KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Y(89)-anti-Lag3 (Clone C9B7W) | Biolegend | Cat# 125202; AB_961187 |
| 115In-anti-Ly6C (Clone HK14) | Biolegend | Cat#128001; RRID: AB_1134213 |
| 141Pr-anti-CD44 (Clone IM7) | Biolegend | Cat#103001; RRID: AB_312952 |
| 142Nd-anti-CXCR5 (Clone L138D7) | Biolegend | Cat#145502; RRID: AB_2561955 |
| 142Nd-anti-Siglec-F (Clone E50-2440) | BD Biosciences | Cat#552125; RRID: AB_394340 |
| 143Nd-anti-IRF2 (EPR4644(2)) | Abcam | Cat#ab229443; RRID: NA |
| 144Nd-anti-Granzyme B (Clone GB11) | ThermoFisher | Cat#MA1-80734; RRID: AB_931084 |
| 145Nd-anti-CTLA-4 (Clone UC10-4B9) | Biolegend | Cat#106302; RRID: AB_313251 |
| 146Nd-anti-EOMES (Clone Dan11mag) | eBioscience | Cat#14-4875-82; RRID: AB_11042577 |
| 147Sm-anti-CD45.2 (Clone 104) | Biolegend | Cat#109802; RRID: AB_313439 |
| 148Nd-anti-CD11b (Clone M1/70) | Fluidigm | Cat#3148003B; RRID: AB_2814738 |
| 148Nd-anti-ICOS (Clone C398.4A) | Fluidigm | Cat#3148019B; RRID: AB_2756435 |
| 149Sm-anti-CD69 (Clone H1.273) | Biolegend | Cat#104502; RRID: AB_313105 |
| 150Nd-anti-Ly6G (Clone 1A8) | Biolegend | Cat#127601; RRID: AB_1089179 |
| 150Nd-anti-CD73 (Clone TY/11.8) | Biolegend | Cat#127202; RRID: AB_1089066 |
| 151Eu-anti-CD25 (Clone 3C7) | Fluidigm | Cat#3151007B; RRID: AB_2827880 |
| 152Sm-anti-CD86 (Clone GL-1) | Biolegend | Cat#105007; RRID: AB_313150 |
| 153Eu-anti-CD8a (Clone 53-6.7) | Fluidigm | Cat#3153012B; RRID: AB_2885019 |
| 153Eu-anti-CD45.1 (Clone A20) | Fluidigm | Cat#3153002B; RRID:AB_268784 |
| 154Sm-anti-BATF (Clone D7C5) | Fluidigm | Cat#3154012A; RRID: AB_2687838 |
| 155Gd-anti-CD103 (Clone 2 × 107) | Biolegend | Cat#121401; RRID: AB_535944 |
| 155Gd-anti-CD103 (Clone M290) | BD Biosciences | Cat#553699; RRID: AB_394995 |
| 156Gd-anti-PD-L1 (Clone M1H5) | eBioscience | Cat#14-5982-82; RRID: AB_467781 |
| 158Gd-anti-RORɣt (Clone Q31-378) | BD Biosciences | Cat#562197; RRID: AB_10894594 |
| 159Tb-anti-CD39 (Clone 24DMS1) | eBioscience | Cat#14-0391-82; RRID: AB_1210501 |
| 160Gd-anti-CD4 (Clone rm4-5) | Biolegend | Cat#100505; RRID: AB_312708 |
| 161Dy-anti-T-bet (Clone 4B10) | Fluidigm | Cat#3161014B; RRID: AB_2858233 |
| 162Dy-anti-Foxp3 (Clone MF-14) | Biolegend | Cat#126401; RRID: AB_1089120 |
| 163Dy-anti-Tim-3 (Clone B8.2C12) | Biolegend | Cat#134002; RRID: AB_1626128 |
| 163Dy-anti-Bcl6 (Clone K112.91) | BD Biosciences | Cat#561520; RRID: AB_10713172 |
| 164Dy-anti-CD62L (Clone MEL-14) | Fluidigm | Cat#3164003B; RRID: AB_2885021 |
| 165Ho-anti-TCRb (Clone H57-597) | Biolegend | Cat#109201; RRID: AB_313424 |
| 166Er-anti-B220 (Clone RA3-6B2) | Invitrogen | Cat#14-0452-82; RRID: AB_467254 |
| 166Er-anti-Blimp1 (Clone ROS195G) | Biolegend | Cat# 648202; RRID:AB_2300132 |
| 167Er-anti-TCF-1 (Clone S33-966) | BD Biosciences | Cat#624084; RRID: NA |
| 168Er-anti-Bcl6 (Clone K112.91) | BD Biosciences | Cat#561520; RRID: AB_10713172 |
| 168Er-anti-PKR (Clone EPR19374) | Abcam | Cat#ab224887; RRID:N/A |
| 169Tm-anti-SLAM (Clone TC15-12F12.2) | Biolegend | Cat#115901; RRID: AB_313680 |
| 170Er-anti-NK1.1 (Clone PK136) | Fluidigm | Cat#3170002B; RRID: AB_2885023 |
| 171Yb-anti-CD80 (Clone 16-10A1) | Fluidigm | Cat#3171008B; RRID: AB_2885024 |
| 172Yb-anti-Ki67 (Clone B56) | BD Biosciences | Cat#550609; RRID: AB_393778 |
| 173Yb-anti-Helios (Clone 22F6) | Biolegend | Cat#137202; RRID: AB_10900638 |
| 174Yb-anti-CD11c (Clone N418) | Biolegend | Cat#117301; RRID: AB_313770 |
| 174Yb-anti-Lag3 (Clone C9B7W) | Fluidigm | Cat#3174019B; RRID:N/A |
| 175Lu-anti-PD1 (Clone RMP-30) | Biolegend | Cat#109101; RRID: AB_313418 |
| 176Yb-anti-Thy1.2 (Clone 53-21) | ThermoFisher | Cat#14-0902-82; RRID: AB_467379 |
| 209Bianti-MHC II (Clone M5/114.15.2) | Fluidigm | Cat#3209006B; RRID: AB_2885025 |
| Y(89)-anti-human CD45 (Clone HI30) | Fluidigm | Cat#3089003B; RRID:N/A |
| Cd(111)-anti-human CD80 (Clone BB1) | BD Biosciences | Cat#555681; RRID:AB_396033 |
| Cd(112)-anti-human CD45RO (Clone UCHL1) | Biolegend | Cat#304202; RRID: AB_314418 |
| Cd(114)-anti-human Helios (Clone 22F6) | Biolegend | Cat#137202; RRID:AB_10900638 |
| In(115)-anti-human SOCS1 (Clone 4H1) | EMD Millipore | Cat#04-002; RRID:AB_612104 |
| In(116)-anti-human Ki67 (Clone Ki-67) | Biolegend | Cat#350502; RRID:AB_10662385 |
| Pr(141)-anti-human CD45RA (Clone HI100) | Biolegend | Cat#304102; RRID:AB_314406 |
| ND(142)-anti-human HLA-DR (Clone L243) | Biolegend | Cat#307602; RRID:AB_314680 |
| ND(143)-anti-IRF2 (Clone EPR4644(2)) | Abcam | Cat#ab229443; RRID:N/A |
| ND(144)-anti-human CD33 (Clone WM53) | Biolegend | Cat#303402; RRID:AB_314346 |
| ND(145)-anti-human CXCR3 (Clone G025H7) | Biolegend | Cat#353706; RRID:AB_10962912 |
| ND(146)-anti-human CD8a (Clone RPA-T8) | Biolegend | Cat#301053; RRID:AB_2562810 |
| Sm(147)-anti-human CD4 (Clone RPA-T4) | Biolegend | Cat#300541; RRID:AB_2562809 |
| ND(148)-anti-human ICOS (Clone DX29) | BD Biosciences | Cat#557801; RRID:AB_396877 |
| Sm(149)-anti-human FoxP3 (Clone 236A-E7) | ThermoFisher | Cat#14-477782; RRID:AB_467556 |
| ND(150)-anti-human CD103 (Clone B-Ly7) | ThermoFisher | Cat#14-103882; RRID:AB_467412 |
| Eu(151)-anti-human CD39 (Clone A1) | Biolegend | Cat#328221; RRID:AB_2563747 |
| Sm(152)-anti-human CD11c (Clone Bu15) | Biolegend | Cat#337221; RRID:AB_2562834 |
| Eu(153)-anti-human CD3 (Clone UCHT1) | Biolegend | Cat#300443; RRID:AB_2562808 |
| Gd(155)-anti-human CD303 (Clone 201A) | Biolegend | Cat#354215; RRID:AB_2563739 |
| Gd(156)-anti-human CD14 (Clone M5E2) | Biolegend | Cat#301843; RRID:AB_2562813 |
| Gd(158)-anti-human CD27 (Clone O323) | Biolegend | Cat#302839; RRID:AB_2562817 |
| Tb(159)-anti-human CD19 (Clone HIB19) | Biolegend | Cat#302247; RRID:AB_2562815 |
| Gd(160)-anti-human CD25 (Clone M-A251) | Biolegend | Cat#356102; RRID:AB_2561752 |
| Dy(161)-anti-human Tbet (Clone 4B10) | Biolegend | Cat#644802; RRID:AB_1595503 |
| Dy(162)-anti-human CD28 (Clone CD28.2) | Biolegend | Cat#302937; RRID:AB_2563737 |
| Dy(163)-anti-human CD137 (Clone 4B4-1) | Biolegend | Cat#309802; RRID:AB_314781 |
| Dy(164)-anti-human CD86 (Clone 2331) | BD Biosciences | Cat#555655; RRID:AB_396010 |
| Ho(165)-anti-human PD1 (Clone EH12.2H7) | Biolegend | Cat#329941; RRID:AB_2563734 |
| Er(166)-anti-human Tim3 (Clone F38-2E2) | Biolegend | Cat#345019; RRID:AB_2563790 |
| Er(167)-anti-human PKR (Clone 6H3A10) | Novus Biological | Cat#NBP2-37242; RRID:N/A |
| Er(168)-anti-human CD73 (Clone AD2) | Biolegend | Cat#344002; RRID:AB_2154067 |
| Tm(169)-anti-human CTLA4 (Clone 14D3) | ThermoFisher | Cat#14-152982; RRID:AB_467512 |
| Er(170)-anti-human CD317 (Clone RS38E) | Biolegend | Cat#348402; RRID:AB_10588013 |
| Yb(171)-anti-human Granzyme B (Clone GB11) | ThermoFisher | (Special order) |
| Yb(172)-anti-human CD127 (Clone EBioRDR5) | ThermoFisher | Cat#14-1278-8; RRID:N/A |
| Yb(173)-anti-human NKP46 (Clone 9 × 102) | Biolegend | Cat#331902; RRID:AB_1027637 |
| Yb(174)-anti-human TCF-1 (Clone S33-966) | BD Biosciences | (Special order) |
| Lu(175)-anti-human CD274 (Clone 29E.2A3) | Biolegend | Cat#329719; RRID:AB_2565429 |
| Yb(176)-anti-human Lag3 (Clone 7H2C65) | Biolegend | Cat#369202; RRID:AB_2616877 |
| Bi(209)-anti-human CD11b (Clone ICRF44) | Fluidigm | Cat#3209003B; RRID:N/A |
| APC anti-mouse/human CD11b (clone M1/70) | Biolegend | Cat#101211; RRID: AB_312794 |
| APC/Fire 750 anti-mouse CD11c (clone N418) | Biolegend | Cat#117351; RRID: AB_2572123 |
| Brilliant Violet 421 anti-mouse CD11c (clone N418) | Biolegend | Cat#117343; RRID: AB_2563099 |
| PerCP/Cyanine5.5 anti-mouse CD45.1 (clone A20) | Biolegend | Cat#110728; RRID:AB_893346 |
| APC anti-mouse CD45.2 (clone 104) | Biolegend | Cat#109814; RRID:AB_389211 |
| PerCP/Cyanine5.5 anti-mouse CD45.2 (clone 104) | Biolegend | Cat#109828; RRID:AB_893350 |
| APC/Fire 750 anti-mouse CD4 (clone GK1.5) | Biolegend | Cat#100459; RRID: AB_2572110 |
| Brilliant Violet 605 anti-mouse CD4 (clone GK1.5) | Biolegend | Cat#100547; RRID:AB_11125962 |
| Brilliant Violet 711 anti-mouse CD8α (clone 53-6.7) | Biolegend | Cat#100747; RRID:AB_11219594 |
| PerCP/Cyanine5.5 anti-mouse CD8α (clone 53-6.7) | Biolegend | Cat#100734; RRID:AB_2075238 |
| PerCP/Cyanine5.5 anti-mouse B220 (clone RA3-6B2) | Biolegend | Cat#103236; RRID:AB_893354 |
| Alexa Fluor 700 anti-mouse B220 (clone RA3-6B2) | Biolegend | Cat#103231; RRID:AB_493716 |
| Brilliant Violet 421 anti-mouse Tcrβ (clone H57-597) | Biolegend | Cat#109229; RRID:AB_10933263 |
| PerCP/Cyanine5.5 anti-mouse Tcrβ (clone H57-597) | Biolegend | Cat#109228; RRID:AB_1575173 |
| Brilliant Violet 421 anti-mouse FoxP3 (clone MF-14) | Biolegend | Cat#126419; RRID:AB_2565933 |
| Alexa Fluor 488 anti-mouse FoxP3 (clone MF-14) | Biolegend | Cat#126406; RRID:AB_1089113 |
| PerCP/Cyanine5.5 anti-mouse NK1.1 (clone PK136) | Biolegend | Cat#108728; RRID:AB_2132705 |
| Pacific Blue anti-mouse Ly6C (clone HK1.4) | Biolegend | Cat#128014; RRID:AB_1732079 |
| PerCP/Cyanine5.5 anti-mouse Ly6G (clone 1A8) | Biolegend | Cat#127616; RRID:AB_1877271 |
| FITC anti-mouse Granzyme B (clone GB11) | Biolegend | Cat#515403; RRID:AB_2114575 |
| Pacific Blue anti-mouse Granzyme B (clone GB11) | Biolegend | Cat#515407; RRID:AB_2562195 |
| PE anti-mouse TCF1 (clone S33-966) | BD Bioscience | Cat#564217; RRID:AB_2687845 |
| APC anti-mouse Tbet (clone 4B10) | Biolegend | Cat#644814; RRID:AB_10901173 |
| FITC anti-mouse Ki67 (clone 35/Ki-67RUO) | BD Bioscience | Cat#556026; RRID:AB_396302 |
| FITC anti-mouse CD44 (clone IM7) | Biolegend | Cat#103006; RRID:AB_312957 |
| Brilliant Violet 421 anti-mouse CD25 (clone PC61) | Biolegend | Cat#102043; RRID:AB_2562611 |
| PECy7 anti-mouse CD62L (clone MEL-14) | Biolegend | Cat#104418; RRID:AB_313103 |
| Brilliant Violet 421 anti-mouse PDL1 (clone 10F.9G2) | Biolegend | Cat#124315; RRID:AB_10897097 |
| PECy7 anti-mouse CD39 (clone (24DMS1) | eBioscience | Cat#25-0391-82; RRID:AB_1210766 |
| APC anti-mouse Lag3 (clone C9B7W) | Biolegend | Cat#125210; RRID:AB_10639727 |
| Brilliant Violet 786 anti-mouse PD1 (clone 29F.1A12) | Biolegend | Cat#135225; RRID:AB_2563680 |
| PE anti-mouse Tox (clone txrx10) | eBioscience | Cat#12-6502-82; RRID:AB_10855034 |
| PE anti-mouse BATF (clone D7C5) | Cell Signaling | Cat#27120; RRID:AB_2798938 |
| PE anti-mouse IRF4 (clone IRF4.3 × 104) | Biolegend | Cat#646403; RRID:N/A |
| Alexa Fluor 488 anti-mouse IRF1 (clone D5E4) | Cell Signaling | Cat#14028; RRID:AB_2798366 |
| PE anti-mouse IRF1 (clone D5E4) | Cell Signaling | Cat#12732; RRID:AB_2798008 |
| PE anti-mouse IRF7 (clone MNGPKL) | eBioscience | Cat#12-5829-80; RRID:AB_2572628 |
| anti-mouse PKR (clone EPR19374) | Abcam | Cat#ab184257; RRID:AB_2916271 |
| Alexa Fluor 647 anti-mouse Stat1 (clone 1/stat1) | BD Bioscience | Cat#558560; RRID:AB_647143 |
| Alexa Fluor 647 anti-mouse Blimp1 (clone 5 × 107) | Biolegend | Cat#150004; RRID:AB_2565618 |
| PE anti-mouse Blimp1 (clone 5 × 107) | Biolegend | Cat#150005; RRID:AB_2565991 |
| Alexa Fluor 647 donkey anti-Rabbit IgG (clone Poly4064) | Biolegend | Cat#406414; RRID:AB_2563202 |
| anti-IRF2 antibody (clone [EPR4644(2)]) | Abcam | Cat#ab124744; RRID:AB_10974405 |
| APC anti-mouse IFNγ (clone XMG1.2) | Biolegend | Cat#505810; RRID:AB_315404 |
| Brilliant Violet TNFα anti-mouse (clone MP6-XT22) | Biolegend | Cat#506328; RRID:AB_2562902 |
| InVivoMAb anti-mouse IFNAR-1 (clone MAR1-5A3) | BioXcell | Cat#BE0241; RRID:AB_2687723 |
| InVivoMAb anti-mouse IFNγ (clone XMG1.2) | BioXcell | Cat#BE0055; RRID:AB_1107694 |
| InVivoMAb anti-mouse PDL1 (clone 10F.9G2) | BioXcell | Cat#BE0101; RRID:AB_10949073 |
| InVivoMAb anti-mouse CD8α (clone 2.43) | BioXcell | Cat#BE0061; RRID:AB_1125541 |
| InVivoMAb anti-mouse CD4 (clone GK1.5) | BioXcell | Cat#BE0003; RRID:AB_1107642 |
| InVivoMAb rat IgG2b isotype control (clone LTF-2) | BioXcell | Cat#BE0090; RRID:AB_1107780 |
| InVivoMAb IgG1 isotype control (clone MOPC-21) | BioXcell | Cat#BE0083; RRID:AB_1107784 |
| Ms CD4 Olgo AMM2056 (clone GK1.5) | BD Bioscience | Cat#940471; RRID:AB_2876318 |
| Ms CD8b Olgo AMM2189 (clone H35-17.2) | BD Bioscience | Cat#940360; RRID:AB_2876231 |
| Ms TCRβ CHN Olgo AMM2021 (clone H57-597) | BD Bioscience | Cat#940125, RRID:AB_2876014 |
| Ms CD3e Olgo AMM2001 (clone 145-2C11) | BD Bioscience | Cat#940107; RRID:AB_2875997 |
| Biological samples | ||
| Human melanoma samples | Princess Margaret Cancer Biobank | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Cell-ID Cisplatin | Fluidigm | Cat#201064 |
| Cell-ID Intercalator-Iridium—125 mM | Fluidigm | Cat#201192A |
| Zombie Aqua Fixable Viability Kit | Biolegend | Cat#423102 |
| Mouse IL-2 Recombinant Protein | GIBCO | Cat#PMC0025 |
| Brefeldin A | Sigma | Cat#B7651-5MG |
| DNase I | Sigma | Cat#DN25-1G |
| Cisplatin | BioVision | Cat#1550 |
| Collagenase I | ThermoFisher | Cat#17018029 |
| Fixation Buffer | Biolegend | Cat#420801 |
| Intracellular Staining Permeabilization Wash Buffer (10X) | Biolegend | Cat#421002 |
| Foxp3/Transcription Factor Staining Buffer Set | eBioscience | Cat#00-5523-00 |
| EasySep Mouse CD8+ T cell Isolation Kit | STEMCELL | Cat#19853 |
| 20-Plex Pd Barcoding Kit | Fluidigm | Cat#201060 |
| Mouse CD45+ (TIL) Microbeads | Miltenyi Biotec | Cat#110-021-618 |
| Fc block | ThermoFisher | Cat#16-9161-73 |
| Recombinant mouse IFNβ | R & D Systems | Cat#12401-1 |
| Deposited data | ||
| ATAC-seq data from human tumor-infiltrating PD1+ CD8+ T cells | (Philip et al., 2017) | GEO accession#: GSE89308 |
| Transcriptional features of Tox-deficient CD8+ T cells | Khan et al., (2019) | GEO accession#: GSE131871 |
| CUT&TAG | This manuscript | GEO accession#: GSE199177 |
| scATAC-Seq | This manuscript | GEO accession#: GSE199177 |
| scRNA-Seq | This manuscript | GEO accession#: GSE199177 |
| Original codes | This manuscript | https://github.com/diala-ar/BrooksLab |
| Experimental models: Cell lines | ||
| MMTV-PyMT cell line | Dr. Christopher PAGE (University Health Network) | N/A |
| PyMG tumor cells | Generated by our lab | N/A |
| B16-F10 tumor cells | Dr. Tracy McGaha (University Health Network) | N/A |
| MC38 tumor cells | Dr. Daniel de Carvalho (University Health Network) | N/A |
| MC38-GP cells | Generated by our lab | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J mice | Jackson laboratory | Cat#000664 |
| LCMV-GP33-specific CD8 TCR transgenic (P14) mice | Bred in our facility | N/A |
| Mouse: Irf2−/− | Provided by Dr. Tak Mak at the University Health Network (Matsuyama et al., 1993), and bred in our facility | N/A |
| Mouse: Irf2+/+ | Bred in our facility | N/A |
| Irf2fll/fl mice | generated and bred in our facility | N/A |
| CD8α-Cre (E8iii-Cre) transgenic mice (C57BL/6-Tg(CD8α-cre)1Itan/J, Stock No. 008766 | The Jackson Laboratory | Stock no. 008766 |
| Software and algorithms | ||
| Flow Jo version 9 and 10 | BD FLOWJO | http://www.flowjo.com/ |
| BD FACSsuite v1.4.0.7047 | BD Biosciences | https://www.bdbiosciences.com/ |
| Cytobank | Cytobank, Inc | https://www.cytobank.org |
| Graphpad Prism v8 and v9 | GraphPad Software, Inc | https://www.graphpad.com/ |
| R | R Core Team | https://www.r-project.org/ |
| UMAP | (McInnes et al., 2018) | RRID:SCR_018217 |
| PhenoGraph | (Levine et al., 2015) | RRID:SCR_016919 |
| diffcyt R | (Weber et al., 2019) | https://bioconductor.org/packages/release/bioc/html/diffcyt.html |
| HOMER v4.8 findMotifsGenome.pl | (Duttke et al., 2019) | N/A |
| Bedtools v2.27.1 getfasta tool | (Quinlan and Hall, 2010) | N/A |
| Ingenuity Pathway Analysis software | Qiagen | N/A |
| Cytoscape | (Shannon et al., 2003) | N/A |
| SeqGeq software | BD Biosciences | N/A |
| BD RhapsodyTM WTA Analysis pipeline | BD Biosciences | https://www.sevenbridges.com |
| SEACR v1.3 | (Meers et al., 2019) | https://github.com/FredHutch/SEACR |
| bowtie v2.4.1 | https://bowtie-bio.sourceforge.net/index.shtml | |
| cellranger-atac count (v 2.0.0) | 10X genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| Integrative genomics viewer (IGV) | https://igv.org/ | |