| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Monoclonal mouse anti-ARF6 AF488 (clone 3A-1) | Santa Cruz Biotechnology | Cat#sc-7971 AF488 |
| Monoclonal mouse anti-Calnexin AF488 (clone AF18) | ThermoFisher Scientific | Cat#MA3–027-A488 |
| Monoclonal mouse anti-GM130 AF488 (clone 35/GM130) | BD Biosciences | Cat#560257 |
| Monoclonal mouse anti-TfR AF488 (clone #29806) | R&D Systems | Cat#FAB2474G-100UG |
| Polyclonal rabbit anti-TGN46 AF488 | Novus Biologicals | Cat#NBP1–49643AF488 |
| Polyclonal sheep anti-EEA1 AF488 | R&D Systems | Cat#IC8047G |
| Polyclonal sheep anti-LAMP1 AF488 | R&D Systems | Cat#IC7985G |
| Polyclonal goat anti-Mouse IgG (H+L) AF594 | ThermoFisher Scientific | Cat#A-11032 |
| Polyclonal goat anti-Rabbit (gG (H+L) AF647 | ThermoFisher Scientific | Cat#A-21245 |
| Monoclonal mouse anti-CD8 (clone 4B11) | Leica | Cat#CD8–4B11-L-CE |
| Monoclonal mouse anti-CD58 (clone TS2/9) | ThermoFisher Scientific | Cat#MA5800 |
| Monoclonal mouse anti-Ki-67 (MIB-1) | Nordic MUbio | Cat#KI500 |
| Monoclonal anti-mouse CD16/32 (clone 93) | Biolegend | Cat#101302 |
| Monoclonal mouse anti-CD2 BV605 (clone RPA-2.10) | Biolegend | Cat#300223 |
| Monoclonal mouse anti-CD279 (PD-1) APC (clone EH12.2H7) | Biolegend | Cat#329908 |
| Monoclonal mouse anti-CD3 PE-Cy7 (clone HIT3a) | Biolegend | Cat#300316 |
| Monoclonal mouse anti-CD4 AF700 (clone RPA-T4) | Biolegend | Cat#300526 |
| Monoclonal mouse anti-CD45RA Brilliant Violet 711 (clone HI100) | Biolegend | Cat#304137 |
| Monoclonal mouse anti-CD45RO Brilliant Violet 570 (clone UCHL1) | Biolegend | Cat#304226 |
| Monoclonal mouse anti-CD48 FITC (clone BJ40) | Biolegend | Cat#336705 |
| Monoclonal mouse anti-CD58 APC (clone TS2/9) | Biolegend | Cat#330918 |
| Monoclonal mouse anti-CD58 BV421 (clone 1C3) | BD Biosciences | Cat#564363 |
| Monoclonal mouse anti-CD58 PE-Cy5 (clone TS2/9) | Biolegend | Cat#330909 |
| Monoclonal mouse anti-CD8 AF488 (clone HIT8a) | Biolegend | Cat#300916 |
| Monoclonal mouse anti-Granzyme B PE-CF594 (clone GB11) | BD Biosciences | Cat#562462 |
| Monoclonal mouse anti-human CD45 Pacific Blue (clone HI30) | Biolegend | Cat#304022 |
| Monoclonal mouse anti-HLA A,B,C BV605 (clone W6/32) | Biolegend | Cat#311432 |
| Monoclonal mouse anti-PD-L1 APC (clone 29E.2A3) | Biolegend | Cat#329708 |
| Monoclonal mouse anti-PD-L1 BV785 (clone 29E.2A3) | Biolegend | Cat#329736 |
| Monoclonal rat anti-Ki-67 eFluor506 (clone SolA15) | ThermoFisher Scientific | Cat#69-5698-82 |
| Monoclonal rat anti-mouse CD45 BV510 (clone 30-F11) | Biolegend | Cat#103138 |
| Monoclonal mouse anti-CD58 (clone TS2/9) | Biolegend | Cat#330923 |
| Monoclonal rat anti-CD2 (LO-CD2b) | Laboratory of Megan Sykes | n/a |
| Monoclonal mouse anti-CD28 (clone CD28.2) | ThermoFisher Scientific | Cat#16-0289-81 |
| Monoclonal mouse anti-CD3 (clone OKT3) | Miltenyi Biotec | Cat#130-093-387 |
| Monoclonal mouse anti-PD-L1 (clone 29E.2A3) | Bio X Cell | Cat#BE0285R001MG |
| Mouse IgG2b isotype control (clone MPC-11) | Bio X Cell | Cat#BE0086R001MG |
| Mouse IgG4, κ isotype control (clone QA16A15) | Biolegend | Cat#403701 |
| Rat IgG2b negative control (clone LTF-2) | EMD Millipore | Cat#MABF1076Z |
| APC Mouse IgG1, κ Isotype Ctrl Antibody (clone MOPC-21) | Biolegend | Cat#981806 |
| APC Mouse IgG2b, κ Isotype Ctrl Antibody (clone MPC-11) | Biolegend | Cat#400319 |
| Brilliant Violet 421™ Mouse IgG2a, κ Isotype Ctrl Antibody (clone MOPC-173) | Biolegend | Cat#400259 |
| Brilliant Violet 605™ Mouse IgG2a, κ Isotype Ctrl Antibody (clone MOPC-173) | Biolegend | Cat#400269 |
| Brilliant Violet 785™ Mouse IgG2b, κ Isotype Ctrl Antibody (clone MPC-11) | Biolegend | Cat#400355 |
| FITC Mouse IgG1, κ Isotype Ctrl (clone MOPC-21) | Biolegend | Cat#981802 |
| Monoclonal mouse anti-CD58 (clone TS2/9) | Abcam | Cat#ab171087 |
| Monoclonal mouse anti-His (clone 27E8) | Cell Signaling Technology | Cat#2366 |
| Monoclonal mouse anti-PD-L1 (clone 405.9A11) | Cell Signaling Technology | Cat#29122 |
| Polyclonal rabbit anti-CMTM6 | MilliporeSigma | Cat#HPA026980 |
| Polyclonal rabbit anti-CMTM6 | Invitrogen | Cat#PA5–55472 |
| Monoclonal rabbit anti-PD-L1 (clone E1L3N) | Cell Signaling Technology | Cat#13684 |
| Monoclonal rabbit anti-V5 (clone D3H8Q) | Cell Signaling Technology | Cat#13202 |
| Monoclonal rabbit anti-CD58 (clone EP15041) | Abcam | Cat#ab196648 |
| Monoclonal rabbit anti-GAPDH (clone 14C10) | Cell Signaling Technology | Cat#2118 |
| IRDye 680RD Goat anti-Mouse IgG (H+L) | Li-Cor | Cat#926–68070 |
| IRDye 680RD Goat anti-Rabbit IgG (H+L) | Li-Cor | Cat#926–68071 |
| IRDye 800CW Goat anti-Mouse IgG (H+L) | Li-Cor | Cat#926–32210 |
| Bacterial and virus strains | ||
| Human CRISPR Knockout Pooled Library (Brunello) | Doench et al.26 | Addgene Virus #73178-LV |
| Chemicals, peptides, and recombinant proteins | ||
| Accutase | Innovative Cell Technologies | Cat#AT104 |
| ACK Lysing Buffer | Quality Biological | Cat#118-156-101 |
| BOND Epitope Retrieval Solution 1 | Leica Biosystems | Cat#AR9961 |
| BONE Epitope Retrieval Solution 2 | Leica Biosystems | Cat#AR9640 |
| Cas9-NLS purified protein | QB3 MacroLab | N/A |
| CellEvent Caspase-3/7 Detection Reagent | ThermoFisher Scientific | Cat#C10423 |
| CFSE | ThermoFisher Scientific | Cat#C34570 |
| Chloroquine diphosphate | Sigma Aldrich | Cat#C6628–25G |
| Collagenase D | Sigma Aldrich | Cat#11088866001 |
| Concanamycin A | Santa Cruz Biotechnology | Cat#sc-202111 |
| Digitonin | Sigma-Aldrich | Cat#D141 |
| DNase I | Sigma Aldrich | Cat#10104159001 |
| Ex Taq DNA Polymerase | TaKaRa | Cat#RR001C |
| Gateway BP Clonase II Enzyme Mix | ThermoFisher Scientific | Cat#11789020 |
| Gateway LR Clonase iI Enzyme Mix | ThermoFisher Scientific | Cat#11791020 |
| Halt Protease and Phosphatase Inhibitor Cocktail | ThermoFisher Scientific | Cat#76445 |
| Human IL-2 | Chiron | Cat#53905-991-01 |
| Insulin-Transferrin-Selenium | ThermoFisher Scientific | Cat#41400–045 |
| Laemmli SDS-Sample Buffer | Boston BioProducts | Cat#BP-111R |
| Matrigel Basement Membrane Matrix, LDEV Free | Corning | Cat#354234 |
| Matrigel Matrix High Concentration, Phenol-Red Free, LDEVfree | Corning | Cat#354262 |
| Opti-MEM I Reduced Serum Medium | ThermoFisher Scientific | Cat#31985062 |
| Polybrene Infection/Transfection Reagent | Sigma-Aldirch | Cat#TR-1003 |
| Recombinant CD58 His-tag protein | VWR | Cat#10797–676 |
| Recombinant CD58/LFA-3 Fc chimera protein | R&D Systems | Cat#10068-CD-050 |
| Recombinant human CMTM6 GST (N-term) protein | Novus Biologicals | Cat#H00054918-P01 |
| Recombinant human IFN-gamma | Abcam | Cat#ab9659 |
| Recombinant human PD-L1/B7-H1 His-tag protein | R&D Systems | Cat#9049-B7–100 |
| RIPA buffer | Sigma Aldrich | Cat#R0278 |
| TaqMan Fast Advanced Master Mix | ThermoFisher Scientific | Cat#4444557 |
| TransIT-LT1 Transfection Reagent | Mirus Bio | Cat#MIR 2300 |
| Zombie NIR | Biolegend | Cat#423105 |
| Zombie Violet | Biolegend | Cat#423113 |
| Critical commercial assays | ||
| Duolink In Situ Detection Reagents FarRed | Sigma-Aldrich | Cat#DUO92013 |
| IFN-gamma ELISA kit | Biolegend | Cat#430104 |
| IL-2 ELISA kit | Biolegend | Cat#431804 |
| QuikChange XL Site-Directed Mutagenesis Kit | Agilent | Cat#200516 |
| SF Cell Line Kit 4D X Kit | Lonza | Cat#197174 |
| Opal 6-Plex Detection Kit - for Whole Slide Imaging | Akoya Biosciences | Cat#NEL871001KT |
| ACTB TaqMan Gene Expression Assay | ThermoFisher Scientific | Assay ID: Hs99999903_m1 |
| CD274 TaqMan Gene Expression Assay | ThermoFisher Scientific | Assay ID: Hs00204257_m1 |
| CD58 TaqMan Gene Expression Assay | ThermoFisher Scientific | Assay ID: Hs01560660_m1 |
| GAPDH TaqMan Gene Expression Assay | ThermoFisher Scientific | Assay ID: Hs02786624 |
| Deposited data | ||
| A375 CD58 CRISPR/Cas9 KO screen data | This paper | GEO: GSE225235 |
| Melanoma scRNA-seq | Sade-Feldman et al.20 | GEO: GSE120575 |
| Melanoma scRNA-seq | Jerby-Arnon et al.7 | GEO: GSE115978 |
| Melanoma scRNA-seq | Pozniak et al.19 | EGA: EGAS00001006488 |
| A375 and 2686 CD58 IP mass spectrometry data | This paper | Proteome Xchange: PXD039710 |
| Experimental models: Cell lines | ||
| Human: 2686 | MD Anderson Cancer Center | N/A |
| Human: MaMel134 | UK-Essen | N/A |
| Human: A375 | ATCC | CRL-1619 |
| Human: WM852 | Rockland | WM852-01-0001 |
| Human: Jurkat | ATCC | TIB-152 |
| Human: HEK293T | ATCC | CRL-3216 |
| Experimental models: Organisms/strains | ||
| Mouse: NOD.Cg-Prkdcscid II2rgtm1Sug Tg(CMV-IL2)4–2Jic/JicTac | Taconic | Taconic: 13440-F |
| Mouse: NOD.Cg-Prkdcscid II2rgtm1Wjl/SzJ | The Jackson Laboratory | JAX: 005557 |
| Biological samples | ||
| Human 2686 TILs | MD Anderson Cancer Center | N/A |
| Human MaMel134 TILs | UK-Essen | N/A |
| Patient melanoma FFPE blocks | New York Presbyterian Hospital/Columbia University Irving Medical Center | N/A |
| Oligonucleotides | ||
| QuikChange CD58 K34A F: TTTTCCAGTTCTGCAACTGCATCCTTTTGTTTTTTCCATAGGACCTCIIIIAA | This paper | N/A |
| QuikChange CD58 K34A R: TTAAAAGAGGTCCTATGGAAAAAACAAAAGGATGCAGTTG CAGAACT GGAAAA | This paper | N/A |
| P5 and P7 primers (See Table S5) | Doench et al. | N/A |
| CD58 crRNA: AATGCTCTGGTATCATGCAT | This paper | N/A |
| CD274 crRNA: ACTGCTTGTCCAGATGACTT | This paper | N/A |
| B2M crRNA: GAGTAGCGCGAGCACAGCTA | This paper | N/A |
| CD2 crRNA: CGATGATCAGGATATCTACA | This paper | N/A |
| CMTM6 crRNA: GGTGTACAGCCCCACTACGG | This paper | N/A |
| Recombinant DNA | ||
| Plasmid: pLEX307 CD58 TM | This paper | N/A |
| Plasmid: pLEX307_CD58_GPI | This paper | N/A |
| Plasmid: pLEX307_CD58_TM_K34A | This paper | N/A |
| Plasmid: pLEX307_CD58_GPI_K34A | This paper | N/A |
| Plasmid: pLEX307_CMTM6 | This paper | N/A |
| Plasmid: pLEX307_CMTM6_V5 | This paper | N/A |
| Plasmid: pLEX307_CMTM6_Ctr_V5 | This paper | N/A |
| Plasmid: pLEX307_CMTM6_Ntr_V5 | This paper | N/A |
| Plasmid: pLEX307_CMTM6_EC1mut_V5 | This paper | N/A |
| Plasmid: pLEX307_CMTM6_EC2mut_V5 | This paper | N/A |
| Plasmid: pLEX307_CMTM6_EC1&2mut_V5 | This paper | N/A |
| Plasmid: pLX311_CD274 | This paper | N/A |
| Plasmid: pLX311_CD274_H1Amut | This paper | N/A |
| Plasmid: pXPR-011 | Doench et al.55 | Addgene #59702 |
| Plasmid: pLEX_307 | Laboratory of David Root | Addgene #41392 |
| Plasmid: pLX_TRC311 | Laboratory of John Doench | Addgene #113668 |
| Plasmid: pDONR221 | ThermoFisher Scientific | Cat#12536017 |
| Plasmid: pxsPAX2 | Laboratory of Dider Trono | Addgene #12260 |
| Plasmid: pMD2.G | Laboratory of Dider Trono | Addgene #12259 |
| Plasmid: pLX_311-Cas9 | Doench et al.55 | Addgene #96924 |
| Software and algorithms | ||
| ImageJ | Schneider et al.58 | https://imagej.net |
| FlowJo v10.8.1 | BD Biosciences | https://www.flowjo.com |
| CellProfiler v4.2.1 | Stirling et al.59 | https://cellprofiler.org |
| Prism v9.5.0 | GraphPad | https://www.graphpad.com |
| MAGeCK v0.5.9.2 | Li et al.48 | https://sourceforge.net/p/mageck/wiki/Home/ |
| InForm v2.5.1 | Akoya Biosciences | https://www.akoyabio.com/phenoimager/software/inform-tissue-finder/ |
| Image Studio Lite v5.2.5 | Li-Cor | https://www.licor.com/bio/image-studio/ |
| MaxQuant v2.0.1.0 | Cox and Mann66 | https://www.maxquant.org/ |
| Perseus | Tyanova et al.67 | https://maxquant.net/perseus/ |
| Andromeda | Cox et al.65 | https://bioinformaticshome.com/tools/proteomics/descriptions/Andromeda.html |
| SnapGene 6.0.5 | Dotmatics | https://www.snapgene.com |
| R v4.1.1 | The R Project | https://www.rproject.org |
| AUCell v1.20.2 | Aibar et al.63 | https://bioconductor.org/packages/release/bioc/html/AUCell.html |
| Seurat v4.1.0 | Hao et al.64 | https://satijalab.org/seurat/ |
| ZEN v3.4.91 | Zeiss | https://www.zeiss.com/microscopy/en/products/software/zeisszen.html |
| Other | ||
| SPRIselect beads | Beckman Coulter | Cat# B23318 |
| Protein A Dynabeads | ThermoFisher Scientific | Cat#10006D |
| Protein G Dynabeads | ThermoFisher Scientific | Cat#10003D |
| 8 well chambered cover glass | Cellvis | Cat#C8–1.5H-N |
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