REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD26 (BA5b)	BioLegend	Cat# 302702, RRID:AB_314286
CD4 (RPA-T4)	Fluidigm	Cat# 3145001B, RRID:AB_2661789
CCR6 (G034E3)	Fluidigm	Cat# 3141003A, RRID:AB_2687639
CD11a (HI111)	Fluidigm	Cat# 3142006B, RRID:AB_2877095
CD45RA (HI100)	Fluidigm	Cat# 3143006B, RRID:AB_2651156
CD11c (Bu15)	Fluidigm	Cat# 3147008B, RRID:AB_2687850
CD16 (3G8)	Fluidigm	Cat# 3148004B, RRID:AB_2661791
CD62L (DREG56)	Fluidigm	Cat# 3153004B, RRID:AB_2810245
TIM3 (F38-2E2)	Fluidigm	Cat# 3154010B, RRID:AB_2893002
CXCR3 (G025H7)	Fluidigm	Cat# 3156004B, RRID:AB_2687646
CCR4 (L291H4)	Fluidigm	Cat# 3158032A, RRID:AB_2893003
CCR7 (G043H7)	Fluidigm	Cat# 3159003A, RRID:AB_2714155
CD28 (CD28.2)	Fluidigm	Cat# 3160003B, RRID:AB_2868400
CTLA4 (14D3)	ThermoFisher	Cat# 14-1529-82, RRID:AB_467512
FoxP3 (PCH101)	Fluidigm	Cat# 3162011A, RRID:AB_2687650
CD45RO (UCHL1)	Fluidigm	Cat# 3165011B, RRID:AB_2756423
CD57 (HCD57)	Fluidigm	Cat# 3172009B, RRID:AB_2888930
HLA-DR (L243)	Fluidigm	Cat# 3173005B, RRID:AB_2810248
CD94 (HP3D9)	Fluidigm	Cat# 3174015B, RRID:AB_2756429
CD127 (A019D5)	Fluidigm	Cat# 3176004B, RRID:AB_2687863
CD27 (L128)	Fluidigm	Cat# 3155001B, RRID:AB_2687645
CD44 (BJ18)	Fluidigm	Cat# 3166001B, RRID:AB_2744692
CD11b (ICRF44)	Fluidigm	Cat# 3209003B, RRID:AB_2687654
CD38 (HIT2)	Fluidigm	Cat# 3167001B, RRID:AB_2802110
Ki-67 (B56)	Fluidigm	Cat# 3168007B, RRID:AB_2800467
PD-1 (EH12.2H7)	Fluidigm	Cat# 3175008B, RRID:AB_2687629
ICOS (C398.4A)	Fluidigm	Cat# 3168024B, RRID:AB_2858237
Pan Cytokeratin antibody [AE1/AE3]	Abcam	Cat# ab27988, RRID:AB_777047
PTEN antibody	GeneTex	Cat# GTX101025, RRID:AB_1241223
JAK2 antibody [EPR108(2)]	Abcam	Cat# ab108596, RRID:AB_10865183
YAP1 antibody [EP1674Y]	Abcam	Cat# ab52771, RRID:AB_2219141
MDM2 (D1V2Z) antibody	Cell Signaling Technology	Cat# 86934, RRID:AB_2784534
Goat Anti-Mouse IgG (H+L) Highly Cross-adsorbed Antibody, Alexa Fluor 488 Conjugated	Molecular Probes	Cat# A-11029, RRID:AB_138404
Goat Anti-Rabbit IgG (H+L) Highly Cross-adsorbed Antibody, Alexa Fluor 555 Conjugated	Molecular Probes	Cat# A-21429, RRID:AB_2535850
DISC. OmniMap ANTI-MS HRP RUO	Roche	Cat# 760-4310, RRID:AB_2885182
DISC. OmniMap ANTI-Rb HRP RUO	Roche	Cat# 760-4311, RRID:AB_2811043
CD3	Roche	Cat# 790-4341, RRID:AB_2335978
CD8	Leica	Cat# CD8-4B11-L-CE, AB_10555292
Granzyme B	Leica	Cat# NCL-L-GRAN-B, RRID:AB_563751
FOXP3	Cell Signaling Technology	Cat# 98377S, RRID:AB_2747370
Ki-67	Agilent	Cat# M724029-2, RRID:AB_2893005
Pan Cytokeratin antibody [AE1/AE3]	Roche	Cat# 760-2135, RRID:AB_2810237
Biological samples
Patient-derived tissues	Table S3	Table S3
Chemicals, peptides, and recombinant proteins
Discovery Inhibitor	Roche	Cat# 760-4840
Citrate Buffer, pH 6.0, 10x, Antigen Retriever	Sigma Aldrich	C9999-1000ML
Critical commercial assays
AllPrep DNA/RNA Mini Kit	QIAGEN	Cat# 80204
mirVana miRNA Isolation Kit, with phenol	Thermo Fischer Scientific	Cat# AM1560
QIAamp DNA FFPE Tissue Kit	QIAGEN	Cat# 56404
FlexiGene DNA Kit	QIAGEN	Cat# 51206
Deposited data
WES of tumor tissues and matched normal tissues	This Paper	SRA: PRJNA744256
RNA-seq of tumor tissues	This Paper	GEO: GSE179730
Mass cytometry data of patient- and healthy donor-derived PBMCs	This Paper	FlowRepository: FR-FCM-Z475
TCR-seq of matched patient-derived tumors and PBMCs	This Paper	https://clients.adaptivebiotech.com/pub/liu-2021-crm
Software and algorithms
cytofkit	Bioconductor	Version: 3.7
R software	CRAN	Version: 3.5.1
GraphPad Prism	https://swcstore.oit.ucla.edu/secure/browse_vendors.php	Version: 7
Cytobank	https://www.cytobank.org/	N/A
tcR	CRAN	Version: 2.2.4.1
BWA	http://bio-bwa.sourceforge.net/	Version: 0.7.15
Picard	https://broadinstitute.github.io/picard/	Version: 1.141
gatk	https://gatk.broadinstitute.org/hc/en-us	Version: 3.8
Samtools	http://www.htslib.org/	Version: 0.1.19
MuTect	https://software.broadinstitute.org/cancer/cga/mutect	Version: 1.1.7
VarScan2	http://varscan.sourceforge.net/	Version: 2.4.3
Oncotator	https://software.broadinstitute.org/cancer/cga/oncotator	Version: 1.9.9.0
Sequenza	http://www.cbs.dtu.dk/biotools/sequenza/	Version: 2.1.2
PHYLIP	https://evolution.genetics.washington.edu/phylip.html	Version: 3.698
POLYSOLVER	https://software.broadinstitute.org/cancer/cga/polysolver_run	Version: 4.2
HISAT2	https://ccb.jhu.edu/software/hisat2/manual.shtml	Version: 2.0.6
HTSeq	https://htseq.readthedocs.io/en/release_0.11.1/count.html	Version: 0.5.4
GeoTcgaData	CRAN	Version: 0.2.5
GSVA	Bioconductor	Version: 1.34.0
CIBERSORTx	https://cibersortx.stanford.edu/	N/A
survival	CRAN	Version: 3.1.8
Phenochart viewer	Akoya Biosciences	Version 1.0.12
inForm software	Akoya Biosciences	Version 2.4.4