KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Monoclonal anti-SAMHD1 mouse antibody clone OTI3F5 (30 μL) | Cedarlane | Cat#TA502024S |
| Polyclonal Anti-SAMHD1 (PHOSPHO THR592) (0.02 mg) antibody | Cedarlane | Cat#8005-0.02MG |
| Goat Anti-Mouse IgG (H + L) Secondary Antibody, HRP (1/2000) | Thermo Fisher | Cat#32340; RRID: AB_1185566 |
| Phospho-mTOR (Ser2448) Antibody (1/1000) | Cell Signaling | Cat#2971S; RRID: AB_330970 |
| mTOR (7C10) Rabbit mAb (1/1000) | Cell Signaling | Cat#2983; RRID: AB_2105622 |
| Anti-phospho-ribosomal protein S6 Ser240/Ser244 (1/500) | EMD Millipore | Cat#07-2113 |
| S6 Ribosomal Protein (5G10) Rabbit mAb (1/1000) | Cell Signaling | Cat#2217 |
| TCF4/TCF7L2 (C48H11) Rabbit (1/1000) | Cell Signaling | Cat#2569; RRID: AB_2199816 |
| Monoclonal Anti-β-actin Antibody Produce in Mouse (1/5000) | Sigma | Cat#A5441; RRID: AB_476744 |
| Anti-rabbit IgG HRP-linked Antibody (1/5000) | Cell Signaling | Cat#7074; RRID: AB_2099233 |
| ITGB7 BUV737 (Clone FIB504) | BD | Cat#749664 |
| GSK3B pS9 Antibody, anti-human/mouse/rat REAfinity APC | Miltenyi | Cat#130-106-901; RRID: AB_2651905 |
| Beta Catenin Monoclonal Antibody (15B8), Alexa Fluor 488 | Invitrogen | Cat#53-2567-41; RRID: AB_10807094 |
| Mouse anti-human CD3 Pacific Blue (Clone UCHT1) | BD | Cat#558117; RRID: AB_397038 |
| Mouse anti-human CD4 Alexa Fluor 700 (Clone RPA-T4) | BD | Cat#557922; RRID: AB_396943 |
| Mouse anti-human CD16 Phycoerythrin-Cyanine 7 (Clone 3G8) | BD | Cat#560918; RRID: AB_10563252 |
| Mouse anti-human CD14 APC (Clone M5E2) | BD | Cat#555399; RRID: AB_398596 |
| Anti-human CD1c (BDCA-1) Phycoerythrin (Clone REA694) | Miltenyi | Cat#130-110-536; RRID: AB_2656038 |
| Anti-human HLA-DR Brilliant Violet 785 (Clone L243) | Biolegend | Cat#307642; RRID: AB_2563461 |
| Mouse Anti-human CD195 Fluorescein Isothiocyanate (Clone 2D7/CCR5) | BD | Cat#555992; RRID: AB_396278 |
| CD184 CXCR4 Allophycocyanine (Clone 12G5) | Biolegend | Cat#306510; RRID: AB_314616 |
| HIV-1 core (p24) antigen-RD1 (Clone KC57) | Beckman Coulter | Cat#6604667; RRID: AB_1575989 |
| RARα | Cell signaling | Cat#62294; RRID: AB_2799625 |
| Phospho-Rpb1 CTD (Ser2) | Cell signaling | Cat#13499; RRID: AB_2798238 |
| Phospho-Rpb1 CTD (Ser5) | Cell signaling | Cat#13523; RRID: AB_2798246 |
| RNA polymerase II | Cell signaling | Cat#2629S |
| Rabbit IgG | Cell signaling | Cat#2729; RRID: AB_1031062 |
| CDK9 | Abcam | Cat#ab239364; RRID: AB_3096172 |
| Bacterial and virus strains | ||
| One Shot Stbl3 Chemically Competent E. coli | Life Technologies | Cat# C737303 |
| 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. Dana Gabuzda (Dana-Farber Cancer Institute, Boston, MA, USA) | N/A |
| VSV-G Plasmid | National Institution of Health (NIH) | Cat#ARP-4693 |
| NL4.3BaLΔenv GFP | National Institution of Health (NIH) | Cat#ARP-12637 |
| NL4.3Env-Vpr- | From Dr. Eric Cohen | N/A |
| ADA-Env | From Dr. Eric Cohen | N/A |
| Blam-Vpr | From Dr. Eric Cohen | N/A |
| VSV-G-Env | From Dr. Eric Cohen | N/A |
| pNL4.3-IRES-GFP | NIH HIV Reagent Program | Cat#ARP-11349 |
| Biological samples | ||
| Leukapheresis collected from HIV-participants | N/A | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Sodium Bicarbonate (NaHCO3) | Sigma | Cat#S5761 |
| Sodium Carbonate (Na2CO3) | Sigma | Cat#223530-500G |
| Thimerosal | Sigma | Cat#T5125-10G |
| Phosphate Buffered Saline (PBS) | Thermo Fisher | Cat#10010023 |
| Tween 20 | Fisher Scientific | Cat#BP337-500 |
| Triton X-100 | Sigma | Cat#X100-500mL |
| Trypan Blue | Thermo Fisher | Cat#15250061 |
| Bovine Serum Albumin (BSA) | BioShop | Cat#ALB001.500 |
| Streptavidin Horseradish Peroxidase (Strep-HRP) | Fisher Scientific | Cat#65R-S104PHRP |
| 3,3′,5,5′-Tetramethylbenzidine (TMB) | Quimigen | Cat#42R-TB10265R-S104PHRP |
| Phosphoric Acid (H3PO4) | Sigma | Cat#PX0996 |
| Nonidet P-40 | Bioshop | Cat#NON505 |
| Tris HCl | BioShop | Cat#TRS002.500 |
| Proteinase K | Fisher Scientific | Cat#25530-015 |
| Molecular Grade Water (H2O) | Wisent | Cat#809-115-CL |
| Guanidine-HC; | Promega | Cat#H5381 |
| Trypsin EDTA with phenol red | Wisent | Cat#075-350 |
| X-tremeGENE HP DNA Transfection Reagent | Roche | Cat#6366244001 |
| Probenecid | Sigma-Aldrich | Cat#P8761 |
| Methanol 99,98% | Fisher Scientific | Cat#BPA4084 |
| ReBlot Plus Strong Antibody Stripping Solution | Sigma | Cat#2504 |
| 4X Laemmli Sample Buffer | Bio-Rad | Cat#1610747 |
| 2-Mercaptoethanol | Sigma | Cat#M6250 |
| Precision Plus Protein Dual Color Standards | Bio-Rad | Cat#1610374 |
| Glycine | BioShop | Cat#GLN001.500 |
| Sodium Chloride | BioShop | Cat#SOD002 |
| 30% Bis-acrylamide Solution | Bioshop | Cat#ACR010.500 |
| UltraPure Tris Buffer | Thermo Fisher | Cat#15504-020 |
| Sodium Dodecyl Sulfate (SDS) | Bio-Rad | Cat#1610302 |
| N,N,N′,N′-Tetramethyl Ethylenediamine (TEMED) | Sigma | Cat#8087420005 |
| Ammonium Persulfate (APS) | Bioshop | Cat#AMP001.100 |
| Radioimmunoprecipitation Assay Buffer (RIPA) 10X | Cell Signaling | Cat#9806S |
| Phosphatase Inhibitor (PhosSTOP) | Roche | Cat#4906845001 |
| Complete, Mini, EDTA-free protease inhibitor | Roche | Cat#11836170001 |
| Formaldehyde solution 37 wt. % in H2O | Sigma | Cat#F1635-500ML |
| Sodium Azide | Bioshop | Cat#SAZ001.250 |
| Fetal Bovine Serum (FBS) | Wisent | Cat#091-150 |
| Dimethyl Sulfoxide (DMSO) | Sigma | Cat#34869-500mL |
| RPMI 1640 Medium (RPMI) | Thermo Fisher | Cat#11875119 |
| All-trans Retinoic Acid (ATRA) | Sigma | Cat#R2625-50MG |
| Sapanisertib (INK128) | Cayman Chemical | Cat#11811-1 |
| PRI-724 (ICG-001) | Selleck | Cat# S8968 |
| PNU-74654 | Selleck | Cat# S8429 |
| Recombinant Human Macrophage Colony Stimulating Factor (M-CSF) | Cedarlane | Cat#216-MC-025 |
| EDTA | Bioshop | Cat#EDT001.1 |
| Phosphate Buffered Saline (PBS) | Thermo Fisher | Cat#10010023 |
| Penicillin/streptomycin (PenStep) | Thermo Fisher | Cat#15140122 |
| Lymphocyte Separation Medium (LSM) | Wisent | Cat#305-010-CL |
| CO2-independent media | Life Technologies | Cat#18045-088 |
| DMEM High glucose, pruvate | Gibco | Cat#11995065 |
| Opti-MEM | Gibco | Cat#31985070 |
| DNAse | Invitrogen | Cat#AM1907 |
| Critical commercial assays | ||
| LDH Assay Kit | Abcam | Cat#ab65393 |
| p24 Enzyme-linked Immunosorbent Assay (ELISA) | Homemade. Hybridome provided by Dr. Michel J. Tremblay95 | N/A |
| QuantiTect SYBR Green RT-PCR Kit | Qiagen | Cat#204243 |
| 10X PCR Buffer/Magnesium Chloride (MgCl2) Buffer/Thermus Aquaticus (TAQ) Polymerase | Thermo Fisher | Cat#18038067 |
| LC480 probe master mix | Roche | Cat#4707494001 |
| QuantiTect SYBR Green RT-PCR Kit | Qiagen | Cat#204243 |
| Deoxynucleoside Triphosphates (dNTP) | Thermo Fisher | Cat#10297018 |
| Promega Wizard Plus DNA Purification System | Fisher Scientific | Cat#PR-A7100 |
| EndoFree Plasmid Maxi Kit | Qiagen | Cat#12362 |
| Memory CD4+ T cell Isolation Kit, human | Miltenyi | Cat#130-091-893 |
| CCF2-AM Substrate and Loading Solution | Life Technologies | Cat#K1032 |
| All Prep DNA/RNA/miRNA Universal Kit | Qiagen | Cat#80224 |
| Detergent Compatible (DC) Protein Assay | Bio-Rad | Cat#5000111 |
| Clarity and Clarity Max ECL Western Blotting Substrates | Bio-Rad | Cat#1705062S |
| Fixation/Permeabilization Kit | BD | Cat#554714 |
| LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (405 nm excitation) | Thermo Fisher | Cat#L34957 |
| Pan Monocyte Isolation Kit | Miltenyi | Cat#130-096-537 |
| CHIP assay kit | EMD Millipore | Cat#17-295 |
| Luna® Universal qPCR Master Mix | NEB | Cat# M3003S |
| GeneJET PCR Purification Kit | Thermo Fisher | Cat# K0702 |
| EZ-10 Spin Column Total RNA Miniprep Super Kit | Bio Basic | Cat#BS584 |
| Prime-Script RT reagent kit | TaKaRa | Cat#RR037A |
| Experimental models: Cell lines | ||
| HT-29 | ATCC | Cat#HTB-38 |
| 293T | ATCC | Cat#CRL-3216 |
| ACH-2 | NIH HIV Reagent Program | Cat#ARP-349 |
| THP-1 | NIH HIV Reagent Program | Cat#ARP-9942 |
| Oligonucleotides | ||
| PPARy | Qiagen | GeneGlobal ID: QT00029841 |
| TCF7L2 | Qiagen | GeneGlobal ID: QT00071120 |
| HIC1 | Qiagen | GeneGlobal ID: QT00203175 |
| CTNNB1 | Qiagen | GeneGlobal ID: QT00077882 |
| GSK3β | Qiagen | GeneGlobal ID: QT00057134 |
| CCND2 | Qiagen | GeneGlobal ID: QT00057575 |
| CDK1 | Qiagen | GeneGlobal ID: QT00042672 |
| SAMHD1 | Qiagen | GeneGlobal ID: QT00084322 |
| RARA | Qiagem | GeneGlobal ID: QT00095865 |
| RXRA | Qiagen | GeneGlobal ID:QT00005726 |
| See Table S1: Oligonucleotides | See Table S1: Oligonucleotides | See Table S1: Oligonucleotides |
| Software and algorithms | ||
| FlowJo version 10 | BD | https://www.flowjo.com/ |
| GraphPad Prism 9 | GraphPad | https://www.graphpad.com/ |
| Image Lab | Bio-Rad | https://www.bio-rad.com/en-ca/product/image-lab-software?ID=KRE6P5E8Z |
| QuantStudio™ Design & Analysis Software | Thermo Fisher | https://www.thermofisher.com/ |
| Other | ||
| MACS LS Columns | Miltenyi | Cat# 130-042-401 |
| Pre-Separation Filters 30 μm | Miltenyi | Cat# 130-041-407 |
| Immobilon-PSQ Polyvinylidene Difluoride (PVDF) | Sigma | Cat#ISEQ00010 |