REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rat anti-human/mouse/rat CD3 (clone CD3-12)	Abcam	ab255972
Mouse anti-human CD8 (clone C8/144B)	Abcam	ab17147 (RRID:AB_443686)
Rabbit anti-human CD68 (clone EPR20545)	Abcam	ab213363 (RRID:AB_2801637)
Donkey anti-rat Alexa Fluor 647 (polyclonal)	ThermoFisher Scientific	A48272 (RRID:AB_2893138)
Donkey anti-mouse Alexa Fluor 488 (polyclonal)	ThermoFisher Scientific	A32766 (RRID:AB_2762823)
Donkey anti-rabbit Alexa Fluor 555 (polyclonal)	ThermoFisher Scientific	A32794 (RRID:AB_2762834)
Anti-human β2m PE (clone BBM.1)	Santa Cruz Biotech	sc-13565 (RRID:AB_626748)
Anti-human HLA-A,B,C PE (clone W6/32)	Biolegend	311406 (RRID:AB_314875)
Anti-human HLA-A,B,C APC (clone W6/32)	Biolegend	311410 (RRID:AB_314879)
Goat anti-mouse IgG PE (polyclonal)	Southern Biotech	1030-09 (RRID:AB_2794297)
Anti-human Fc block (clone Fc1)	BD Biosciences	564220 (RRID:AB_2728082)
Anti-human CD3 FITC (clone SK7)	Biolegend	344804 (RRID:AB_2043993)
Anti-human CD8 Brilliant Violet 785 (clone SK1)	Biolegend	344740 (RRID:AB_2566202)
Anti-human CD4 PerCP/Cy5.5 (clone SK3)	Biolegend	344608 (RRID:AB_1953236)
Anti-human CD28 (clone CD28.2)	BD Biosciences	555725 (RRID:AB_396068)
Anti-human CD49d (clone 9F10)	BD Biosciences	555501 (RRID:AB_2130052)
Human TruStain FcX	Biolegend	422302 (RRID:AB_2818986)
Anti-human CD8 FITC (clone SK1)	Biolegend	344704 (RRID:AB_1877178)
Anti-human CD3 Brilliant Violet 421 (clone SK7)	Biolegend	344834 (RRID:AB_2565675)
TotalSeq™-C0251 anti-human hashtag 1 (clone LNH-94, 2M2)	Biolegend	394661 (RRID:AB_2801031)
TotalSeq™-C0252 anti-human hashtag 2 (clone LNH-94, 2M2)	Biolegend	394663 (RRID:AB_2801032)
TotalSeq™-C0253 anti-human hashtag 3 (clone LNH-94, 2M2)	Biolegend	394665 (RRID:AB_2801033)
TotalSeq™-C0254 anti-human hashtag 4 (clone LNH-94, 2M2)	Biolegend	394667 (RRID:AB_2801034)
Anti-human CD11b Brilliant Violet 421 (clone ICRF44)	Biolegend	301324 (RRID:AB_11219589)
Anti-human CD19 PE/Dazzle594 (clone HIB19)	Biolegend	302252 (RRID:AB_2563560)
Anti-mouse TCRβ chain PE (clone H57-597)	Biolegend	109208 (RRID:AB_31343)
Anti-mouse TCRβ chain APC/Fire750 (clone H57-597)	Biolegend	109246 (RRID:AB_2629697)
Anti-human CD3 (clone OKT3)	Miltenyi	130-093-387 (RRID:AB_1036144)
Anti-human CD28 (clone 15E8)	Miltenyi	130-093-375 (RRID:AB_1036134)
Anti-human CD3 APC/Cy7 (clone SK7)	Biolegend	344818 (RRID:AB_10645474)
Anti-human CD279 (PD-1) PE (clone EH12.2H7)	Biolegend	329906 (RRID:AB_940483)
Anti-human CD366 (TIM-3) PE/Cy7 (clone F38-2E2)	Biolegend	345014 (RRID:AB_2561720)
Anti-human CD197 (CCR7) FITC (clone G043H7)	Biolegend	353216 (RRID:AB_10916386)
Anti-human CD45RA Brilliant Violet 421 (clone HI100)	Biolegend	304130 (RRID:AB_10965547)
Anti-human CD45RO Brilliant Violet 650 (clone UCHL1)	Biolegend	304232 (RRID:AB_2563462)
Anti-human CD3 Brilliant Violet 785 (clone SK7)	Biolegend	344842 (RRID:AB_2616891)
Anti-human IFNγ Alexa Fluor 647 (clone 4S.B3)	Biolegend	502516 (RRID:AB_493031)
Anti-human TNFα Brilliant Violet 605 (clone MAb11)	Biolegend	502936 (RRID:AB_2563884)
Anti-human CD69 PerCP/efluor710 (clone FN50)	ThermoFisher Scientific	46-0699-42 (RRID:AB_2573694)
Anti-human IL-2 PE (clone MQ1-17H12)	Biolegend	500307 (RRID:AB_315094)
FastImmune™ CD28/CD49d (clone L293, L25)	BD Biosciences	347690 (RRID:AB_647457)
LEGENDplex™ human Th panel detection antibodies	Biolegend	741041
Anti-human CD8a FITC (clone RPA-T8)	Biolegend	301006 (RRID:AB_314124)
Anti-mouse TCRβ chain APC (clone H57-597)	Biolegend	109212 (RRID:AB_313435)
Rabbit anti-GFP (polyclonal)	Rockland Immunochemicals	600-401-215 (RRID:AB_828167)
Goat anti-mCherry (polyclonal)	Biorbyt	orb11618 (RRID:AB_2687829)
Camelid anti-tagBFP Alexa Fluor 647 (clone 1H7)	Antibodies Online	ABIN6953244
Donkey anti-rabbit Alexa Fluor 488 (polyclonal)	ThermoFisher Scientific	A32790 (RRID:AB_2762833)
Donkey anti-goat Alexa Fluor 555 (polyclonal)	ThermoFisher Scientific	A32816 (RRID:AB_2762839)
Anti-human CD4 Alexa Fluor 700 (clone SK3)	Biolegend	344622 (RRID:AB_2563150)
Anti-human CD137 (4-1BB) APC (clone 4B4-1)	Biolegend	309810 (RRID:AB_830672)
Anti-human CD197 (CCR7) APC/Cy7 (clone G043H7)	Biolegend	353212 (RRID:AB_10916390)
Biological samples
FLC patient TILs (FLC-SJ1)	University of Maryland (approval #HP-00080263, Pro00008980)	N/A
FLC patient PBMCs (FLC-SJ1)	University of Maryland (approval #HP-00080263, Pro00008980)	N/A
FLC patient ascites fluid (FLC-SJ3)	University of Tennessee Health Science Center (approval #17-05064-XP, Pro00003992)	N/A
FLC patient tumor (FLC-SJ2, FLC-SJ4, FLC-SJ5)	Molecular Analysis of Solid Tumors (MAST, NCT01050296, approval #Pro00001240)	N/A
Healthy donor PBMCs	St. Jude Blood Donor Center (Dept. of Pathology protocol # BDC035)	N/A
Chemicals, peptides, and recombinant proteins
FBS	Gibco	16140–071
OCT embedding matrix	Sakura	4583
Vector® trueVIEW™ autofluorescence quenching reagent with DAPI	Vector	SP-8500-15
HLA class I easYmers	Immudex	Table S2
DNAJB1-PRKACA fusion peptides	Genscript	Table S2
Streptavidin beads, 6–8 μm	Spherotech	SVP-60-5
Lenti-X concentrator	Takara	631232
Puromycin	Sigma-Aldrich	P9620
G418	Gibco	10131–035
Protease inhibitor tablets	ThermoFisher Scientific	A32963
CaptivA® protein A resin	Repligen	CA-HF-0100
Human serum AB	Gemini BioProducts	100–512
Human IL-2	Stemcell Technologies	78036
X-VIVO 15 serum-free hematopoietic cell medium	Lonza	04-418Q
Human GM-CSF	Miltenyi Biotec	130-095-372
Human IL-4	R&D Systems	204-IL-010
Human Flt3-L	R&D Systems	308-FKN-025
R848	InvivoGen	tlrl-r848-5
Salmonella Minnesota lipopolysaccharide (LPS)	InvivoGen	tlrl-smlps
Human IL-1β	R&D Systems	201-LB-010
Human IL-2	R&D Systems	202-IL-050
Human IL-7	R&D Systems	207-IL-025
Human IL-15	PeproTech	200–15
Dasatinib	Sigma-Aldrich	CDS023389
Ghost Violet 510 viability dye	Tonbo Biosciences	13-080-T100
Collagenase IV	Worthington Biochemical	LS004188
DNase I	Worthington Biochemical	LS002145
TotalSeq™-C0954 PE streptavidin	Biolegend	405267
Human IL-7	PeproTech	200–07
Retronectin	Takara	T100A
PE streptavidin	Biolegend	405203
APC streptavidin	Biolegend	405207
Brilliant Violet 421 streptavidin	Biolegend	405226
PE/Cy7 streptavidin	Biolegend	405206
GolgiPlug (containing brefeldin A)	BD Biosciences	555029
GolgiStop (containing monensin)	BD Biosciences	554724
Cell stimulation cocktail	ThermoFisher Scientific	00-4970-93
LEGENDplex™ human IFNγ capture beads B3	Biolegend	740545
LEGENDplex™ human TNFα capture beads B7	Biolegend	740711
LEGENDplex™ human IL-2 capture beads A5	Biolegend	740934
Annexin V Brilliant Violet 421	Biolegend	640924 (RRID:AB_2893503)
Annexin V binding buffer	Biolegend	422201
Human IL-7	Biolegend	715302
Human IL-15	Biolegend	715902
NucView 530 caspase-3 substrate	Biotium	10408
LEGENDplex™ streptavidin-PE	Biolegend	740452
D-luciferin	Perkin Elmer	122799
Vectashield Vibrance® mounting media with DAPI	Vector	H-1800
Critical commercial assays
10x Chromium Single Cell 5′ Library & Gel Bead Kit v1	10x Genomics	1000006
10x Chromium Single Cell 5′ Library Construction Kit	10x Genomics	1000020
10x Chromium Single Cell V(D)J Enrichment Kit, Human T cell	10x Genomics	1000005
10x Chromium Single Cell Chip A Kit	10x Genomics	1000009
10x Chromium i7 Multiplex Kit	10x Genomics	120262
10x Chromium Single Cell 5′ Feature Barcode Library Kit	10x Genomics	1000080
10x Chromium i7 Multiplex Kit N Set A	10x Genomics	1000084
10x Chromium Next GEM Single Cell 5′ Library & Gel Bead Kit v1.1	10x Genomics	1000165
10x Chromium Next GEM Chip G Single Cell Kit	10x Genomics	1000127
10x Chromium Single Index Kit T Set A	10x Genomics	1000213
10x Chromium Single Index Kit N Set A	10x Genomics	1000212
SuperScriptVILO cDNA synthesis kit	ThermoFisher Scientific	11754250
In-Fusion® snap assembly cloning kit	Takara	638947
Cytofix/Cytoperm fixation kit	BD Biosciences	554714
Deposited data
Raw single-cell GEX and TCR data	This paper	SRA: PRJNA1070700
Immunopeptidomics data	This paper	PRIDE: PXD042316
FLC patient bulk RNAseq	Dinh et al.18	EGA: EGAS00001004169
FLC patient bulk RNAseq	Francisco et al.43	GEO: GSE181922
IPD-IMGT/HLA database	Barker et al.79	https://www.ebi.ac.uk/ipd/imgt/hla/
Uniprot annotated proteome UP000005640	Uniprot	https://www.uniprot.org/proteomes/UP000005640
Human HLA allele frequencies in US populations	Gonzalez-Galarza et al.44	http://allelefrequencies.net/hla.asp
Human reference genome GRCh38	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/
Cell Ranger human reference, GRCh38 (Ensembl 84)	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build
Cell Ranger human reference, GRCh38 (Ensembl 93)	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build
Cell Ranger human V(D)J reference vdj_IMGT_human	10x Genomics	N/A
Cell Ranger human V(D)J reference vdj_IMGT_human-None	10x Genomics	N/A
Cell Ranger human V(D)J reference vdj_GRCh38_alts_ensembl-3.1.0-3.1.0	10x Genomics	N/A
Single-chain TCR repertoire data from HCV-infected patient SR5	Mazouz et al.56	immuneACCESS: Mazouz_Shoukry_2021 https://clients.adaptivebiotech.com/pub/mazouz-2021-ji (https://doi.org/10.21417/SM2021JI)
Single-chain TCR repertoire data from SARS-CoV-2-infected donor M	Minervina et al.57	Zenodo: 4065547 https://zenodo.org/record/4065547
Single-chain TCR repertoire data from SARS-CoV-2-vaccinated donors 01a, 04, 20, 22	Mudd et al.54	GEO: GSE183393
IMGT/GENE-DB	Giudicelli et al.80	https://www.imgt.org/genedb/
Experimental models: Cell lines
HEK 293T	ATCC	Cat#: CRL-3216 (RRID:CVCL_0063)
K562	ATCC	Cat#: CCL-243 (RRID:CVCL_0004)
2D3 Jurkat	A kind gift from Fumihiro Fujiki (Osaka University Graduate School of Medicine, Suita, Japan)	N/A
A549.eGFP.ffLuc	A kind gift from Christopher DeRenzo (St. Jude Children’s Research Hospital, Memphis, TN)	N/A
W6/32 hybridoma	ATCC	HB-95 (RRID:CVCL_7872)
Experimental models: Organisms/strains
Mouse: NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)	St. Jude NSG colony	N/A
Oligonucleotides
Human TRAV/TRBV external primers	Wang et al.81	See Table S5
Human TRAC/TRBC external reverse primers	Wang et al.81	See Table S5
Human TRAV/TRBV internal forward primers	Wang et al.81	See Table S5
Human TRAC/TRBC internal reverse index primers	Wang et al.81	See Table S5
Recombinant DNA
pLVX-EF1α-IRES-Puro	Takara	631253
pSPAX2	A kind gift from Didier Trono	Addgene plasmid #12260 (RRID:Addgene_12260)
pMD2.G	A kind gift from Didier Trono	Addgene plasmid #12259 (RRID:Addgene_12259)
HLA class I sequences	Genscript	See “Generation of aAPCs” for alleles
TCRαβ sequences	Genscript	Table S4
pSFG	A kind gift from Stephen Gottschalk (St. Jude Children’s Research Hospital, Memphis, TN)	N/A
pEq-Pam3(-E)	A kind gift from Stephen Gottschalk (St. Jude Children’s Research Hospital, Memphis, TN)	N/A
pRD114	A kind gift from Stephen Gottschalk (St. Jude Children’s Research Hospital, Memphis, TN)	N/A
pLVX- EF1α-IRES-G418	This paper	N/A
Software and algorithms
NIS Elements software, version 5.30.05	Nikon Instruments	N/A
HLApers	Aguiar et al.82	github.com/genevol-usp/HLApers
kallisto	Bray et al.83	http://pachterlab.github.io/kallisto/
OptiType	Szolek et al.84	github.com/FRED-2/OptiType
NetMHCcons v1.1	Karosiene et al.85	https://services.healthtech.dtu.dk/services/NetMHCcons-1.1/
NetMHCpan v4.1b	Reynisson et al.45	https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/
NetMHCIIpan v4.1	Reynisson et al.45	https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.1/
FlowJo v10.7.2	BD Biosciences	https://www.flowjo.com/
PEAKs Xpro v10.6	Bioinformatic Solutions	N/A
Cell Ranger v2.2, v3.1.0, v4.0.0	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/release-notes
Seurat v4.2.0	Hao et al.86	https://satijalab.org/seurat/
conga v0.1.1 TCRdist implementation (tcrdist_cpp)	Schattgen et al.87	https://github.com/phbradley/conga
data.table R package v1.14.6	N/A	https://rdatatable.gitlab.io/data.table/
dplyr R package v1.1.0	N/A	https://dplyr.tidyverse.org
stringdist R package v0.9.10	N/A	https://github.com/markvanderloo/stringdist
igraph R package v1.3.5	N/A	https://r.igraph.org/
gephi v0.9.7	N/A	https://gephi.org/
stitchr Python package v1.0.2	Heather et al.88	https://github.com/JamieHeather/stitchr
RTCA Software Pro	Agilent	N/A
Prism v9	GraphPad	N/A
Assay Analyzer	Berkeley Lights	N/A
Living Image	Caliper Life Sciences	N/A
ggplot2 package v3.3.6	N/A	https://ggplot2.tidyverse.org/
rstatix package v0.7.0	N/A	https://github.com/kassambara/rstatix
Other
0.45 μm SFCA syringe filter	ThermoFisher Scientific	723–9945
Amicon 5 kDa MWCO filter	Millipore-Sigma	UFC8010
Omix C18 stage tips	Agilent	A5700310
96-well RTCA E-plate	Agilent	300600910