | 25 (22–27; 19–30) | 23 (22–26; 18–36) | 0.62 |
| Ethnicity | ||||
| Caucasian | 17 (85.0) | 9 (90.0) | 8 (80.0) | 1.00 |
| African | 2 (10.0) | 1 (10.0) | 1 (10.0) | |
| Maghrebi | 1 (5.0) | 0 (0.0) | 1 (10.0) | |
| HLA typing B57/01, negative (n = 19) | 19 (100.0) | 9 (100.0) | 10 (100.0) | - |
| Smoking, smoker, or ex-smoker | 10 (50.0) | 4 (40.0) | 6 (60.0) | 0.66 |
| Time since first positive HIV serology, years | 12.6 (6.8–18.2; 3.5–25.4) | 9.8 (7.3–13.3; 3.5–25.4) | 15.6 (7.6–18.5; 3.5–21.5) | 0.58 |
| Cumulative time of untreated HIV infection, years | 0.9 (0.1–3.5; 0.0–17.2) | 1.8 (0.1–5.0; 0.0–17.2) | 0.6 (0.1–2.1; 0.0–6.1) | 0.47 |
| Cumulative time of viral suppression, years | 7.4 (4.8–9.2; 2.9–16.5) | 5.6 (4.7–7.7; 3.3–16.2) | 7.9 (5.8–12.4; 2.9–16.5) | 0.32 |
| Continuous time of viral suppression before study, years | 3.9 (3.3–5.8; 0.4–10.2) | 4.4 (3.7–6.9; 3.3–10.2) | 3.4 (3.2–4.9; 0.4–7.9) | 0.12 |
| Time on DTG-containing ART regimen before study, years | 3.5 (3.4–3.7; 2.2–3.9) | 3.5 (3.4–3.8; 2.2–3.9) | 3.5 (3.3–3.5; 2.7–3.8) | 0.41 |
| Nadir CD4+ count, cells/mm3 | 277 (147–410; 24–747) | 277 (205–340; 24–521) | 292 (136–508; 30–747) | 0.65 |
| First measured plasma viral load, log10 HIV RNA copies/ml | 4.52 (3.91–5.35; 2.48–6.60) | 4.52 (4.36–4.96; 3.00–6.60) | 4.55 (3.69–5.38; 2.48–5.70) | 0.85 |
| CD4+ count, cells/mm3 | 775 (659–1144; 225–1383) | 732 (672–970; 225–1267) | 886 (668–1217; 492–1383) | 0.39 |
| CD8+ count, cells/mm3 | 745 (637–1288; 377–2017) | 723 (535–931; 377–2017) | 939 (690–1310; 501–1853) | 0.39 |
| CD4/CD8 ratio | 0.94 (0.66–1.47; 0.32–2.24) | 1.00 (0.64–1.36; 0.32–1.82) | 0.93 (0.69–1.56; 0.35–2.24) | 0.82 |
| Total HIV DNA in PBMCs, copies/106 cells | 175.5 (70.0–467.3; 15.1–1090) | 99.4 (37.4–231.5; 15.1–333.0) | 421.0 (139.5–764.3; 61.8–1090) | 0.015 |
| Intact HIV DNA in PBMCs, copies/106 cells | 55.2 (19.2–87.0; 5.17–624.2) | 29.5 (16.2–97.1; 10.3–624.2) | 58.6 (44.7–144.7; 5.17–292.6) | 0.36 |
| US HIV RNA in PBMCs, copies/μg total RNA | 92.1 (13.3–290.3; 2.53–1580) | 72.2 (12.2–253.8; 6.18–486) | 124.6 (17.0–591.0; 2.53–1580) | 0.58 |
| US RNA/total DNA ratio in PBMCs | 0.40 (0.07–1.47; 0.03–3.96) | 1.21 (0.11–2.81; 0.04–3.96) | 0.33 (0.06–0.70; 0.03–2.73) | 0.21 |
| Total HIV DNA in rectal tissue, copies/106 cells | 477.0 (271.3–971.5; 7.27–1720) | 547.0 (291.0–1215; 53.4–1720) | 403.0 (194.6–952.5; 7.27–1510) | 0.44 |
| Plasma DTG concentration, ng/mL | 3287 (2602–5087; 237–6593) | 3560 (2953–4455; 1969–5536) | 3266 (2245–5983; 237–6593) | 0.82 |
| Tissue DTG concentration, ng/g | 634 (533–830; 303–1810) | 737 (534–852; 482–1810) | 581 (535–714; 303–1037) | 0.44 |
| Plasma 3TC concentration, ng/ml | 316 (148–731; 50–1616) | 431 (214–941; 102–1616) | 246 (117–439; 50–1156) | 0.26 |
| Tissue 3TC concentration, ng/g | 2114 (1417–2345; 90–4495) | 2193 (1590–2784; 1215–4495) | 2114 (1233–2317; 900–3187) | 0.50 |
| CDC classification | - | |||
| A1 | 4 (20.0) | 1 (10.0) | 3 (30.0) | |
| A2 | 9 (45.0) | 6 (60.0) | 3 (30.0) | |
| A3 | 3 (15.0) | 1 (10.0) | 2 (30.0) | |
| B3 | 1 (5.0) | 0 (0.0) | 1 (10.0) | |
| C3 | 3 (15.0) | 2 (20.0) | 1 (10.0) | |
| HBV status | - | |||
| Immune | 12 (60.0) | 8 (80.0) | 4 (40.0) | |
| Non-immune, not infected | 5 (25.0) | 2 (20.0) | 3 (30.0) | |
| Isolated HBc Ab | 2 (10.0) | 0 (0.0) | 2 (20.0) | |
| Cured hepatitis B | 1 (5.0) | 0 (0.0) | 1 (10.0) | |
| HCV status | 1.00 | |||
| Not infected | 19 (95.0) | 10 (10.0) | 9 (90.0) | |
| Recovered | 1 (5.0) | 0 (0.0) | 1 (10.0) |
-
*
Mann–Whitney tests were used for continuous variables and Fisher’s exact tests were used for categorical variables.
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†
Data are medians (interquartile ranges, followed by ranges) for continuous variables and numbers (percentages) for discrete variables.
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Table 1—source data 1
Numerical data corresponding to Table 1.
- https://cdn.elifesciences.org/articles/106931/elife-106931-table1-data1-v1.xlsx
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | APC/Fire 810 anti-human CD3 (Mouse monoclonal) | Sony Biotechnology | Cat# 2324290 | 1:25 |
| Antibody | PE/Fire 700 anti-human CD4 (Mouse monoclonal) | Sony Biotechnology | Cat# 2323330 | 1:25 |
| Antibody | PerCP anti-human CD8a (Mouse monoclonal) | Sony Biotechnology | Cat# 2104610 | 1:25 |
| Antibody | PE Mouse anti-human CD279 (PD-1) (Mouse monoclonal) | BD Biosciences | Cat# 560795; RRID:AB_2033989 | 1:25 |
| Antibody | BV421 Mouse anti-human TIGIT (Mouse monoclonal) | BD Biosciences | Cat# 747844; RRID:AB_2872307 | 1:25 |
| Antibody | BB515 Mouse anti-human HLA-DR (Mouse monoclonal) | BD Biosciences | Cat# 564516; RRID:AB_2732846 | 1:25 |
| Antibody | BV711 Mouse anti-human CD38 (Mouse monoclonal) | BD Biosciences | Cat# 563965; RRID:AB_2738516 | 1:25 |
| Commercial assay or kit | DNA-free DNA Removal Kit | Thermo Fisher Scientific | Cat# AM1906 | |
| Commercial assay or kit | TaqMan β-Actin Detection Reagents | Thermo Fisher Scientific | Cat# 401846 | |
| Commercial assay or kit | TaqMan Ribosomal RNA Control Reagents | Thermo Fisher Scientific | Cat# 4308329 | |
| Commercial assay or kit | Puregene Cell Kit | QIAGEN | Cat# 158043 | |
| Commercial assay or kit | ReliaPrep gDNA Tissue Miniprep System | Promega | Cat# A2051 | |
| Commercial assay or kit | ProcartaPlex Human Inflammation Panel, 20plex | Thermo Fisher Scientific | Cat# EPX200-12185-901 | |
| Commercial assay or kit | Human CD14 ELISA Kit – Quantikine | R&D Systems | Cat# DC140 | |
| Chemical compound, drug | Platinum Quantitative PCR SuperMix-UDG | Thermo Fisher Scientific | Cat# 11730-025 | |
| Chemical compound, drug | SuperScript III reverse transcriptase | Thermo Fisher Scientific | Cat# 18080-085 | |
| Chemical compound, drug | Random primers | Thermo Fisher Scientific | Cat# 48190-011 | |
| Chemical compound, drug | RNaseOUT Recombinant Ribonuclease Inhibitor | Thermo Fisher Scientific | Cat# 10777-019 | |
| Chemical compound, drug | ddPCR Supermix for Probes (No dUTP) | Bio-Rad | Cat# 1863024 | |
| Chemical compound, drug | BglI restriction enzyme | Thermo Fisher Scientific | Cat# ER0071 | |
| Chemical compound, drug | TaqMan Gene Expression Assay, IL-1β | Thermo Fisher Scientific | Cat# 4331182 | Hs01555410_m1 |
| Chemical compound, drug | TaqMan Gene Expression Assay, IL-6 | Thermo Fisher Scientific | Cat# 4331182 | Hs00174131_m1 |
| Chemical compound, drug | TaqMan Gene Expression Assay, IFN-γ | Thermo Fisher Scientific | Cat# 4331182 | Hs00989291_m1 |
| Chemical compound, drug | TaqMan Gene Expression Assay, IL-17α | Thermo Fisher Scientific | Cat# 4331182 | Hs00174383_m1 |
| Chemical compound, drug | TaqMan Gene Expression Assay, TNF-α | Thermo Fisher Scientific | Cat# 4331182 | Hs00174128_m1 |
| Chemical compound, drug | TaqMan Gene Expression Assay, GAPDH | Thermo Fisher Scientific | Cat# 4331182 | Hs02758991_g1 |
| Software, algorithm | Prism 10.2.0 | GraphPad Software | https://www.graphpad.com/ RRID:SCR_002798 | Statistics |
| Software, algorithm | IBM SPSS Statistics 28.0.1.0 | IBM | https://www.ibm.com/products/spss-statistics RRID:SCR_016479 | Statistics |
| Software, algorithm | QuantaSoft 1.7.4 | Bio-Rad | RRID:SCR_025696 | ddPCR data analysis |
| Software, algorithm | Rotor-Gene 2.3.5 | QIAGEN | RRID:SCR_015740 | qPCR data analysis |
| Software, algorithm | FlowJo 10.8.1 | Becton Dickinson | https://www.flowjo.com/ RRID:SCR_008520 | Flow cytometry data analysis |
Appendix 2—table 1
Comparison of models for the virological markers (between-group analysis).
| Dependent variable | Explanatory variables | Treatment only(repeated-measures model) | Treatment + time point(as discrete variable) | Treatment + time(as continuous variable) | |||
|---|---|---|---|---|---|---|---|
| Estimate (95% CI) | p* | Estimate (95% CI) | p | Estimate (95% CI) | p | ||
| Total DNA (log10 fold change from baseline) | Treatment, intensified vs. control group | −0.38 (−0.55 to −0.21)† | 2.3 × 10–5 | −0.38 (−0.55 to −0.20) | 5.8 × 10–5 | −0.38 (−0.56 to −0.20) | 6.5 × 10–5 |
| Time, per day | - | - | - | 0.15 | 0.001 (−0.002 to 0.004) | 0.41 | |
| US RNA (log10 fold change from baseline) | Treatment, intensified vs. control group | −0.56 (−0.98 to −0.14) | 0.010 | −0.49 (−0.94 to −0.04) | 0.035 | −0.49 (−0.93 to −0.05) | 0.028 |
| Time, per day | - | - | - | 0.99 | −0.001 (−0.008 to 0.006) | 0.82 | |
| US RNA/total DNA ratio (log10 fold change from baseline) | Treatment, intensified vs. control group | −0.36 (−0.77 to 0.06) | 0.090 | −0.29 (−0.73 to 0.16) | 0.20 | −0.28 (−0.71 to 0.16) | 0.21 |
| Time, per day | - | - | - | 0.91 | −0.002 (−0.009 to 0.005) | 0.62 | |
-
*
p values were calculated by type III tests of fixed effects.
-
†
Control group is assigned zero value.
Appendix 2—table 2
Comparison of models for the virological markers (within-group analysis).
| Dependent variable | Group | Explanatory variables | Intercept only (repeated-measures design) | Intercept + time point | ||
|---|---|---|---|---|---|---|
| Estimate (95% CI) | p* | Estimate (95% CI) | p | |||
| Total DNA (log10 fold change from baseline) | Intensified group | Intercept | −0.21 (−0.33 to −0.08) | 0.0022 | −0.17 (−0.44 to 0.11) | 0.0016 |
| Time point | - | - | - | 0.40 | ||
| Control group | Intercept | 0.16 (0.05 to 0.27) | 0.0053 | 0.24 (0.01 to 0.48) | 0.019 | |
| Time point | - | - | - | 0.42 | ||
| US RNA (log10 fold change from baseline) | Intensified group | Intercept | −0.54 (−0.75 to −0.33) | 6.0 × 10–5 | −0.62 (−1.19 to −0.06) | 0.0069 |
| Time point | - | - | - | 0.60 | ||
| Control group | Intercept | 0.05 (−0.26 to 0.37) | 0.73 | 0.24 (−0.44 to 0.92) | 0.71 | |
| Time point | - | - | - | 0.88 | ||
| US RNA/total DNA ratio (log10 fold change from baseline) | Intensified group | Intercept | −0.47 (−0.67 to −0.27) | 2.2 × 10–4 | −0.53 (−1.09 to 0.03) | 0.029 |
| Time point | - | - | - | 0.59 | ||
| Control group | Intercept | 0.01 (−0.29 to 0.32) | 0.94 | −0.07 (−0.76 to 0.62) | 0.81 | |
| Time point | - | - | - | 0.86 | ||
-
*
p values were calculated by type III tests of fixed effects.
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Doubling dolutegravir dosage reduces the viral reservoir in ART-treated people with HIV
eLife 14:RP106931.
https://doi.org/10.7554/eLife.106931.3
