KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| CD45-BV510 | Biolegend | Cat# 368526, RRID: AB_2687377 |
| CD3-BV650 | Biolegend | Cat# 304044, RRID: AB_2563812 |
| CD8-PerCP-Cy5.5 | Biolegend | Cat# 344710, RRID: AB_2044010 |
| CD8-BV510 | Biolegend | Cat# 344732, RRID: AB_2564624 |
| PD-1-APC/Fire 750 | Biolegend | Cat# 329954, RRID: AB_2616721 |
| CD39-APC | Biolegend | Cat# 328210, RRID: AB_1953234 |
| CD39-PE/Cy7 | Biolegend | Cat# 328212, RRID: AB_2099950 |
| CD4-Alexa Fluor 700 | Biolegend | Cat# 357418, RRID: AB_2616933 |
| FOXP3-FITC | Invitrogen | Cat# 11-4776-42, RRID: AB_1724125 |
| CXCR5-PE | Biolegend | Cat# 356904, RRID: AB_2561813 |
| GITR-APC | Biolegend | Cat# 371206, RRID: AB_2616843 |
| CXCR4-PerCP-Cy5.5 | Biolegend | Cat# 306516, RRID: AB_10642818 |
| Anti-β2M-PE | Biolegend | Cat# 316306, RRID: AB_492839 |
| Human TruStain FcX™ Blocking Buffer | Biolegend | Cat# 422302, RRID: AB_2818986 |
| CD8 antibody for IHC | Dako | Cat# M7103, RRID: AB_2075537 |
| CD20 antibody for IHC | Thermofisher | Cat# PA5-16701, RRID: AB_10980806 |
| CD3 antibody for IHC | Abcam | Cat# ab16669, RRID: AB_443425 |
|
| ||
| Biological samples | ||
|
| ||
| Tumor tissue from NSCLC patients | Biospecimens from patients with informed consent at Memorial Sloan Kettering Cancer Center | This study |
|
| ||
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| RPMI | Corning | Cat# 10-041-CV |
| Human serum | Gemini Biosciences | Cat# 100-512-100 |
| Penicillin/streptomycin | Gibco | Cat# 15140122 |
| Amphotericin | Gibco | Cat# 15290026 |
| Glutamax | Gibco | Cat# 35050061 |
| Minimum essential amino acids | Millipore Sigma | Cat# M7145 |
| Sodium pyruvate | Gibco | Cat# 11360070 |
| Tumor Dissociation Kit, human | Miltenyi | Cat# 130-095-929 |
| EasySep™ Human CD8++ T Cell Isolation Kit | Stem Cell Technologies | Cat# 17953 |
| DNase I Solution (1 mg/mL) | Stem Cell Technologies | Cat# 100-0762 |
| AIM V Media | ThermoFisher Scientific | Cat# 12055083 |
| Gentamycin | Gibco | Cat# 15750078 |
| IL-2 | Peprotech | Cat# 200-02 |
| IL-7 | Peprotech | Cat# 200-07 |
| IL-15 | Peprotech | Cat# 200-15 |
| CEF MHC I Control Peptide Pool “Plus” | Jpt Peptide Technologies | Cat# PM-CEF-002 |
| Cell Trace Violet | Invitrogen | Cat# C34557 |
| Dynabeads™ Human T-Activator CD3/CD28 for T Cell Expansion and Activation | Invitrogen | Cat# 11132D |
| Bambanker Serum Free Cell Freezing Medium | Wako Chemicals | Cat# 101974-112 |
| Dapi, for nucleic acid staining | Sigma-Aldrich | Cat# D9542-50MG |
| LIVE/DEAD Violet | Invitrogen | Cat# L34955 |
| U-Load Dextramer® MHC I Kit (HLA-A*01:01, A*02:01, A*03:01, C*07:01) | Immudex | Custom Orders |
| Streptavidin Coated Polystyrene Particles, 6.0-8.0 μm | Spherotech | Cat# SVP-60-5 |
| Recombinant peptides (9-10mers) | Gensript | Custom Orders |
| Flex-T HLA-A*01:01 Monomer UVX | Biolegend | Cat# 280001 |
| Flex-T HLA-A*07:01 Monomer UVX | Biolegend | Cat# 280133 |
| TotalSeq™-C0951 PE Streptavidin | Biolegend | Cat# 405261 |
| TotalSeq™-C0952 PE Streptavidin | Biolegend | Cat# 405263 |
| TotalSeq™-C0953 PE Streptavidin | Biolegend | Cat# 405265 |
| TotalSeq™-C0954 PE Streptavidin | Biolegend | Cat# 405267 |
| TotalSeq™-C0955 PE Streptavidin | Biolegend | Cat# 405269 |
| TotalSeq™-C0961 PE Streptavidin | Biolegend | Cat# 405155 |
|
| ||
| Critical commercial assays | ||
|
| ||
| Chromium Chip A | 10X Genomics | Cat# PN-230027 |
| Next GEM Chip K | 10X Genomics | Cat# PN-1000286 |
| Chromium Single Cell 5′ Reagent Kit | 10X Genomics | Cat# PN-1000006 |
| Next GEM Single Cell 5′ Kit v2 | 10X Genomics | Cat# PN-1000263 |
| Chromium Single Cell V(D)J Enrichment Kit Human T Cell | 10X Genomics | Cat# PN-1000005 |
| Chromium Single Cell 5′ Feature Barcode Library Kit | 10X Genomics | Cat# PN-1000080 |
| NovaSeq 6000 SP Reagent Kit v1.5 | Illumina | Cat# 20028401 |
| NovaSeq 6000 S1 Reagent Kit v1.5 | Illumina | Cat# 20028319 |
| NovaSeq 6000 S4 Reagent Kit v1.5 | Illumina | Cat# 20028312 |
| NovaSeq 6000 S2 Reagent Kit v1.5 | Illumina | Cat# 20028316 |
| aMPure XP beads | Beckman Coulter | Cat# A63882 |
| AllPrep DNA/RNA Mini Kits | Qiagen | Cat# 80204 |
|
| ||
| Deposited data | ||
|
| ||
| This work (bulk TCR sequencing of longitudinal blood samples, MANAFEST experiments, and sorted multimer+ TILs) | Adaptive Biotechnologies ImmuneAccess | https://doi.org/10.21417/JAP2023CC URL: clients.adaptivebiotech.com/pub/pai-2023-cc |
| This work (scRNA/TCR-seq of resected biospecimens, multimer+ TILs) | NIH GEO | GSE185206 |
| Single cell data from neoadjuvant lung cancer trial | NIH GEO | GSE176021 |
| Single cell data from resection sample | DNA Data Bank of Japan | JGAS000480 |
|
| ||
| Software and algorithms | ||
|
| ||
| FlowJo | TreeStar | Version 10.8.1 |
| Prism | Graphpad | Version 9.0.0 |
| Halo | Indica Labs | Version 3.3.2541 |
| CiberSortx | Stanford | https://cibersortx.stanford.edu |
| R | R | Version 3.6.1 |
| Seurat | https://github.com/satijalab/seurat | Version 3.1.1 |
| CellRanger | 10X Genomics | Version 3.1.0 |
| CellRanger Multi | 10X Genomics | Version 7.0.0 |