Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Mouse TCR-β BUV395 (clone H57-597) | BD | Cat# 742485 |
| Anti-Mouse CD103 BUV496 (clone M290) | BD | Cat# 741083 |
| Anti-Mouse CD44 BUV563 (clone IM7) | BD | Cat# 741227 |
| Anti-Mouse PD-1 BUV615 (clone J43) | BD | Cat# 752299 |
| Anti-Mouse Nrp1 BUV661 (clone V46-1954) | BD | Cat# 752461 |
| Anti-Mouse/Human Ki67 BUV737 (clone B56) | BD | Cat# 567130 |
| Anti-Mouse CD4 BUV805 (clone GK1.5) | BD | Cat# 612900 |
| Anti-Mouse CD39 BV421 (clone Y23-1185) | BD | Cat# 567105 |
| Anti-Mouse IA-IE Pacific Blue (clone M5/114.15.2) | BioLegend | Cat# 107620 |
| Anti-Mouse ST2 BV480 (clone U29-93) | BD | Cat# 746701 |
| Anti-Mouse CD8 Pacific Orange (clone 5H10) | ThermoFisher Scientific | Cat# MCD0830 |
| Anti-Mouse CD62L BV570 (clone MEL-14) | BioLegend | Cat# 104433 |
| Anti-Mouse CD11c BV605 (clone N418) | BioLegend | Cat# 117334 |
| Anti-Mouse ICOS BV650 (clone C398.4A) | BioLegend | Cat# 313550 |
| Anti-Mouse KLRG1 BV750 (clone 2F1) | BD | Cat# 746972 |
| Anti-Mouse PD-L1 BV785 (clone MIH5) | BD | Cat# 741014 |
| Anti-Mouse iNOS FITC (clone REA982) | Miltenyi Biotec | Cat# 130-116-357 |
| Anti-Mouse CD45 A532 (clone 30-F11) | ThermoFisher Scientific | Cat# 58-0451-82 |
| Anti-Mouse CD19 NB610 (clone 1D3) | ThermoFisher Scientific | Cat# M004T02B06 |
| Anti-Mouse Ly6C PerCP-Cy5.5 (clone HK1.4) | BioLegend | Cat# 128012 |
| Anti-Mouse CD206 PerCPeF710 (clone MR6F3) | ThermoFisher Scientific | Cat# 46-2069-42 |
| Anti-Mouse/Human TOX PE (clone REA473) | Miltenyi Biotec | Cat# 130-120-716 |
| Anti-Mouse Ly6G SYG563 (clone 1A8) | BioLegend | Cat# 127668 |
| Anti-Mouse Helios PE-Dazzle 594 (clone 22F6) | BioLegend | Cat# 137232 |
| Anti-Mouse CD80 PE-Cy5 (clone 16-10A1) | BioLegend | Cat# 104712 |
| Anti-Mouse FoxP3 PE-Cy7 (clone FJK-16s) | ThermoFisher Scientific | Cat# 25-5773-82 |
| Anti-Mouse/Human B220 PE/Fire 810 (clone RA3-6B2) | BioLegend | Cat# 103287 |
| Anti-Mouse/Human TCF-1 APC (clone C63D9) | Cell Signaling Technologies | Cat# 37636S |
| Anti-Mouse CD69 SNIR685 (clone H1.2F3) | BioLegend | Cat# 104558 |
| Anti-Mouse/Human CD11b A700 (clone M1/70) | BioLegend | Cat# 101222 |
| Anti-Mouse F4/80 APC/Fire 750 (clone BM8) | BioLegend | Cat# 123152 |
| Anti-Mouse NK1.1 APC/Fire 810 (clone S17016D) | BioLegend | Cat# 156519 |
| TruStain FcX PLUS (clone S17011E) | BioLegend | Cat# 156604 |
| Anti-Mouse Ter-119 PE (clone TER-119) | BioLegend | Cat# 116208 |
| Anti-Mouse/Human CD11b PE (clone M1/70) | BioLegend | Cat# 101208 |
| Anti-Mouse Gr-1 PE (clone RBC-8C5) | BioLegend | Cat# 108408 |
| Anti-Mouse CD3ε PE (clone 145-2C11) | BioLegend | Cat# 100308 |
| Anti-Mouse CD5 PE (clone 53-7.3) | BioLegend | Cat# 100608 |
| Anti-Mouse/Human B220 PE (clone RA3-6B2) | BioLegend | Cat# 103208 |
| Anti-Mouse CD117 (c-kit) APC (clone 2B8) | BioLegend | Cat# 105812 |
| Anti-Mouse Sca-1 BV421 (clone D7) | BioLegend | Cat# 108127 |
| Anti-Human CD4 BV421 (clone OKT-4) | BioLegend | Cat# 317434 |
| Anti-Human CD25 APC (clone M-A251) | BioLegend | Cat# 356110 |
| Anti-Human CD127 PE (clone A019D5) | BioLegend | Cat# 351304 |
| Anti-Mouse CD25 BV421 (clone PC61) | BioLegend | Cat# 102043 |
| Anti-Mouse CD3 BV711 (clone 145-2C11) | BioLegend | Cat# 100349 |
| Anti-Mouse CD8 PE (clone 53-6.7) | BioLegend | Cat# 100708 |
| Anti-Mouse CD127 PE-Cy7 (clone SB/199) | BioLegend | Cat# 121119 |
| Anti-Mouse CD4 APC (clone GK1.5) | BioLegend | Cat# 100411 |
| InVivoMAb Anti-Mouse PD-1 (clone RMP1-14) | BioXCell | Cat# BE0146 |
| Bacterial and virus strains | ||
| NEBstable Competent E. coli | NEB | Cat# C3040H |
| Endura Electrocompetent cells | Lucigen | Cat# 60242-1 |
| Biological samples | ||
| Healthy donor PBMC buffy coats | New York Blood Center | https://www.nybc.org/ |
| ccRCC Nephrectomy Specimens | Columbia University Irving Medical Center | |
| Chemicals, peptides, and recombinant proteins | ||
| Recombinant Human IL-2 | PeproTech | Cat# 200-02 |
| Recombinant Mouse TPO | PeproTech | Cat# 315-14 |
| Recombinant Mouse SCF | PeproTech | Cat# 250-03 |
| Recombinant Mouse Flt3-L | PeproTech | Cat# 250-31L |
| Recombinant Mouse IL-7 | PeproTech | Cat# 217-17 |
| RetroNectin Recombinant Human Fibronectin | Takara Bio | Cat# T100B |
| FDA-approved and Investigational Oncology Drug Compound Library | Selleckchem | Cat# N/A (custom) |
| Gemcitabine (Ly-188011) | Selleckchem | Cat# S1714 |
| Triapine | Selleckchem | Cat# S7470 |
| Floxuridine (NSC 27640) | Selleckchem | Cat# S1299 |
| SYTOX Green Ready Flow Reagent | ThermoFisher Scientific | Cat# R37168 |
| CellTrace Violet Proliferation Kit | ThermoFisher Scientific | Cat# C34557 |
| Ficoll-Paque PLUS (1.077 g/mL) | GE Healthcare | Cat# 17144003 |
| Mitomycin C | Millipore Sigma | Cat# 10107409001 |
| DNase I | Roche/Sigma | Cat# 10104159001 |
| Collagenase D | Roche/Sigma | Cat# 11088866001 |
| LiveDead Fixable Blue Dye | ThermoFisher Scientific | Cat# L34962 |
| BD Brilliant Stain Buffer Plus | BD | Cat# 566385 |
| FoxP3 Fixation/Permeabilization Kit | eBioscience/Thermo | Cat# 00-55214-00 |
| TruStain Monocyte Blocker | BioLegend | Cat# 426103 |
| Fugene HD | Pro mega | Cat# E2312 |
| RNAseA | Qiagen | Cat# 19101 |
| Biotium EVAGREEN DYE 20X IN WATER 1 ML | Fisher Scientific | Cat# NC0521178 |
| GeneJET Gel Extraction Kit | Fisher Scientific | Cat# FERK0692 |
| Gibson Assembly® Master Mix | NEB | Cat# E2611L |
| KAPA HiFi HotStart PCR Kit, with dNTPs | Kapa Biosystems | Cat# KK2502 |
| NucleoBond® Xtra Midi EF (50 preps) | Macherey-Nagel | Cat# 740420.50 |
| Puradisc 25 mm PES Syringe Filters | Cytiva | Cat# 6780-2504 |
| RIPA BUFFER | Teknova | Cat# R3792 |
| Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) | Invitrogen | Cat# 15593031 |
| KAPA HiFi HotStart ReadyMix (2X) | Kapa Biosystems | Cat# KK2612 |
| Critical commercial assays | ||
| CD4+ T cell Isolation Kit, Human | Miltenyi Biotec | Cat# 130-096-533 |
| Human Treg Expander DynaBeads | Gibco | Cat# 11129D |
| Human Tumor Dissociation Kit | Miltenyi Biotec | Cat# 130-095-929 |
| Mouse Tumor Dissociation Kit | Miltenyi Biotec | Cat# 130-096-730 |
| 10x Chromium Next GEM Single Cell 3’ Kit v3.1 | 10x Genomics | Cat# 1000269 |
| Deposited data | ||
| Sorted T-cell Populations RNA-Seq From Patient Blood & Tumor | This Manuscript | DOI: 10.17632/vnrsbb4gk9.1 |
| Overexpression Screen Single-Cell RNA-Seq Data | This Manuscript | DOI: 10.17632/vnrsbb4gk9.1 |
| Gemcitabine Treatment Single-Cell RNA-Sequencing Data | This Manuscript | DOI: 10.17632/vnrsbb4gk9.1 |
| sgRNA counts from CRISPR KO experiment | This Manuscript | DOI: 10.17632/vnrsbb4gk9.1 |
| Drug Screen PLATE-Seq Data | This Manuscript | DOI: 10.17632/vnrsbb4gk9.1 |
| T-cell ARACNe Network | This Manuscript | DOI: 10.17632/vnrsbb4gk9.1 |
| Experimental models: Cell lines | ||
| MC38 | Kerafast | Cat# ENH204-FP |
| MCA205 | Millipore Sigma | Cat# SCC173 |
| HEK293T | ATCC | Cat# CRL-11268 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | Strain# 000664 |
| Mouse: H11-Cas9 (Igs2tm1.1(CAG-cas9*)Mmw/J) | The Jackson Laboratory | Strain# 027650 |
| Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ | The Jackson Laboratory | Strain# 005557 |
| Mouse: Rag1-KO (B6.129S7-Rag1tm1Mom/J | The Jackson Laboratory | Strain# 002216 |
| Mouse FoxP3-YFP/Cre (B6.129(Cg)-Foxp3tm4(YFP/icre)Ayr/J | The Jackson Laboratory | Strain# 016959 |
| Recombinant DNA | ||
| pXPR_053 | Addgene | Cat# 113591 (PubMed 30971695 |
| PsPAX2 | Addgene | Cat# 12260 (gift from Didier Trono) |
| pMD2.G | Addgene | Cat# 12259 (gift from Didier Trono) |
| Tet-O-FUW-EGFP | Addgene | Cat# 30130 (PubMed 20107439) |
| Tet-O-FUW-EGFP-P2A-mCherry | This paper | N/A |
| FUW-M2rtTA | Addgene | Cat# 20342 (PubMed 18786421) |
| Human CSRNP2 ORF clone | GenScript | Cat# OHu04521 |
| Human TRPS1 ORF clone | GenScript | Cat# OHu21177 |
| Human BANP ORF clone | GenScript | Cat# OHu10822 |
| Human MAFB ORF clone | GenScript | Cat# OHu25119 |
| pFUW-tetO-NR4A3 | Addgene | Cat# 139818 (PubMed 30530727) |
| GFP-FBXL10 (KDM2B) | Addgene | Cat# 126542 (PubMed 29985131) |
| KLF4 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| STAT4 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| NR4A1 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| EGR1 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| ZEB2 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| EGR3 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| PBX4 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| ID2 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| FOSL2 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| NR3C1 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| GLI1 in pENTR223.1 | Jussi Taipale lab | PubMed 23332764 |
| Tet-O-FUW-CSRNP2-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-TRPS1-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-BANP-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-MAFB-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-NR4A3-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-KDM2B-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-KLF4-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-STAT4-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-NR4A1-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-EGR1-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-ZEB2-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-EGR3-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-PBX4-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-ID2-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-FOSL2-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-NR3C1-P2A-mCherry | This paper | N/A |
| Tet-O-FUW-GLI1-P2A-mCherry | This paper | N/A |
| Software and algorithms | ||
| R v3.6.2 | https://cran.r-project.org/bin/macosx/ | |
| ARACNe | Margolin, et al. | http://califano.c2b2.columbia.edu/aracne |
| VIPER | Alvarez, et al. | http://califano.c2b2.columbia.edu/viper |
| GraphPad Prism v9 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo v10.8.1 | BD | https://www.flowjo.com/ |
| Single-Cell VIPER | Obradovic, et al. | https://github.com/Aleksobrad/single-cell-rcc-pipeline |
| Custom Analysis Scripts | This paper | DOI: 10.17632/vnrsbb4gk9.1 |