KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| Purified NA/LE Mouse Anti-Human CD3 (Clone UCHT1) | BD | Cat# 555329; RRID: AB_395736 |
| Purified NA/LE Mouse Anti-Human CD28 (Clone CD28.2) | BD | Cat# 555725; RRID: AB_396068 |
| HIV-1 core (p24) antigen-FITC (Clone KC57) | Beckman Coulter | Cat# 6604665; RRID: AB_1575987 |
| Mouse anti-human CD4 Alexa Fluor 700 (Clone RPAT4) | BD | Cat# 557922; RRID: AB_396943 |
| Mouse anti-human CD4 PerCP-Cy5.5 (Clone RPAT4) | BioLegend | Cat# 300530; RRID: AB_893328 |
| Mouse anti-human CD3 Pacific Blue (Clone UCHT1) | BD | Cat# 558117; RRID: AB_397038 |
| Mouse anti-human CCR6 PE (Clone 11A9) | BD | Cat# 559562; RRID: AB_397273 |
| Mouse anti-human CCR5 PE (Clone 2D7/CCR5) | BD | Cat# 555993; RRID: AB_396279 |
| Mouse anti human IFN-γ Alexa Fluor 700 (Clone B27) | BD | Cat# 557995; RRID: AB_396977 |
| Mouse anti human CXCR4 APC (Clone 12G5) | Thermo Fisher | Cat# 17–9999–42; RRID: AB_1724113 |
| Mouse anti human Ki67 BV421 (Clone B56) | BD | Cat# 562899; RRID: AB_2686897 |
| Rat anti human Integrinβ7 PE-Cy 5 (Clone FIB504) | BD | Cat# 551059; RRID: AB_394026 |
| Mouse anti human CD56 FITC (Clone HCD56) | eBioscience | Cat# 318304; RRID: AB_604100 |
| Mouse anti human IL-17A PE (Clone eBio64DEC17) | eBioscience | Cat# 12–7179–42; RRID: AB_1724136 |
| Mouse anti human IL-22 PE-Cyanine7 (Clone 22URTI) | eBioscience | Cat# 25–7229–42; RRID: AB_10853346 |
| Mouse anti human CD8 FITC (Clone BW135/80) | Miltenyi Biotech | Cat# 130–080–601; RRID: AB_244336 |
| Mouse anti human CD19 FITC (Clone LT19) | Miltenyi Biotech | Cat# 130–091–328; RRID: AB_244222 |
| Mouse anti human CD45RA APCeFluor780 (Clone HI100) | eBioscience | Cat# 47–0458–42; RRID: AB_10853641 |
| LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (405 nm excitation) | Invitrogen | Cat# L34957 |
| Rabbit anti human AhR | Abcam | Cat# ab190797; RRID: AB_2894707 |
| Rabbit anti human AhR | Cell Signaling | Cat# 83200; RRID: AB_2800011 |
| Rabbit anti human ARNT | Cell Signaling | Cat# 5537; RRID: AB_10694232 |
| Normal Rabbit IgG | Cell Signaling | Cat# 2729; RRID: AB_1031062 |
| Monoclonal anti-βActin (clone AC15) | Sigma | Cat# A5441; RRID: AB_476744 |
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| Bacterial and virus strains | ||
|
| ||
| HIV-1 THRO plasmid (pTHRO.c/2626), subtype B | NIH AIDS Reagent Program (Contribution of Dr. John Kappes and Dr. Christina Ochsenbauer) | Cat#11745 |
| NL4.3BaL HIV plasmid | From Dr Roger J Pomerantz (Thomas Jefferson University, Philadelphia, Pennsylvania, USA) and Dr. Michel J. Tremblay (Université Laval, Québec City, QC, Canada) | N/A |
|
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| Biological samples | ||
|
| ||
| Leukaphereses of ART treated and untreated people living with HIV | Recruited at the Montreal Chest Institute, McGill University Health Center and Center Hospitalier de l’Université de Montréal via the collaboration of Dr Jean-Pierre Routy’s group | N/A |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Dulbecco’s Modified Eagle’s medium (DMEM) | Thermo Fisher | Cat# 11995065 |
| Roswell Park Memorial Institute (RPMI) | Thermo Fisher | Cat# 11875–093 |
| Penicillin/Streptomycin | Gibco | Cat# 15140–122 |
| Fetal Bovine Serum (FBS) | Sigma | Cat# F2442 |
| Bovine Serum Albumin (BSA) | BioShop | Cat# ALB001 |
| Phosphate Buffered Saline (PBS) | Thermo Fisher | Cat# 20012050 |
| Tween 20 | Thermo Fisher | Cat# BP337–500 |
| PVDF membrane | Millipore Sigma | Cat# ISEQ00010 |
| RIPA Buffer 10X | NEB | Cat# 9806S |
| rhIL-2 | R&D Systems | Cat# 202–IL–050 |
| rhIL-10 | R&D Systems | Cat# 217–IL |
| rhIL-22 | R&D Systems | Cat# 782–IL–010 |
| CH-223191 | Sigma | Cat# C8124 |
| FICZ | Sigma | Cat# SML1489 |
| DNAzol™ Reagent | Invitrogen | Cat# 10503027 |
| T7 Endonuclease I - 250 units | NEB | Cat# M0302S |
| Phusion® High-Fidelity DNA Polymerase | NEB | Cat# M0530S |
| UltraComp ebeads | eBioscience | Cat# 01–2222–42 |
| Formaldehyde 37% | Sigma | Cat#F79500 |
| LC480 probe master mix | Roche | Cat# 4707494001 |
| Amersham ECL Prime Western Blotting System | Cytiva | Cat# RPN2232 |
| Brefeldin A | Sigma | Cat# B7651 |
| PMA | Sigma | Cat# P1585 |
| Ionomycin | Sigma | Cat# I0634 |
| Luna Universal qPCR Master Mix | NEB | Cat# M3003E |
| TMB Peroxidase Substrate | Fitzgerald | Cat# 42R–TB102 |
| Streptavidin Poly-HRP40 | Fitzgerald | Cat# 65R–S104PHRP–200UG |
|
| ||
| Critical commercial assays | ||
|
| ||
| Memory CD4+ T cell Isolation Kit, human | Miltenyi | Cat#130–091–893 |
| Fixation/Permeabilization Solution Kit (Cytofix/Cytoperm) | BD | Cat# 554714 |
| Human IL-10 DuoSet ELISA | R&D Systems | Cat# DY217B |
| Human IL-17A (homodimer) ELISA Ready-SET-Go | Thermo Fisher | Cat# 88–7176–86 |
| Human IL-22 DuoSet ELISA | R&D Systems | Cat# DY782 |
| Human IFN-γ ELISA | Thermo Fisher | Cat# 88–7316–86 |
| QuantiTect SYBR Green RT-PCR Kit | Qiagen | Cat# 204245 |
| Human T cell Nucleofector® Kit | Lonza | Cat# VPA–1002 |
| Rneasy Plus Mini Kit | Qiagen | Cat# 74136 |
| CHIP assay kit | EMD Millipore | Cat# 17–295 |
| Luna® Universal qPCR Master Mix | NEB | Cat# M3003S |
| MyTaq Extract PCR kit | Bioline | Cat# BIO–21126 |
| High-fidelity enzyme Q5 | NEB | Cat# M0530L |
| QIAEX II Gel extraction kit | Qiagen | Cat# 20021 |
| GeneJET PCR Purification Kit | Thermo Fisher | Cat# K0702 |
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| Deposited data | ||
|
| ||
| RNA-Sequencing dataset | This paper | GEO: GSE198078 |
| Original western blot images relative to Figures 1, S1 and S2. | This paper; Mendeley Data | https://data.mendeley.com/datasets/4ry9gxv7tp/1 |
| Gene Ontology: Biological Processes database | Broad Institute | https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=BP |
| Homo Sapiens database GRCh 37 version75 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/ |
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| Experimental models: Cell lines | ||
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| ACH-2 cell line | NIH HIV Reagent Program | Cat# ARP–349 |
| 293T cells | ATCC | Cat# CRL–3216 |
| TZM-bl cells | NIH HIV Reagent Program | Cat# ARP–8129 |
| HIV-p24 Abs producing hybridome | From Dr. Michel J. Tremblay (Université Laval, Québec City, QC, Canada) | N/A |
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| Oligonucleotides | ||
|
| ||
| See Table S3: Oligonucleotides | This paper | N/A |
|
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| Software and algorithms | ||
|
| ||
| Kallisto software version 0.44.0 | Pachter Lab | https://pachterlab.github.io/kallisto/ |
| FlowJo version 10 | BD | https://www.flowjo.com/ |
| GraphPad Prism 7 | GraphPad | https://www.graphpad.com/ |
| Microsoft Excel v16 | Microsoft Office | https://www.microsoft.com/en-ca/microsoft-365/excel |
| Snapgene software | Snapgene | https://www.snapgene.com/ |
| TIDE software | Tide | https://tide.nki.nl/ |
| ICE software | Synthego | https://ice.synthego.com/ |
| QuantStudio™ Design & Analysis Software | Thermo Fisher | https://www.thermofisher.com/ |