KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| NKG2A – blocking antibody (20D5) | Innate Pharma | N/A |
| PD-1 – blocking antibody (clone RMP1–14, InvivoPlus) | BioXCell | BP0146; RRID: AB_10949053 |
| NK1.1 – depletion antibody (clone PK136, InvivoPlus) | BioXCell | BP0036; RRID: AB_1107737 |
| InVivoMAb anti-mouse IFNγR (CD119) (GR-20) | BioXcell | BE0029; RRID: AB_1107576 |
| Purified CD16/CD32 (2.4G2) | BD Pharmingen | Cat#: 553141; RRID: AB_394656 |
| NKG2A – PE (16a11) | eBioscience | Cat#: 12–5897–81; RRID: AB_466024 |
| CD94 – V450 (18d3) | eBioscience | Cat#: 48–0941–82; RRID: AB_11218905 |
| PD-1 – FITC (RMP1–30) | eBioscience | Cat#: 11–9981–82; RRID: AB_465467 |
| TIM-3 – APC (RMT3–23) | BioLegend | Cat#: 119706; RRID: AB_2561656 |
| Lag-3 – PE-Cy7 (eBioC9B7W) | eBioscience | Cat#: 16–2231–81; RRID: AB_494125 |
| CD45.1 – APC (A20) | BioLegend | Cat#: 110714; RRID: AB_313503 |
| CD45.2 – APC-Cy7 (104) | eBioscience | Cat#: 47–0454–82; RRID: AB_1272175 |
| CD3 – PE-CF594 (145–2C11) | BD Horizon | Cat#: 562286; RRID: AB 11153307 |
| CD4 – BV605 (RM4–5) | BioLegend | Cat#: 100547; RRID: AB_11125962 |
| CD8 – AF700 (53–6.7) | eBioscience | Cat#: 56–0081–82; RRID: AB_494005 |
| NK1.1 – BV650 (PK136) | BD Horizon | Cat#: 564143 |
| Qa-1 – biotin (6A8.6F10.1A6) | BD Pharmingen | Cat#: 559829; RRID: AB_397345 |
| Streptavidin – APC | eBioscience | Cat#: 17–4317–82 |
| Db – PE (28–14–8) | BioLegend | Cat#: 114507; RRID: AB_313588 |
| CD274 (PDL1) – BV421 (MIH5) | BD Horizon | Cat#: 564716 |
| IFN-γ – APC (XMG1.2) | BioLegend | Cat#: 505810; RRID: AB_315404 |
| CD8α – PE (53–6.7) | BioLegend | Cat#: 100708; RRID: AB_312747 |
| CD3 – V450 (UCHT1) | BD Biosciences | Cat#: 560365; RRID: AB_1645570 |
| CD8 – APC-Cy7 (SK1) | BD Biosciences | Cat#: 348813 |
| CD56 – AF700(B159) | BD Biosciences | Cat#: 557919; RRID: AB_396940 |
| CD4 – PE-CF594 (RPA-T4) | BD Biosciences | Cat#: 562281; RRID: AB_11154597 |
| CD94 – FITC (131412) | R&D Systems | Cat#: FAB1058F; RRID: AB_2133132 |
| TIM-3 – BV605 (F38–2E2) | BioLegend | Cat#: 345017; RRID: AB_2562194 |
| CD279 (PD-1) – PE-Cy7 (EH12.2H7) | BioLegend | Cat#: 329917; RRID: AB_2159325 |
| CD159a (NKG2A) – PE (Z199) | Beckman-Coulter | Cat#: IM3291U; RRID: AB_10643228 |
| CD103 – BV605 (Ber-ACT8) | BD Biosciences | Cat#: 350218 |
| CD45RO – BV786 (UCHL1) | BioLegend | Cat#: 304234; RRID: AB_2563819 |
| CCR7 – Pacific Blue (G043H7) | BioLegend | Cat#: 353210; RRID: AB_10918984 |
| CD127 – AF488(A019D5) | BioLegend | Cat#: 351314; RRID: AB_10898315 |
| KLRG-1 – PE/Dazzle594 (14C2A07) | BioLegend | Cat#: 368608; RRID: AB_2572135 |
| Perforin – PerCP/Cy5.5 (B-D48) | BioLegend | Cat#: 353314; RRID: AB_2571971 |
| Granzyme B – FITC (GB11) | BioLegend | Cat#: 515403; RRID: AB_2114575 |
| IFN-γ – PE/Dazzle594 (4S.B3) | BioLegend | Cat#: 502546; RRID: AB_2563627 |
| CTLA-4 – PerCP/Cy5.5 (BNI3) | BioLegend | Cat#: 369608; RRID: AB_2629674 |
| TIGIT – PE/Dazzle594 (A15153G) | BioLegend | Cat#: 372716; RRID: AB_2632931 |
| CD45 – 89Y (HI30) | Fluidigm | Prod#: 3089003B |
| CCR6 – 141Pr (G034E3) | Fluidigm | Prod#: 3141003A; RRID: AB_2687639 |
| NKG2A – 142Nd (Z199) | Beckman Coulter | Cat#: IM2750; RRID: AB_131495 |
| C-Kit – 143Nd (104D2) | Fluidigm | Prod#: 3143001B; RRID: AB_2687630 |
| CD11b – 144Nd (ICRF44) | Fluidigm | Prod#: 3144001B; RRID: AB_2714152 |
| CD4 – 145Nd (RPA-T4) | Fluidigm | Prod#: 3145001B; RRID: AB_2661789 |
| CD8a – 146Nd (RPA-T8) | Fluidigm | Prod#: 3146001B; RRID: AB_2687641 |
| Nkp44 – 147Sm (P44–8) | BioLegend | Cat#: 325102; RRID: AB_756094 |
| CD16 – 148Nd (3G8) | Fluidigm | Prod#: 3148004B; RRID: AB_2661791 |
| CD25 – 149Sm (2A3) | Fluidigm | Prod#: 3149010B |
| IgM – 150Nd* (MHM88) | BioLegend | Cat#: 314527 |
| CD123 – 151Eu (6H6) | Fluidigm | Prod#: 3151001B; RRID: AB_2661794 |
| TCRγ/δ – 152Sm (11F2) | Fluidigm | Prod#: 3152008B; RRID: AB_2687643 |
| CD7 – 153Eu (CD7–6B7) | Fluidigm | Prod#: 3153014B |
| CD163 – 154Sm (GHI/61) | Fluidigm | Prod#: 3154007B; RRID: AB_2661797 |
| CD103 – 155Gd* (Ber-ACT8) | BioLegend | Cat#: 350202 |
| CRTH2 – 156Gd* (BM16) | BioLegend | Cat#: 350102; RRID: AB_10639863 |
| CD122 – 158Gd* (TU27) | BioLegend | Cat#: 339015; RRID: AB_2563712 |
| CCR7 – 159Tb (G043H7) | Fluidigm | Prod#: 3159003A; RRID: AB_2714155 |
| CD14 – 160Gd (M5E2) | Fluidigm | Prod#: 3151009B |
| KLRG-1 – 161Dy* (REA261) | Miltenyi Biotech | N/A customized order |
| CD11c – 162Dy (Bu15) | Fluidigm | Prod#: 3162005B; RRID: AB_2687635 |
| CD20 – 163Dy* (2H7) | BioLegend | Cat#: 302343; RRID: AB_2562816 |
| CD’S’ – 164Dy (HP-3G10) | Fluidigm | Prod#: 3164009B; RRID: AB_2687651 |
| CD127 – 165Ho (A019D5) | Fluidigm | Prod#: 3165008B |
| CD8b – 166Er* (SIDI8BEE) | eBioscience | Cat#: 14–5273–82 |
| CD27 – 167Er (O323) | Fluidigm | Prod#: 3167002B |
| HLA-DR – 168Er* (L243) | BioLegend | Cat#: 307651; RRID: AB_2562826 |
| CD45RA – 169Tm (HI100) | Fluidigm | Prod#: 3169008B |
| CD3 – 170Er (UCHT1) | Fluidigm | Prod#: 3170001B; RRID: AB_2661807 |
| CD2B – 171Yb* (CD2B.2) | BioLegend | Cat#: 302937; RRID: AB_2563737 |
| CD3B – 172Yb (HIT2) | Fluidigm | Prod#: 3172007B |
| CD45RO – 173Yb* (UCHL1) | BioLegend | Cat#: 304239; RRID: AB_2563752 |
| NKp46 – 174Yb* (9E2) | BioLegend | Cat#: 331902; RRID: AB_1027637 |
| PD-1 – 175Lu (EH 12.2H7) | Fluidigm | Prod#: 3175008B; RRID: AB_2687629 |
| CD56 – 176Yb (NCAM16.2) | Fluidigm | Prod#: 3176008B; RRID: AB_2661813 |
| Bacterial and Virus Strains | ||
| Biological Samples | ||
| Human Head and Neck Squamous Cell Carcinoma (HNSCC) | Vanderbilt University Medical Center | IRB #030062, NCT00B9B63B |
| Oropharyngeal Squamous Cell Carcinoma (OPSCC) | Leiden University Medical Center | (Heusinkveld et al., 2012) (P07–112) |
| Cervical Carcinoma (CxCa) | Leiden University Medical Center | CIRCLE study (de Vos van Steenwijk et al., 2010) |
| Chemicals, Peptides, and Recombinant Proteins | ||
| H-2Db HPV16 E749−57 peptide (RAHYNIVTF) tetramer – APC | Peptide synthesis facility of department IHB, LUMC | |
| H-2Db MC38 Adpgk peptide (ASMTNMELM) tetramer – APC | Peptide synthesis facility of department IHB, LUMC | |
| H-2Db MC38 Dpagtl peptide (SIIVFNLL) tetramer – APC | Peptide synthesis facility of department IHB, LUMC | |
| H-2Db MC38 Repsl peptide (AQLANDVVL) tetramer – APC | Peptide synthesis facility of department IHB, LUMC | |
| LIVE/DEAD™ Fixable Yellow Dead Cell Stain Kit | Invitrogen™ | L34959 |
| Liberase™ TL Research Grade | Roche | 05401020001 |
| Concanavalin A (Type IV) | Sigma | C2010 |
| Phorbol myristate acetate | Sigma | P9139 |
| Recombinant IFN-γ | BioLegend | 57530B |
| GolgiPlug Protein transport inhibitor | BD Biosciences | 555029 |
| Lipofectamine™ 2000 Transfection Reagent | Invitrogen | 1166B027 |
| Permeabilization Buffer 10X | eBioscience | Cat#: 00-B333–56 |
| IC Fixation Buffer | eBioscience | Cat#: 00-B222–49 |
| Monensin Solution (1,000X) | BioLegend | Cat#: 420701 |
| Cell Stimulation Cocktail (500X) | Invitrogen | Cat#: 00–4970–93 |
| HPV16 E743–77 peptide (GQAEPDRAHYNIVTFCCKCDSTLRLCVQSTHVDIR) | Peptide synthesis facility of department IHB, LUMC | |
| short HPV16 E749–57 peptide (RAHYNIVTF) | Peptide synthesis facility of department IHB, LUMC | |
| human gp10020–39 peptide (AVGALKVPRNQDWLGVPRQL) | Peptide synthesis facility of department IHB, LUMC | |
| gp10025–33 peptide (EGSRNQDWL) | Peptide synthesis facility of department IHB, LUMC | |
| MC38 peptide Adpgk (PVHLELASMTNMELMSSIVHQ) | Peptide synthesis facility of department IHB, LUMC | |
| MC38 peptide Dpagt1 (EAGQSLVISASIIVFNLLELEGDYR) | Peptide synthesis facility of department IHB, LUMC | |
| MC38 peptide Reps1 (ELFRAAQLANDVVLQIMEL) | Peptide synthesis facility of department IHB, LUMC | |
| RMA Env-encoded CD4 T cell epitope (EPLTSLTPRCNTAWNRLKL) | Peptide synthesis facility of department IHB, LUMC | |
| RMA Gag-encoded CD8 T cell epitope (CCLCLTVFL) | Peptide synthesis facility of department IHB, LUMC | |
| human recombinant IL-2 (Proleukin® 18 × 106 IE) | Novartis | RVG 13354 |
| Aldara™ 5% crème (Imiquimod) | MEDA Pharma B.V | Cat#: 620362216 |
| CpG (ODN 1826) | Invivogen | Cat#: tlrl-1826 |
| Incomplete Freunds Adjuvant (IFA; Difco) | BD | Cat#: 263910 |
| Critical Commercial Assays | ||
| Tumor Dissociation Kit, human | Milteny Biotec | 130–095–929 |
| gentleMACS™ Octo Dissociator | Milteny Biotec | 130–095–937 |
| mouse CD3ɛ MicroBead kit | Milteny Biotec | 130–094–973 |
| Deposited Data | ||
| The Cancer Genome Atlas (TCGA) | Firehose, The Broad Institute | https://portal.gdc.cancer.gov/ |
| Experimental Models: Cell Lines | ||
| TC-1 | Provided by Prof. T.C. Wu (John Hopkins University, Baltimore, USA) | RRID: CVCL_4699 |
| B16F10 | ATCC | CRL-6475; RRID: CVCL 0159 |
| RMA | Provided by Prof. K. Kärre (Karolinska Institute, Stockholm, Sweden) | RRID: CVCL_J385 |
| MC38 | Provided by Prof. Marco Colonna (Washington University School of Medicine, St. Louis, USA) | RRID: CVCL_B288 |
| R1 | Provided by Prof. Paola Ricciardi- Castagnoli | |
| KPC | Provided by Dr. Thorsten Hagemann, Queen Mary University of London | |
| Experimental Models: Organisms/Strains | ||
| Mouse: Qa-1b−/− (targeted mutation of the H2-T23 gene) | Jackson Laboratory; provided by Dr. M. Vocanson (Lyon, France) | Stock#: 007907; RRID: IMSR_JAX:007907 |
| Mouse: TCR transgenic mice gp10025–33/H-2Db bred to express congenic marker CD45.1 (Ly5.1) | Provided by Dr. N.P. Restifo (NIH, Bethesda, USA) | |
| Mouse: C57BL/6 | Charles River Laboratories France | |
| Oligonucleotides | ||
| sgRNA sequence for Qa-1: 5’-GGCTATGTCATTCGCGGTCC-3’ | This paper | N/A |
| Recombinant DNA | ||
| sgRNA expression vector | Addgene | 41824 |
| plasmid containing Cas9 WT | Addgene | 41815 |
| Software and Algorithms | ||
| R version 3.4.2 (package survival) | R Project | https://www.r-proiect.org; RRID:SCR_001905 |
| The Cancer Genome Atlas (TCGA) | Firehose, The Broad Institute | https://portal.gdc.cancer.gov/ |
| GraphPad Prism v7 | GraphPad | https://www.graphpad.com/scientificsoftware/prism; RRID: SCR_002798 |
| FlowJo v10 | TreeStar | https://www.flowjo.com/solutions/flowjo; RRID: SCR_008520 |
| CRISPR gRNA Design | Zhang Lab, MIT | http://crispr.mit.edu |
| Cytobank | Cytobank | https://www.cytobank.org/; RRID:SCR_014043 |
| Other | ||
*
Custom metal conjugation