KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| Mouse anti-human CD58 (TS2/9) | Biolegend | Cat# 330924; RRID: AB_2832649 |
| Rabbit anti-human CD58 (EP15041) | Abcam | Cat# ab196648; RRID: AB_2943462 |
| Goat anti-human CD58 | R&D systems | Cat# AF1689; RRID: AB_354933 |
| Rabbit anti-human CD58 (for IHC) | Novus Biologicals | Cat# NBP2-90097; RRID: AB_2943463 |
| Rabbit anti-human CD58 (for IHC) | SinoBiological | Cat# 12409-R126; RRID: AB_2860423 |
| Mouse anti-human PD-L1 (405.9A11) | Cell signaling technology | Cat# 29122; RRID: AB_2798970 |
| Rabbit anti-human PD-L1 (E1L3N) | Cell signaling technology | Cat# 13684S; RRID: AB_2687655 |
| Mouse anti-human CMTM6 (RCT6) | Absea | Cat# K06143M03F06C; RRID: AB_2943464 |
| Mouse anti-human CMTM6 (6B2) | This study (Generated by Absea) | RRID: AB_2943461 |
| Rabbit anti-human CMTM6 | Atlas Antibodies | Cat# HPA026980; RRID: AB_10602801 |
| Mouse anti-human HSP90 (F-8) | Santa Cruz | Cat# sc13119; RRID: AB_675659 |
| Goat anti-Mouse IgG (H + +L) | Jackson ImmunoResearch | Cat# 115-035-146; RRID: AB_2307392 |
| Goat anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | Cat# 111-035-144; RRID: AB_2307391 |
| Goat anti-Mouse light chain specific | Jackson ImmunoResearch | Cat# 115-005-174 RRID: AB_2338460 |
| Mouse anti-Rabbit light chain specific | Jackson ImmunoResearch | Cat# 211-032-171; RRID: AB_2339149 |
| Mouse anti-Goat IgG | Santa Cruz | Cat# sc2354; RRID: AB_628490 |
| Donkey anti-Goat IgG (H+L) | Invitrogen | Cat# A16005; RRID: AB_2534679 |
| humanized anti-human PD-L1 | Genentech | RRID: AB_2943467 |
| Mouse anti-human CD137-PE/Cyanine7 (4B4-1) | Biolegend | Cat# 309818, RRID: AB_2207741 |
| Mouse anti-human CD69-APC/FireTM 750 (FN50) | Biolegend | Cat# 310946; RRID: AB_2616709 |
| Mouse anti-human CD3-Alexa Fluor 700 (SK7) | Biolegend | Cat#344822; RRID: AB_2563420 |
| Mouse anti-human CD2-APC (RPA-2.10) | Biolegend | Cat# 300214; RRID: AB_10895925 |
| Mouse anti-human CD28-FITC (CD28.2) | Biolegend | Cat# 302906; RRID: AB_314308 |
| Mouse anti-human CD279-PE (EH12.2H7) | Biolegend | Cat# 329906; RRID: AB_940483 |
| Mouse anti-human CD274-PE (29E.2A3) | Biolegend | Cat# 329706; RRID: AB_940368 |
| Mouse anti-human CD58-APC (TS2/9) | Biolegend | Cat# 330918; RRID: AB_2650886 |
| Mouse anti-human CD58 BUV395 (Clone L306.4) | BD Biosciences | Cat# 745571; RRID: AB_2743091 |
| Mouse anti-human CD274-APC (29E.2A3) | Biolegend | Cat# 329708; RRID: AB_940360 |
| Mouse anti-HLA-A, B, C-APC (W6/32) | Biolegend | Cat# 311410; RRID: AB_314879 |
| Rat anti-human IL-2-PE/Cy7 (MQ1-17H12) | Biolegend | Cat# 500326; RRID: AB_2125593 |
| Mouse anti-human TNF-α-Brilliant Violet 785 (MAb11) | Biolegend | Cat# 502948; RRID: AB_2565858 |
| Mouse anti-human IFN-γ-Brilliant Violet 421 (4S.B3) | Biolegend | Cat# 502532; RRID: AB_2561398 |
| Mouse BD HorizonTM Customs BYG584-P CMTM6 (6B2) | This study (Fluorophore conjugation by BD) | RRID: AB_2943461 |
| Mouse IgG1, Isotype Control antibody (MOPC-21) | Biolegend | Cat# 400102; RRID: AB_2891079 |
| Humanized Human IgG1, Isotype Control antibody (QA16A12) | Biolegend | Cat# 403502; RRID: AB_2927629 |
| Goat anti-Rabbit IgG (H+L) Highly Cross-adsorbed Secondary antibody, Alexa Fluor™ Plus 488 |
Invitrogen | Cat# A32731; RRID: AB_2633280 |
| Goat anti-Mouse IgG (H+L) Cross-adsorbed Secondary antibody, Alexa Fluor 555 |
Invitrogen | Cat# A21422; RRID: AB_2535844 |
| Goat anti-Rabbit IgG (H+L) Highly Cross-adsorbed Secondary antibody, Alexa Fluor Plus 647 |
Invitrogen | Cat# A32733; RRID: AB_2633282 |
| Human/Mouse/Rat EEA1 Alexa Fluor® 488-conjugated antibody | R&D systems | Cat# IC8047G; RRID: AB_2943466 |
| Alexa Fluor 647 Mouse anti-Human Transferrin R (CD71) (OKT9) | BD Biosciences | Cat# 566724; RRID: AB_2869830 |
| Alexa Fluor 647 anti-human CD107a (LAMP-1) antibody (H4A3) | Biolegend | Cat# 328611; RRID: AB_1227507 |
|
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| Bacterial and virus strains | ||
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| One Shot™ Stbl3™ Chemically Competent E. coli | ThermoFisher Scientific | Cat # C737303 |
|
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| Biological samples | ||
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| Human melanoma tumor material | Netherlands Cancer Institute | N03LAM/CFMBP547 |
| Human colon tumor material | Nanjing Drum Tower hospital/Nanjing University | ZDX22001 |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Recombinant Human CD2 Fc Chimera Protein | R&D systems | 1856-CD-050 |
| MART-1 ELA mutant epitope peptide | This study | N/A |
| Digitonin | Millipore | Cat# 300410 |
| Prolong Glass Antifade Mountant | Thermo Fisher Scientific | Cat# P36984 |
| Proteinase inhibitor | Roche | Cat# 11836170001 |
| Proleukin S (IL-2) | Novartis | N/A |
|
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| Critical commercial assays | ||
|
| ||
| First Strand cDNA Synthesis Kit | Thermo Fisher Scientific | Cat# K1641 |
| Bioscience intracellular fixation & permeabilization buffer set | Thermo Fisher Scientific | Cat# 88-8824-00 |
| LIVE / DEAD ™ Fixable Near-IR Dead Cell Stain Kit | Thermo Fisher Scientific | Cat# L10119 |
|
| ||
| Experimental models: Cell lines | ||
|
| ||
| RKO | ATCC | N/A |
| A375 | ATCC | N/A |
| 8505C | DSMZ | N/A |
| Ramos | DSMZ | N/A |
| BJAB | DSMZ | N/A |
| OCI-AML2 | DSMZ | N/A |
| HAP1 | Carette et al.59 | N/A |
|
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| Experimental models: Organisms/strains | ||
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| ||
| NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ | The Jackson Laboratory | RRID:IMSR_JAX:005557 |
|
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| Oligonucleotides | ||
|
| ||
| Human-GAPDH-qPCR-F: AAGGTGAAGGTCGGAGTCAA |
Sigma | N/A |
| Human-GAPDH-qPCR-R: AATGAAGGGGTCATTGATGG |
Sigma | N/A |
| Human-CD58-qPCR-F: GACACTGTGTCAGGTAGCCTCA |
Sigma | N/A |
| Human-CD58-qPCR-R: GCACAAGTTAGTGTGGGAGATGG |
Sigma | N/A |
|
| ||
| Recombinant DNA | ||
|
| ||
| Plasmid: pMD2.G | Addgene | Cat #12259 |
| Plasmid: psPAX2 | Addgene | Cat #12260 |
| Plasmid: pCMV-VSV-G | Addgene | Cat #8454 |
| Plasmid: gag/pol | Addgene | Cat #14887 |
| Plasmid: padVantage | Promega | E171A |
| Plasmid: pLentiCRISPRv2 | Addgene | Cat #52961 |
| Plasmid: pLentiCas9-Blast | Addgene | Cat #52962 |
| Plasmid: plentiGuide-Puro | Addgene | Cat #52963 |
| Plasmid: pLentiGuide-GFP-2A-GFP | This study | N/A |
| Plasmid: pLentiGuide-BFP-2A-BFP | This study | N/A |
| Plasmid: pLentiCRISPRv2-sgNT (non-targeting)(GTATTACTG ATATTGGTGGG) | This study | sgRNA sequence is extracted from Human CRISPR Knockout Pooled Library (Brunello) Addgene: 73178 |
| Plasmid: pLentiCRISPRv2-sgCMTM6#1 (CCGGGTCCTCCTCCGTAGTG) | This study | sgRNA sequence is extracted from Human CRISPR Knockout Pooled Library (Brunello) Addgene: 73178 |
| Plasmid: pLentiCRISPRv2-sgCMTM6#2 (TCACAATGTACTTTATGTGG) | This study | sgRNA sequence is extracted from Human CRISPR Knockout Pooled Library (Brunello) Addgene: 73178 |
| Plasmid: pLentiCRISPRv2-sgCD58(GCAGCAGGCAGACCACGCTG) | This study | sgRNA sequence is extracted from Human CRISPR Knockout Pooled Library (Brunello) Addgene: 73178 |
| Plasmid: pLentiCRISPRv2-sgPD-L1(CACCACCAATTCCAAGAGAG) | This study | sgRNA sequence is extracted from Human CRISPR Knockout Pooled Library (Brunello) Addgene: 73178 |
| Plasmid: pLentiGuide-GFP-2A-Puro-sgNT (non-targeting) (GTATTACTGATATTGGTGGG) | This study | sgRNA sequence is extracted from Human CRISPR Knockout Pooled Library (Brunello) Addgene: 73178 |
| Plasmid: pLentiGuide-BFP-2A-Puro-sgCMTM6#2 (TCACAATGT ACTTTATGTGG) |
This study | sgRNA sequence is extracted from Human CRISPR Knockout Pooled Library (Brunello) Addgene: 73178 |
| Plasmid: pLKO.1 puro | Addgene | Cat #8453 |
| shCMTM6 hairpin sequence (CCGGCCTTTCTTCTGAGTCTCCT TACTCGAGTAAGGAGACTCAGAA GAAAGGTTTTTTG) |
The RNAi Consortium shRNA Library | TRCN0000127888 |
| shCD58-1 hairpin sequence (CCGGGCCTCACTATCTACAACTT AACTCGAGTTAAGTTGTAGATAGT GAGGCTTTTTG) | The RNAi Consortium shRNA Library | TRCN0000057543 |
| shCD58-2 hairpin sequence (CCGGGCGGTCATTCAAGACACG GGTCTCGAGATCTGTGTCTTGAAT GACCGCTTTTTG) |
The RNAi Consortium shRNA Library | TRCN0000057544 |
| shCD58-3 hairpin sequence (CCGGGTGCTGTATATGAATGGT ATTCTCGAGAATACCATTCATAT ACAGCACTTTTTG) | The RNAi Consortium shRNA Library | TRCN0000057545 |
| shCD58-4 hairpin sequence (CCGGGTGTTGTGTATGGGAATG TAACTCGAGTTACATTCCCATAC ACAACACTTTTTG) | The RNAi Consortium shRNA Library | TRCN0000057546 |
| shCD58-5 hairpin sequence (CCGGGCATTGACTAATGGAAGC ATTCTCGAGAATGCTTCCATTAGT CAATGCTTTTTG) | The RNAi Consortium shRNA Library | TRCN0000057547 |
| shCD58-6 hairpin sequence (CCGGACGTAACTCAACCAGTAT ATACTCGAGTATATACTGGTTGA GTTACGTTTTTTG) | The RNAi Consortium shRNA Library | TRCN0000312623 |
| shCD58-7 hairpin sequence (CCGGTACTCTTAGCAATCCATTA TTCTCGAGAATAATGGATTGCTA AGAGTATTTTTG) | The RNAi Consortium shRNA Library | TRCN0000312555 |
| shCD58-8 hairpin sequence (CCGGGAAGACAACAGCATAACT AAACTCGAGTTTAGTTATGCTGT TGTCTTCTTTTTG) | The RNAi Consortium shRNA Library | TRCN0000312624 |
| Plasmid: pCDH-CMV-MCS-EF1-Hygro | System Bioscience | CD515B-1 |
| Plasmid: pCDH-CMV-MCS-EF1-Puro | System Bioscience | CD510B-1 |
| Plasmid: pCDH-CMV-MCS-mPGK-Blast | This study | N/A |
| Plasmid: pMP71-CD33Hul95-CD28zCAR | This study | N/A |
| Plasmid: pCDH-Hygro-CD58 (ENST00000457047.6) | This study | N/A |
| Plasmid: pCDH-Puro-CMTM6 (ENST00000205636.4) | This study | N/A |
| Plasmid: pCDH-MART-1epi-2A-RFP | This study | N/A |
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| Software and algorithms | ||
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| Matlab | The MathWorks | RRID: SCR_001622 |
| FlowJo v10 | FlowJo, LLC | RRID: SCR_008520 |
| R (v 4.2.2) | R project | RRID: SCR_001905 |
| ggplot2 | Wickham | https://ggplot2.tidyverse.org |
| Graphpad prism | Dotmatics | RRID:SCR_002798 |
| Zeiss ZEN 3.7 | Zeiss | RRID:SCR_013672 |
| Image Lab V6.1 | Bio-rad | http://www.bio-rad.com/en-us/sku/1709690-image-lab-software; RRID:SCR_014210 |
| Riorender | Biorender | https://www.biorender.com/ |
| Image_ColorChannel_Intensity | This paper | Mendeley Data: https://doi.org/10.17632/zcky9dypsr.1 |
| Deposited data | ||
| Data generated in this study | This paper | Mendeley Data: https://doi.org/10.17632/zcky9dypsr.1 |