Patients were not selected on viral load (VL). Subjects included were 29 males, four females, with a median age of 38.69 (25–67), 4 median years of infection (<1–17), a median CD4+ count of 240.2 (51–336) and median VL of 101 669 (45≥500 000). For longitudinal studies, these patients were sampled prior to and 1, 4, 8–12 months post-initiation of HAART (Supporting Information Table

2). In addition, 31 chronically infected asymptomatic treatment-naive I-BET-762 cost HIV+ subjects were studied (Supporting Information Table 3). Chronic untreated patients were identified as being treatment naïve with a stable CD4+ count above 300, as measured on at least two occasions (from time of diagnosis and at 6–12 monthly intervals) prior to sampling, not requiring therapy. This group had a median age of 37.87 (26–53), eight of which were females and 23 were males, with a median CD4+ T-cell count of 672.5 (277–1439) and median VL of 17 451 (<50–18 779) and 5.5 (1–16) median years of infection. Control HIV sero-negative blood samples were purchased from the National Blood Pirfenidone Transplantation Service at St George’s Hospital Tooting, UK, and tested in parallel with samples from HIV+ subjects. For controls subjects, where information was available the intention was to match the patients as closely as possible in terms of age, and to attempt to match in terms of gender if possible. Although all recruited patients were studied, not all

subjects could be analysed for all parameters included in this study, which was linked to blood volume, yield and CD4+ T-cell count at the time of experimentation. Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation (Lymphoprep: Axis-Shield PoC AS, Oslo, Norway). CD4+CD45RO+CD25− effector and CD4+CD45RO+CD25+ Treg-cell populations were isolated using Dynabeads T regulatory cell isolation kit (Invitrogen, Paisley, UK) as described previously 15. Purity of isolated fractions was confirmed by immunostaining Nitroxoline to be >95% for effector and Treg populations (Supporting Information Fig. 5). All assays were carried out in RPMI-1640 Glutamax 25 mM HEPES media

(Invitrogen), 10% human AB serum (Lonza, Sweden), and supplemented with 20 μg/mL Gentamycin (Sigma-Aldrich, UK) as described previously 15 by co-cultuting 2.5×103 effector cells, with at least two ratios of Treg cells. Cells were stimulated with Dynal anti-human CD3/CD28 coated magnetic beads (bead: effector cell ratio, 2:1) (Invitrogen) for 5 days. Each well received 0.5 μCi of (3 H)-thymidine (Perkin Elmer, UK) for the last 16 h of culture. As described previously 15 2×104 effector cells were cultured with varying ratios of Treg cells and stimulated with 2:1 (bead:effector cell) Dynal anti-human CD3/CD28 coated magnetic beads. After the addition of Brefeldin A (Sigma-Aldrich) cultures were maintained for 16 h before ICS for IFN-γ (PE-IFN-γ) and Interleukin-2 (APC-IL-2, both BD Pharmingen, UK) or appropriate isotype control mAbs.